Branchio-Oto-Renal Spectrum

Branchio-oto-renal syndrome and branchio-otic syndrome (EYA1, SIX1): an autosomal dominant disorder of the development of second pharyngeal arch derivatives, the ear and the kidney, with hearing loss in more than 90% of those affected, preauricular pits, cervical fistulae or cysts and congenital anomalies of the kidney and urinary tract.

Literature and regulatory information updated: 10 October 2026.

0. Initial Reference Table

Data on bilateral renal hypoplasia or aplasia (CAKUT, congenital anomalies of the kidney and urinary tract) relevant to differential diagnosis, to the assessment of relatives and to recurrence risk are in sections 6 and 8. The oculo-auriculo-vertebral spectrum and craniofacial microsomia appear here only as differential diagnoses [37–39].

1. Introduction

1.1. From clinical observation to syndrome

The association between branchial fistulae, preauricular pits and deafness was recorded by Heusinger in 1864, but only a century later was it recognised as a hereditary entity with renal involvement [4]. In 1975, Melnick, Bixler, Silk, Yune and Nance described “autosomal dominant branchio-oto-renal dysplasia” in a family in which the father and three of six children had mixed deafness, pinna malformation, branchial fistula and renal anomalies [4, 40]. In 1978, Fraser, Ling, Clogg and Nogrady published a pedigree with serial audiograms documenting the onset and rapid progression of deafness in the twin sister of an affected child, and reviewed the literature for counselling purposes: affected individuals could have preauricular pits, lacrimal duct stenosis, deafness, branchial fistulae or cysts, malformations of the external, middle and inner ear and renal anomalies ranging from mild hypoplasia to agenesis [41]. The combination of the two names gave rise to the eponym Melnick-Fraser syndrome, which Smith's Recognizable Patterns of Human Malformation still uses as its heading [3]. Other historical designations were branchio-otic dysplasia, branchio-oto-ureteral syndrome, “preauricular pits, cervical fistulae and deafness” and “ear pits-deafness syndrome” [4].

In 1980, Fraser, Sproule and Halal examined 421 white children in schools for the deaf in Montreal: 19 had preauricular pits and, of the 9 families who accepted family study with audiograms and intravenous urography, the syndrome was identified in 4 and may have been present in others [28]. This work produced the two estimates that still circulate in all reference sources, about 2% of children with profound deafness and a frequency of about 1/40,000, as well as the estimate of severe renal dysplasia in about 6% of heterozygotes and the observation that a preauricular pit at birth is associated with a probability of at least 1 in 200 of severe deafness [2, 3, 28]. In 1995, Chen and colleagues characterised the phenotype of 45 individuals and described in the temporal bone cochlear hypoplasia (four-fifths of normal size, with only two turns), enlargement of the vestibular aqueduct, bulbous internal auditory canals and acutely angled promontories [42].

1.2. Molecular milestones

In 1997, Abdelhak and colleagues identified by positional cloning at 8q13.3 the EYA1 gene, the human homologue of the Drosophila eyes absent gene, and defined a new gene family by the conserved C-terminal region of 271 amino acids (eyaHR, eya homologous region) that it shares with EYA2 and EYA3; in the mouse, Eya1 was expressed in all components of the inner ear from the otic placode onwards and, in the kidney, in the metanephric mesenchyme surrounding the ureteric branches [43]. In the same year, the same group described the genomic structure (16 coding exons over 156 kb) and showed that variants clustered in the eyaHR [44], and Vincent and colleagues demonstrated, in two families with an exclusively branchio-otic phenotype, that BO syndrome and BOR syndrome are allelic defects of EYA1 [45]. In 2004, Ruf and colleagues mapped the BOS3 locus to 14q23.1 and identified SIX1 variants in four families, all disrupting the EYA1–SIX1 interaction and, in the homeodomain, DNA binding [46]. Also in 2004, Chang and colleagues proposed the clinical criteria still in use and showed that about 20% of EYA1 variants were genomic rearrangements not detected by analysis of the coding sequence [47].

In 2007, Hoskins and colleagues reported SIX5 missense variants in 5 of 95 patients without a variant in EYA1 or SIX1 [48]. This association was called into question when Krug and colleagues, screening 140 French patients from 124 families, found no SIX5 variants and identified a three-exon deletion of EYA1 in a patient previously described as carrying SIX5 p.(Thr552Met) [27]. In 2018, the ClinGen (Clinical Genome Resource) hearing loss expert panel classified the SIX5–BOR association as disputed, and in 2025 GeneReviews ceased to regard SIX5 as a causal gene [1, 12]. Whole genome sequencing, applied systematically for the first time in a Korean cohort published in 2024, revealed cryptic inversions and balanced complex rearrangements of EYA1 and raised the diagnostic yield to about 90% [26]. In 2025 the first causal deep intronic variant of EYA1 was described, identified by whole genome sequencing after six years of negative testing in a Danish family [49].

1.3. Current nomenclature and definition of the entities

Since 2025 GeneReviews has used the designation branchio-oto-renal spectrum (BORSD) to bring together branchio-oto-renal syndrome (BORS), in which renal anomalies are present, and branchio-otic syndrome (BOS), in which they are absent [1]. The distinction between the two has no strict nosological value, because within the same family, with the same variant, some individuals have BORS and others BOS [1, 50]. The OMIM (Online Mendelian Inheritance in Man) classification keeps separate entries, BOR1 (113650) and BOS1 (602588) for EYA1, BOS3 (608389) and DFNA23 (605192) for SIX1, BOS2 (120502) for a locus at 1q31 with no gene identified and BOR2 (610896) for SIX5; Orphanet distributes the spectrum between ORPHA:107 and ORPHA:52429 [2, 14, 15, 17–19, 21, 22]. OMIM has no BOR3 entry for SIX1 [17].

For clinical purposes, the spectrum is defined by the presence of clinical criteria (section 5) or by identification of a heterozygous pathogenic or likely pathogenic variant in EYA1 or SIX1, or of a deletion or structural variant of 8q13.2-q13.3 that includes EYA1, in a patient with suggestive findings [1]. The atypical form, with two major criteria with or without one minor criterion, has been characterised in Japanese cohorts and has a lower genetic yield [50]. Otofaciocervical syndrome, caused by contiguous gene deletions that include EYA1, is regarded by GeneReviews as an allelic disorder; a 2025 preprint proposes treating it as the extreme of a phenotypic continuum of EYA1 [1, 13]. Nonsyndromic DFNA23 deafness was described in an individual with a SIX1 variant who in fact had a solitary hypodysplastic kidney, and ClinGen grouped it with the spectrum because there is no difference in mechanism or inheritance [1, 5, 51].

2. Molecular Genetics and Pathophysiology

2.1. The EYA1–SIX1 developmental module

EYA1 is located at 8q13.3 (GRCh38, chr8:71,197,432–71,592,025, minus strand); the MANE Select transcript is NM_000503.6 (ENST00000340726.8), which encodes the 592-amino-acid protein NP_000494.2 [8]. Historical descriptions of 16 coding exons and a 559-amino-acid protein refer to an alternative isoform; NM_000503.5 and NM_000503.6 produce the same c. numbering and the same protein, according to VariantValidator [44, 50, 52]. The protein has an N-terminal proline-, serine- and threonine-rich transactivation domain and a C-terminal EYA domain (eyaHR) with phosphatase activity [4, 43]. EYA1 has no DNA-binding domain of its own: it is recruited by SIX family factors, chiefly SIX1, and converts the SIX1 complex from a transcriptional repressor into an activator; it also acts as a tyrosine phosphatase for histone H2AX phosphorylated at Tyr-142, a mark that decides between DNA repair and apoptosis [9, 53]. Li and colleagues showed that the phosphatase activity of Eya regulates the transcriptional effects of the Six1–Dach–Eya axis in mammalian organogenesis [53].

SIX1 is located at 14q23.1; the MANE Select transcript is NM_005982.4 (ENST00000645694.3), which encodes the 284-amino-acid protein NP_005973.1 [8]. GeneGuidance gives NM_001425142 as the reference transcript, but the MANE Select confirmed in Ensembl is NM_005982.4, and this is the one used for nomenclature in this article [8, 10]. SIX1 is a transcription factor with a SIX protein-interaction domain and a DNA-binding homeodomain; it has no activation domain, recruits EYA1 and EYA2 and carries them into the nucleus, binds the MEF3 motif and regulates, among others, MYOG, MYC, CCND1 and CCNA1 [10, 46]. Pathogenic variants impair formation of the EYA1–SIX1–DNA complex, either by altering DNA binding or by loss of interaction with EYA1 [5, 46].

EYA1 and SIX1 form a transcriptional complex essential to the development of the ear, the pharyngeal arches and the kidney; its disruption perturbs morphogenesis, proliferation and cell specification [1, 53]. EYA1 is expressed in the otic placode, the branchial arches and the metanephric mesenchyme, and in the human embryo between the 4th and 6th weeks of development [1, 43, 50]. The pinna forms from six swellings (hillocks of His), derived from the mesenchyme of the first and second pharyngeal arches around the first branchial groove, which appear at around the 6th week; imperfect fusion of these swellings gives rise to preauricular pits [1, 39]. Cervical fistulae, sinuses and cysts are remnants of the second arch and second pharyngeal pouch [1]. In the kidney, agenesis must occur before 31 days of development, and the absence of fetal urine production triggers the oligohydramnios sequence (Potter sequence), with pulmonary hypoplasia [54]. Mice with loss of Eya1 or Six1 recapitulate the spectrum, and recent mouse studies show the interaction between muscle and cartilage in external ear formation in Eya1 and Tbx1 mutants and the role of SIX1 in homeostasis of the adult cochlear sensory epithelium [1, 55, 56].

2.2. Variant mechanism and gene-disease validity

For EYA1, the mechanism is haploinsufficiency: ClinGen assigns it sufficient evidence of haploinsufficiency (score 3, reviewed in 2020) and no evidence of triplosensitivity, most of the variants described are loss-of-function variants and the pLI index (probability of loss-of-function intolerance) in the gnomAD (Genome Aggregation Database) v4.1 is 1.0 [24, 25]. The ClinGen validity curation for EYA1 and branchio-oto-renal syndrome, approved in November 2017, is definitive, with maximum genetic (12/12) and experimental (6/6) scores; it includes OMIM phenotypes 113650 and 602588 in the same entity and excludes otofaciocervical syndrome [23]. The experimental evidence included the Xenopus model in which the mutant mRNA has a dominant-negative effect, the spontaneous mouse with insertion of an IAP element in intron 7 of Eya1, which has deafness and renal anomalies, the phosphatase activity and the interaction with SIX1 [23].

For SIX1, the ClinGen curation is likewise definitive (2017), but with a genetic score of 7.75/12, based on 13 probands with missense variants and on segregation in four families (total LOD 13.26) [5]. ClinGen finds no evidence of haploinsufficiency for SIX1, the gene's pLI is 0.26 and almost all variants described are missense variants in the SIX domain or the homeodomain, which led the authors of the Japanese cohort to postulate a dominant-negative effect [24–26]. In Xenopus, the variants p.(Val17Glu), in the SIX domain, and p.(Tyr129Cys), in the homeodomain, have distinct effects on gene expression in the neural crest, placodes and otic vesicle; p.(Tyr129Cys) is the least effective at rescue and increases abnormal cartilages also in wild-type embryos, suggesting a dominant-negative effect (preclinical study) [57].

2.3. SIX5: a refuted association

The SIX5 hypothesis arose from the observation of four heterozygous missense variants in five of 95 patients without a variant in EYA1 or SIX1, two of which reduced EYA1–SIX5 binding and transactivation in vitro [48]. Screening of 140 French patients found no SIX5 variants and revealed a three-exon deletion of EYA1 in a patient previously attributed to SIX5 p.(Thr552Met) [27]. In the ClinGen reappraisal, none of the published variants scored: p.(Thr552Met), p.(Gly365Arg), p.(Ala296Thr) and p.(Ala158Thr) were more frequent in gnomAD than the prevalence of the disease allows or had an alternative cause, and p.(Pro606Leu) had no evidence of pathogenicity; the two mouse models with Six5 deletion have cataracts without ear or kidney anomalies [1, 12]. The classification changed from limited to disputed in January 2018 [12]. The Japanese (78 probands tested), Korean (23 families) and Japanese otological referral (38 patients) cohorts found no SIX5 variants [25, 26, 50]. Normalised, the historical variant corresponds to NM_175875.5:c.1655C>T p.(Thr552Met), which has conflicting classifications in ClinVar [52, 58]. OMIM keeps the BOR2 entry (610896) linked to SIX5, with no mode of inheritance assigned, although its text records the deletion of exons 3 to 5 of EYA1 found by Krug in the patient carrying p.(Thr552Met), who had been tested only by direct sequencing [19]. Orphanet still lists SIX5 as a gene associated with ORPHA:107, Gene2Phenotype (G2P) keeps a definitive classification based solely on the 2007 study, and some reference texts continue to attribute 2–2.5% of cases to SIX5 [2, 3, 6, 59]. In current practice, a SIX5 variant in a patient with branchial, auricular or renal anomalies should not be accepted as the explanation of the phenotype, and investigation should continue in EYA1, including structural variants [1, 6]. SIX5 is adjacent to DMPK, but myotonic dystrophy type 1 results from the CTG expansion in the 3' untranslated region of DMPK and not from coding variants of SIX5 [6].

2.4. Spectrum of EYA1 variants

ClinVar lists 187 pathogenic, 81 likely pathogenic and 282 variants of uncertain significance (VUS) for EYA1, a count that reflects testing volume and not the frequency of the variants in the disease [9]. Recent reviews cite from more than 237 to more than 290 pathogenic variants described, most in the EYA domain [4, 60]. According to HGMD (Human Gene Mutation Database), consulted in June 2026 by the authors of a Chinese cohort, 14.4% of pathogenic or likely pathogenic EYA1 variants are missense, 16.9% splicing and 9.9% large deletions, the remainder being truncating [22]. In the Japanese national cohort, 27 EYA1 variants in 52 probands included 10 nonsense, 7 splicing, 4 frameshift and 1 copy loss, with only 4 missense or in-frame insertions [25]. The variants described are, as a rule, private: in the Orten series, 56 of the 70 different variants in 89 families were unique to one family [61].

Copy number variants (CNV) and structural variants carry a weight that does not exist in most monogenic diseases. Vervoort and colleagues showed that genomic rearrangements of EYA1 explained a large fraction of families, and Chang and colleagues estimated that 20% of EYA1 variants were genomic rearrangements [47, 62]. In the Japanese cohort of Masuda, 6 of the 13 distinct variants (46%) were large deletions detected only by MLPA (multiplex ligation-dependent probe amplification) [50]. Brophy and colleagues, using array comparative genomic hybridisation (aCGH) in 32 probands without a point variant, found 5 total or partial deletions of EYA1 (14%), four of them with almost identical breakpoints in blocks of human endogenous retroviral sequences (HERV), which defines a hotspot for non-allelic homologous recombination (NAHR) [63]. The recurrent HERV-mediated deletion of about 2.7 Mb at 8q13.2-q13.3 and other non-recurrent deletions may include neighbouring genes and produce an extended phenotype [1, 64, 65]. In the Korean cohort studied by whole genome sequencing, structural variants accounted for 13% of families: one intragenic deletion, one complex genomic rearrangement and one cryptic inversion, the last two balanced, with no change in dosage and undetectable by exome, CNV algorithms or MLPA; in the same authors' literature review, deletions represented 88.9% of published structural variants, complex rearrangements, cryptic inversions and Alu insertions 3.7% each, and structural variants about 9% of all variants detected [26]. As early as 1997 a de novo Alu insertion in an EYA1 exon had been described, with a poly(A) tail unstable between generations [44]. Pericentric inversions of chromosome 8 that disrupt EYA1 require high-resolution karyotyping or fluorescence in situ hybridisation (FISH) [1, 66]. In a large Brazilian family with branchio-otic syndrome without renal anomaly, linked to 8q13 with negative EYA1 sequencing, aCGH revealed a heterozygous duplication of 71.8 kb (exons 4 to 10), confirmed by quantitative polymerase chain reaction (PCR) in 14 of 15 affected individuals and absent in 13 unaffected individuals; it was the first large causal duplication described in the spectrum [67].

Non-coding variants add a further layer. In the Danish family of Lorans and colleagues, with four affected individuals in three generations and negative testing over six years (Sanger sequencing of EYA1, SIX1, SIX5 and SOX10, MLPA of EYA1, aCGH and three panels), whole genome sequencing identified NM_000503.6:c.556+2123C>T in intron 7, absent from gnomAD v4.1, HGMD, ClinVar and LOVD (Leiden Open Variation Database); the minigene assay showed inclusion of a 117 bp pseudo-exon with a frameshift, and the variant was reclassified as likely pathogenic (PM2_supporting, PVS1_strong, PP4, PP1) [49]. In a Chinese fetus, NM_000503.6:c.640-15G>A, de novo, was initially a VUS (SpliceAI 0.87) and became likely pathogenic after the minigene revealed four aberrant transcripts with intron retention or deletions at the start of exon 9 [68]. This variant, described as novel, already existed in ClinVar with conflicting classifications [58].

2.5. SIX1 variants

SIX1 variants are almost all missense and are located in the SIX domain or the homeodomain; no SIX1 CNV have been described in the spectrum [1, 26]. In screening 247 families, Kochhar and colleagues found five novel variants, all in the SIX domain, and one already known variant, c.328C>T, in five unrelated families [69]. Normalised, this recurrent variant corresponds to NM_005982.4:c.328C>T p.(Arg110Trp), classified as pathogenic in ClinVar without conflicts [52, 58]. The same variant was described in a mother and son with deafness without other signs of the spectrum [5]. In the Japanese national cohort, 11 SIX1 variants in 14 probands were mostly missense, 8 of them novel [25]. A Tunisian family with a SIX1 variant had five heterozygotes with moderate to profound deafness and pits in four, without other second arch, temporal bone or renal anomalies, a phenotype that GeneReviews prefers to classify as mild spectrum rather than nonsyndromic deafness [1, 70].

Conversions between the published protein nomenclature and c. HGVS were confirmed in VariantValidator on GRCh38, and the classifications in ClinVar, on 10 October 2026 [52, 58].

2.6. Genotype-phenotype correlations

Intra- and interfamilial variability limits actionable correlations: within the same family and with the same variant, some individuals have isolated deafness and others the complete picture, and severity does not correlate with variant type or with the domain affected [1, 27, 50, 61]. In the Masuda cohort, the same deletion of exons 2 and 3 of EYA1 appeared in families with typical and atypical phenotypes [50]. There are, however, consistent differences between genes. In the otological meta-analysis of 295 patients, EYA1-related deafness was mainly mixed, moderate to severe, with or without renal anomaly, whereas SIX1-related deafness was more often profound sensorineural [29]. SIX1 variants are always associated with hearing loss, sensorineural or mixed, and in a Korean series they were linked to apparently nonsyndromic deafness and atypical forms [1, 74]. In the Japanese national cohort, fistulae (p = 0.0003), deafness (p = 0.0442), middle ear anomalies (p = 0.0036), mixed deafness and hearing asymmetry (p = 0.0089) were more frequent with EYA1, and none of the 14 probands with SIX1 had second arch, renal or external ear anomalies [25]. In the Korean cohort, most patients with an atypical phenotype had SIX1 variants [26]. In the temporal bone, offset of the cochlear turns was observed in 100% of ears with EYA1 and in 12.5% of ears with SIX1, in which a short, “spiky” apical turn predominates [31]; a turn alignment ratio below 0.476 separates the two situations (section 5) [30]. In a Chinese series of 13 patients with EYA1, cochlear nerve deficiency occurred in 5 of 11 carriers of truncating variants or deletions and in none of the 2 with splicing variants, a difference without statistical significance (p = 0.487) [22]. Deletions extending to genes neighbouring EYA1 are associated with short stature, developmental delay and musculoskeletal defects [3, 65].

2.7. Penetrance and expressivity

In large pedigrees, penetrance is apparently complete, with highly variable expressivity, and some authors have described the disease as fully penetrant since Chen 1995 [1, 4, 49]. Fraser had already observed that few obligate carriers had no sign at all, that about 7% of heterozygotes had deafness without pits or fistulae and that the offspring of affected individuals with pits or fistulae had about an 80% probability of deafness [41]. Incomplete penetrance does exist: in the 2026 Chinese series, the deletion of exons 12 to 18 of EYA1 was present in the father and brother of the proband, both without any major criterion [22]. In the family with 18 heterozygotes for a SIX1 variant, all had deafness, but only six had pits and three branchial cysts [1, 46]. The sources consulted do not identify genetic modifiers of expressivity.

2.8. Allelic disorders and contiguous gene phenotypes

Otofaciocervical syndrome was described in patients with contiguous gene deletions that include EYA1: long face with a narrow nose, high-arched palate, folded protruding ears (lop ears), long neck, sloping shoulders and clavicles, winged, low-set and laterally placed scapulae, tetralogy of Fallot and hearing loss [1, 11]. A canonical EYA1 splice variant in a patient with the phenotype suggested that point variants could also cause it, but the analysis was limited to the coding exons, which does not allow the conclusion to be sustained [1]. A 2025 preprint, with a new patient with a de novo 8q13.2q13.3 microdeletion, reviewed all cases with an EYA1 alteration and concluded that all variant types can give rise to the spectrum, to otofaciocervical syndrome or to hybrid phenotypes, and that all published patients with otofaciocervical syndrome and an EYA1 variant had renal anomalies; the authors propose a diagnostic continuum with renal, otological and skeletal surveillance [13]. A contiguous gene deletion at 8q13 links Duane anomaly type 1 with the spectrum, and molecular analysis of otofaciocervical syndrome narrowed the Duane critical region to 1 cM [11, 75]. Azuma and colleagues identified, in 2000, three EYA1 missense variants in patients with congenital cataract and anterior segment anomalies of the eye, two of them with other features of the spectrum; OMIM includes this phenotype in the BOS1 entry (602588) and adds “with or without cataracts” to the designation of the BOR1 entry (113650) [1, 14, 15]. In the gene entry, OMIM flags otofaciocervical syndrome (166780) with “?”, that is, as a provisional association [16]. For SIX1, no phenotype is known other than the spectrum and DFNA23, which ClinGen grouped with it [1, 5]. A missense variant of ANLN, the gene for an actin-binding protein, was described in a three-generation Chinese family with branchio-otic syndrome and classified by the authors as likely pathogenic; this is an isolated report that does not establish ANLN as a gene of the spectrum [3].

3. Clinical Spectrum and Manifestations by System

3.1. Data sources and what they measure

The GeneReviews clinical description is based on more than 400 published individuals, chiefly in the series of Chang (2004), Morisada (2014) and the meta-analysis of Chen (2021) [1]. Frequencies vary considerably between cohorts, because each is recruited in a different setting: otorhinolaryngology and deafness series underestimate renal anomalies, nephrology series underestimate branchio-otic forms, and cohorts with genetic testing depend on the inclusion criteria. The Japanese national cohort of Goto and colleagues, recruited between September 2021 and August 2023 in 45 hospitals, almost all otorhinolaryngology departments, brought together 169 patients from 129 families, but renal data were missing in 79 patients and second arch data in 70 [25]. The systematic review by Biggs and colleagues brought together 482 patients from at least 95 families in 64 studies, mostly series or isolated cases without objective measures, which precluded meta-analysis [34].

Table sources: [1, 25, 26, 50].

3.2. Hearing

Hearing loss is the most constant manifestation, present in more than 90% of those affected [1]. In GeneReviews, the loss is mixed in 52%, conductive in 33% and sensorineural in 29% (the percentages add up to more than 100% in the original), and severity is mild in 27%, moderate in 22%, severe in 33% and profound in 16% [1, 3]. In the systematic review by Biggs, with the type documented in 308 patients, the loss was mixed in 157 (51%), sensorineural in 89 (29%) and conductive in 62 (20%) [34]. In the Japanese national cohort, analysed per ear, mixed (38.6%) and sensorineural (32.7%) loss predominated, with moderate severity in 39.7%, mild in 17.8%, profound in 15.8% and severe in 15.2%; 26.7% of patients had an asymmetry greater than 20 dB between ears [25]. The loss is usually bilateral and asymmetric [4, 29].

The type of loss reflects the malformed region. In Japanese ears with isolated middle ear malformation, 41.7% had conductive and 37.5% mixed loss; with isolated inner ear malformation, 66.7% had sensorineural and 23.3% mixed loss; with combined malformations, 55.7% had mixed loss; without visible malformation, 41.5% had sensorineural and 26.8% mixed loss [25]. Otitis media can worsen hearing disproportionately in these patients [4].

Age at onset ranges from birth to adulthood. In the Japanese national cohort, 63.9% of patients noticed symptoms before 6 years of age, 13.0% between 6 and 18 years and 7.1% after 19 years [25]. The loss is stable in about 70% of families and progressive in about 30%, correlating with an enlarged vestibular aqueduct; progression typically begins in childhood or adolescence and may be sudden [1, 3]. In 32 Dutch patients from 6 families, with serial audiograms over 3 to 30 years and individual analysis in 16, there was significant progression in 10 and significant fluctuation in 7; substantial fluctuation was observed only in patients followed from a young age, and an enlarged endolymphatic duct or sac on magnetic resonance imaging (MRI) was associated with higher sensorineural thresholds [76]. In the Japanese national cohort, 43.0% of patients reported progression, confirmed by serial audiograms in some of them [25]. In Fraser's original description, a twin child had onset and rapid progression documented on serial audiograms [41]. The vestibular system may be involved, and motor delay in a deaf child should prompt its investigation [77].

3.3. External, middle and inner ear

In the pinna, preauricular pits are the most frequent finding (82%), followed by folded protruding ear (lop ear, 36%) and preauricular tags (13%) [1]. An anteverted or cup-shaped pinna, due to malformation or absence of the helix and antihelix, is characteristic [1]. Malformations range from severe microtia to minor anomalies (cup-shaped, folded, flattened or hypoplastic ear), and the external auditory canal may be narrow, slanting upwards or malformed, which makes otoscopy difficult [3]. In the Japanese national cohort, lop ear occurred in 5.4% and microtia in 7.6% of patients, and canal stenosis and atresia in 3.8% and 1.7% [25]. Pits may become intermittently infected, and the definitive treatment is surgical excision [1].

In the middle ear, anomalies include malformation, malposition, dislocation or fixation of the ossicles and reduction or malformation of the middle ear space [1]. In the Japanese national cohort, 26.9% of patients had ossicular malformations, 8.0% ossicular fixation and 10.8% both; one congenital cholesteatoma was observed [25]. Computed tomography (CT) also shows an underdeveloped mastoid tip, a low tegmen, reduced pneumatisation of the mastoid cortex and facial recess and a patulous Eustachian tube [34]. The Kumarasamy review also lists ankylotia, absence of the oval window, serous otitis media, tympanic perforation, absence of Körner's septum, tympanic plate defects and a large emissary vein [4].

In the inner ear, cochlear hypoplasia is the most frequent anomaly (25.9% in the Japanese national cohort), followed by enlarged vestibular aqueduct (5.4% in that cohort, 24–50% in other series) and hypoplasia of the lateral semicircular canal [1, 25, 50]. The “unwound” cochlea corresponds to anteromedial rotation and displacement of the middle and apical turns relative to the basal turn: in a series of 9 children compared with 50 controls with sensorineural deafness, it was present in 8, with a sensitivity of 89% and a specificity of 100% [78]. Medialisation of the facial nerve relative to the cochlea has been described in 78–100% of patients and in none of the controls with other causes of deafness [34]. Other anomalies are a hypoplastic apical turn (incomplete partition type II), a funnel-shaped or enlarged internal auditory canal, membranous labyrinth dysplasia on MRI and cochlear nerve hypoplasia [1, 34]. In a Chinese series of 13 patients with EYA1 studied by high-resolution CT and MRI of the internal auditory canal, 5 (38.5%) and 7 of 26 ears (26.9%) had cochlear nerve deficiency, defined as a small or absent nerve on MRI or a cochlear nerve canal of less than 1.4 mm on CT; in the earlier literature, the cochlear aperture measured 1.42 ± 0.37 mm in 38 patients versus 2.05 ± 0.24 mm in 21 controls [22]. In a Boston series covering more than 12 years of CT, 2 of 8 patients had bilateral fetal orientation of the vestibular aqueduct, a sign of endolymphatic sac hypoplasia, and none had Ménière's disease [79].

3.4. Second pharyngeal arch and neck

Second arch anomalies occur in about 50% of those affected in the classic series [1]. The sinus or fistula is a small skin opening, sometimes pinpoint, at the anterior border of the sternocleidomastoid, usually in the lower third of the neck; it may open into the tonsillar fossa or pillars or end blindly, and when it has neither a skin nor a mucosal opening it presents as a cyst, a painless cervical mass anterior to the sternocleidomastoid [1]. Fistulae may go unnoticed until deafness is recognised or may become infected and require surgery [3]. The frequency varies widely between cohorts, from 16.2% in the Japanese national series, in which data were missing in 70 patients, to 66% in the Korean cohort [25, 26]. Branchial pigmented patches may also be present on the neck [39]. In the Masuda cohort, branchial anomalies distinguished typical (72%) from atypical (6%) forms and were the finding most strongly associated with detection of a variant (section 5) [50].

3.5. Kidney and urinary tract

Congenital anomalies of the kidney and urinary tract (CAKUT) occur in 67% of patients in clinical series: renal agenesis in 29%, hypoplasia in 19%, dysplasia in 14%, pelviureteric junction obstruction in 10%, calyceal cyst or diverticulum in 10%, and caliectasis, pyelectasis, hydronephrosis and vesicoureteral reflux (VUR) in 5% each, unilateral or bilateral and in any combination [1]. The spectrum ranges from minor dysplasia (tapered upper poles, blunted calyces, duplication of the collecting system) to bilateral renal agenesis [3]. The most severe forms end in pregnancy loss or neonatal death from the oligohydramnios sequence; less severe forms can cause progressive dysfunction up to end-stage chronic kidney disease [1, 54]. Otological and genetic series show lower frequencies, 27.8% in the Japanese national cohort, 15% in the Korean cohort and 17% of variant carriers in that of Masuda, whereas in the series of Unzaki and Krug, according to Masuda, the frequency was 53% [25, 26, 50]. The Japanese authors attribute the difference to recruitment in otorhinolaryngology, because patients with renal dysfunction tend to be followed in paediatrics or nephrology [25]. In the Japanese series of Unzaki, more than half the patients with EYA1 had renal hypodysplasia or kidney failure of unknown cause, with highly variable renal phenotypes within the same family [80]. Renal cysts are part of the spectrum: the Oxford reference includes branchio-oto-renal syndrome among the conditions to consider when renal cysts raise suspicion of autosomal dominant polycystic kidney disease, with renal anomalies including agenesis, duplex kidney and cysts, and branchial sinuses or cysts in some carriers [81].

Besides malformation, there is glomerular disease. Focal segmental glomerulosclerosis (FSGS) has been described in biopsies from patients with the spectrum, and proteinuria, haematuria and glomerulosclerosis may contribute to the risk of end-stage chronic kidney disease independently of CAKUT [1, 72, 82]. In a 2025 review, the 7 published renal biopsies showed FSGS in 4, mesangial proliferation in 2 and membranous nephropathy in 1; 5 of the 6 patients tested had an EYA1 variant [60]. In a 32-year-old Japanese man with a preauricular pit, mixed deafness, a malpositioned right kidney and proteinuria, biopsy of the left kidney showed secondary FSGS of the perihilar variant; trio exome sequencing identified no causal variant, and renal function remained stable for 11 years on an angiotensin II receptor blocker (ARB) [82]. Three Chinese children aged 8 and 9 years were referred to nephrology for proteinuria (23.8–68.9 mg/kg in 24 hours) and kidney failure (glomerular filtration rate, GFR, estimated, eGFR, of 8.9–36.0 mL/min/1.73 m²); they had had auricular and branchial fistulae since early childhood that had been disregarded, all had EYA1 variants, and the diagnostic delay was 8 to 9 years from the extrarenal signs [72]. In a family with EYA1 c.1050+5G>A, the 4-year-old proband had steroid-resistant proteinuria, and the mother and brother, without an initial structural anomaly, developed proteinuria and a decline in GFR over 8 years [22, 71].

The untreated renal natural history is documented mainly in families. In a three-generation Greek-Cypriot family followed for 27 years, the 10 genetically affected members had early-onset deafness, 9 had pits and 8 had undergone surgery for branchial clefts without a family diagnosis; 4 reached end-stage chronic kidney disease at 36, 14, 17 and 17 years of age, with minimal or absent proteinuria, owing to unilateral renal agenesis with contralateral hypodysplasia or severe bilateral hypodysplasia [83]. Fraser estimated severe renal dysplasia in about 6% of heterozygotes, and the Smith text reports chronic kidney failure in about 6% of patients, without a denominator [3, 28]. These figures come from small, old series and should not be read as a validated lifetime risk; the sources consulted do not describe a cohort with systematic renal follow-up from birth. Ruf and colleagues described renal carcinoma in 2 of the 18 heterozygotes of a family with a SIX1 variant; the association has not been described in other families and requires more data [1, 46].

3.6. Other manifestations

Aplasia or hypoplasia of the lacrimal duct causes epiphora [1, 3]. A short or cleft palate can cause feeding or speech difficulties, and retrognathia breathing or feeding difficulties [1]. Facial asymmetry is usually mild, owing to unilateral mandibular or malar hypoplasia, and hemifacial microsomia has been described in two studies [1, 34]. Facial palsy is occasional, and in two Chinese twins it was associated with a structural anomaly of the facial nerve [1, 22]. Occasional findings include gustatory lacrimation (“crocodile tears”, from aberrant regeneration of cranial nerve VII fibres), euthyroid goitre, microdontia of the permanent teeth, bifid uvula, vocal cord paresis, mitral valve prolapse, congenital dislocation of the hip, intestinal non-rotation, pancreatic duplication cyst, imperforate anus, benign intracranial tumour and linear temporoparietal naevus [3, 4]. Congenital heart disease was described in four studies of the systematic review and atrial septal defect in 3 of the 13 Chinese patients assessed [22, 34]. Clinical Cardiogenetics includes branchio-oto-renal syndrome type 1 (EYA1, AD) among the syndromes associated with left ventricular non-compaction or hypertrabeculation, on the basis of a published report and with no estimated frequency [84]. Cognition is normal in the classic form; developmental delay suggests a contiguous gene deletion [3, 65].

3.7. Fetal phenotype

The prenatal phenotype differs from the postnatal one because deafness and pits are practically invisible on ultrasound. In a review of 17 prenatal cases with an EYA1 variant, 6 (35.3%) had urinary anomalies (bilateral pyelectasis, small kidneys, bilateral renal agenesis or bilateral hydronephrosis), 4 (23.5%) amniotic fluid abnormalities, 3 of them oligohydramnios, 4 (23.5%) heart defects (echogenic intracardiac focus, interrupted aortic arch, ventricular septal defect, tetralogy of Fallot) and 2 (11.8%) ear anomalies; about 30% had no ultrasound anomaly at all [68, 85]. Pyelectasis may regress during pregnancy [68]. Amniotic fluid abnormalities and heart defects are more prevalent in prenatal than in postnatal cases, and missense variants in a critical region of the eyaHR that affect protein stability are associated with greater severity [85]. In a 26-week fetus, the findings were a 0.6 × 0.4 × 0.6 cm facial cyst below the left labial commissure, suggestive of a branchial cyst, and a small, dysmorphic left ear (1.4 × 0.7 cm versus 2.1 × 1.5 cm on the right), with no urinary anomaly detected [68].

4. Clinical Recognition and Warning Signs

4.1. Prenatal period

Prenatal suspicion arises mainly in the presence of renal anomalies and amniotic fluid abnormalities. The Oxford Desk Reference recommends considering the spectrum in all fetuses and newborns with renal agenesis, looking for branchial fistulae after birth, asking about a family history of deafness and requesting renal ultrasound in the parents [86]. Bilateral renal agenesis presents with severe oligohydramnios from 14 weeks, and a deepest vertical pocket of less than 1 cm between 16 and 24 weeks is associated with perinatal mortality above 95%, mainly from pulmonary hypoplasia [86]. A lateral facial or cervical cyst and a small or dysmorphic ear are less frequent ultrasound findings that can guide fetal exome sequencing, and about 30% of fetuses with an EYA1 variant have no ultrasound anomalies [68].

4.2. Newborn and infant

Universal newborn hearing screening identifies some of the cases. The 2019 Joint Committee on Infant Hearing (JCIH) position statement keeps the 1-3-6 goals (screening completed by 1 month, audiological diagnosis by 3 months and start of early intervention by 6 months) and recommends that programmes already meeting them move to 1-2-3 months [87]. Because newborn screening does not identify mild, neural, progressive or late-onset losses, the statement includes craniofacial and physical conditions associated with deafness (risk factor 8) and the more than 400 syndromes associated with abnormal hearing thresholds (risk factor 9) among the indicators requiring audiological follow-up even when screening is normal; for most risk factors, diagnostic assessment should take place by 9 months [87]. The otorhinolaryngological examination should include the pinnae (microtia), canal patency (atresia), the tympanic membranes and the presence of preauricular pits or cysts, and branchio-oto-renal syndrome appears in the statement both among syndromes with sensorineural deafness and visible physical anomalies and among those associated with conductive deafness [87].

Preauricular pits or tags occur in 0.5–1% of newborns, and about 20% of these have associated anomalies; 17% of infants with apparently isolated pits or tags have conductive or sensorineural hearing loss, so hearing assessment is always indicated [88]. Fraser estimated that a preauricular pit at birth is associated with a probability of at least 1 in 200 of severe deafness, which justifies taking a family history and hearing surveillance [28]. In a series of 42 patients with an external ear anomaly and renal ultrasound, 12 (29%) had a renal anomaly, 11 of them in the context of a multiple malformation syndrome; the frequency was 33% in syndromic patients and 11% (1 in 9) in isolated ear anomalies [89]. The authors recommended renal ultrasound in the presence of preauricular pits, cup ears or any ear anomaly accompanied by at least one of the following: other malformations or dysmorphic features, a family history of deafness, ear or renal malformations in the family, or maternal gestational diabetes [88, 89]. The Oxford Desk Reference adds bilateral pits or tags as an indication [88].

4.3. Child, adolescent and adult

In childhood, the most common presentation is deafness, often mixed, in a child with preauricular pits or with a cervical opening that drains intermittently [1, 3]. Targeted questioning about a family history of deafness, operated fistulae, ear anomalies and kidney disease is decisive, because the case may appear isolated owing to failure to recognise the signs in relatives; in the Greek-Cypriot family, 8 of the 10 affected individuals had undergone surgery for branchial clefts without the family diagnosis having been made [1, 83]. Hearing aids should be removed during the examination, because the earmoulds cover the pits [39]. The renal presentation may be late and misleading: the children in the Lin series reached nephrology at 8–9 years of age with proteinuria and kidney failure, and an 8-year-old boy with congenital sensorineural deafness and a preauricular pit was treated for four months for irritable bowel syndrome because of recurrent flank pain before bilateral hydronephrosis, proteinuria, pyuria and microscopic haematuria were identified [72, 90]. In adults, incidentally discovered proteinuria or chronic kidney disease may be the entry point, as in the case in section 10 [60, 82]. The combination of deafness with proteinuria or kidney failure often leads to suspicion of Alport syndrome, which fistulae and pits help to rule out [60, 83].

4.4. Warning and emergency signs

5. Diagnosis: Criteria, Tests and Algorithms

5.1. Clinical criteria

The criteria of Chang and colleagues, published in 2004 on the basis of genotype-phenotype analyses of families with EYA1 variants, remain the reference and were supported by the 2021 meta-analysis [1, 29, 47].

Table sources: [1, 25, 47]. GeneReviews groups pits and pinna malformations within the major criterion of second arch anomalies; Chang, Goto and Niu list them as separate major criteria [1, 22, 25].

The clinical diagnosis is established with three or more major criteria, with two major and two minor criteria, or with one major criterion and a first-degree relative who meets the criteria [1, 34]. A 2026 review transcribes the second requirement as “two or more major criteria”, which does not correspond to the original [4, 34]. A family history compatible with autosomal dominant inheritance supports the diagnosis, but its absence does not exclude it [1]. Atypical forms, defined by Masuda and colleagues as two major criteria, or two major and one minor, do not meet the criteria but may have a pathogenic variant [50]. The Japanese national cohort included patients with two major criteria and a causal variant, and its authors propose revising the criteria to incorporate the genetic result and to make middle and inner ear anomalies, present in 63.8% and 71.1% of patients, major criteria [25]. A molecular diagnosis can be made even without complete clinical criteria [1].

5.2. Factors predicting a positive genetic result

In the Masuda cohort, detection of a pathogenic or likely pathogenic EYA1 variant was 86% in typical patients and 33% in atypical patients (25% in the article's abstract; p = 0.0001), and 79% versus 17% per family [50]. Detection was 94% in patients with a branchial anomaly versus 33% in the others (p = 0.0002), and 100% in patients with mixed deafness in at least one ear versus 30% in the others (p = 0.0005); cochlear hypoplasia and enlarged vestibular aqueduct were associated with detection rates of 78% and 84% [50]. Krug obtained 76% in typical and 9% in atypical cases, and Orten 31% in families meeting the criteria and 7% in “questionable” ones, both without whole genome sequencing [27, 61]. In the Korean cohort with whole genome sequencing, the yield was similar in typical (96%) and atypical (93%) cases, because most atypical cases had SIX1 variants [26]. In the Japanese national cohort, 84.6% of the 78 probands tested received a diagnosis; 81.6% of the cohort met the full criteria [25].

5.3. Audiological assessment and temporal bone imaging

Complete hearing assessment includes auditory brainstem responses (ABR), otoacoustic emissions and age-appropriate pure-tone audiometry; if the loss is fluctuating or progressive, CT or MRI of the temporal bones is indicated to look for an enlarged vestibular aqueduct [1]. The 2022 recommendation of the American College of Medical Genetics and Genomics (ACMG) characterises the loss by type, age at onset, progression or fluctuation, laterality, symmetry, severity, configuration, vestibular function and presence of auditory neuropathy, and regards temporal bone imaging as an adjunct, especially if the diagnosis is uncertain or there is cochlear implant candidacy, auditory neuropathy or progressive loss, weighing radiation and sedation [32]. High-resolution CT better assesses the bony structures of the canal and middle ear and is superior in atresia; MRI shows the inner ear, cochlear nerves and brain without radiation; detection of cochlear nerve deficiency or a severe inner ear malformation affects the prognosis with hearing aids or cochlear implant [87].

Offset of the cochlear turns is the best-performing imaging marker. Juliano and colleagues compared 40 individuals with the spectrum and 40 controls and defined the turn alignment ratio (TAR), measured on CT or MRI, with a cut-off of 0.476: sensitivity 1.0 and specificity 0.986; all EYA1 carriers except one cochlea, and all patients of unknown genotype, had a TAR below the cut-off, and all SIX1 carriers except one, as well as all controls, had a TAR above it [30]. GeneReviews regards a TAR below 0.476 as diagnostic of the EYA1-related spectrum [1]. Absence of offset does not exclude the diagnosis and may suggest a SIX1 genotype [31]. Assessment of the cochlear nerve by high-resolution MRI is necessary before cochlear implantation, because aplasia of the nerve is the only absolute contraindication [1, 22].

5.4. Renal assessment

The initial assessment includes renal ultrasound (agenesis, hypoplasia, dysplasia), dimercaptosuccinic acid (DMSA) scintigraphy if scarring is suspected, urea and creatinine to estimate GFR, and urinalysis for proteinuria and haematuria; study of the urinary tract uses diuretic renography with mercaptoacetyltriglycine (MAG3) for pelviureteric junction obstruction and voiding cystourethrography for VUR [1]. GeneReviews also mentions intravenous urography, which recent sources do not cite [1]. In children, the 2024 KDIGO (Kidney Disease: Improving Global Outcomes) guideline recommends estimating GFR with the CKD-EPI, CKiD U25 or EKFC equations, using cystatin C if muscle mass is low, requesting urinary protein/creatinine and albumin/creatinine ratios at initial screening (tubular proteinuria is more frequent in children) and regarding an eGFR below 90 mL/min/1.73 m² as “low” from 2 years of age [91, 92].

The indication for renal ultrasound differs between sources. For the ACMG, in the absence of a specific syndromic suspicion, urinalysis and renal ultrasound can await the genetic result [32]. When pits, fistulae or pinna malformation are present with another Wang criterion, ultrasound is indicated straight away, and GeneReviews, the systematic review by Biggs and the review by Kumarasamy advocate renal investigation in all patients with suspected spectrum, even without symptoms [1, 4, 34, 60, 89]. The two positions are compatible: the ACMG position applies to the child with deafness without syndromic signs, and the others to the child with branchial or auricular signs.

5.5. Genetic testing strategy

The 2022 ACMG recommendation, which replaces the 2014 guideline, advocates pre-test counselling and targeted genetic testing when there are findings suggestive of a syndrome, with the choice between single gene, panel, exome, genome, karyotype, microarray or CNV analysis by next-generation sequencing (NGS) according to the clinical picture; in hearing loss without syndromic signs, it recommends a comprehensive panel including the genes of the ClinGen hearing loss panel and, if negative, exome or genome; a negative result does not exclude a genetic cause [32, 93]. GeneReviews describes two approaches [1]. In the targeted approach, EYA1 and SIX1 are sequenced and, if the result is negative, targeted deletion and duplication analysis is performed; in a multigene panel that includes EYA1, SIX1 and the genes of the differential, deletion and duplication analysis is highly recommended. In the genomic approach, exome sequencing is mainly used; most point variants are detectable by exome, but EYA1 structural variants are more accessible by whole genome sequencing [1, 26]. Chromosomal microarray detects large deletions and duplications of 8q13.2-q13.3 and is the indicated test when there is developmental delay, short stature or an otofaciocervical phenotype; in childhood renal hypoplasia or dysplasia, microarray has a diagnostic rate of about 10% and is proposed as first line [1, 37, 65].

Source: GeneReviews, table 1 [1]. The columns indicate the proportion of known variants detected by each method and not the clinical sensitivity of each test; exome and genome sequencing also detect deletions and duplications through read depth or breakpoints, but with lower sensitivity than targeted analysis [1].

The Korean cohort shows the contribution of each step: panel or exome gave a diagnosis in 18 of 23 families (78.3%), CNV analysis on the exome and MLPA added one (82.6%), and PCR-free whole genome sequencing added two (91.3%), a gain of 8.7% [26]. The following table summarises the published diagnostic yield, which depends mainly on inclusion criteria and methods.

Table sources: [25–27, 47, 50, 61, 63, 69, 80]. The yields of Krug (45 of 124 families, 36%) and Brophy (5 of 32, 16%) were recalculated from the numerators, because the Cho table gives 46% and 14% [26, 27, 63].

5.6. Test limitations

Sanger sequencing and panels or exomes without CNV analysis do not detect multiexon or whole-gene deletions, which account for about 20% of EYA1 variants [1, 47]. MLPA and allele-specific PCR detect partial or complete deletions, but not complex rearrangements, cryptic inversions or Alu element insertions [1, 26]. Microarray detects large deletions, but the apparent size depends on probe density at 8q13.2-q13.3, and balanced rearrangements, including pericentric inversions of chromosome 8, require high-resolution karyotyping or FISH [1, 66]. Deep intronic variants are detected only by whole genome sequencing and require RNA or minigene studies for classification; because EYA1 is not expressed in accessible tissues, sequencing of the patient's RNA is not always possible [49, 68]. Testing on leucocyte DNA does not detect exclusively gonadal mosaicism and may not detect low-level somatic mosaicism [1]. About 10% of patients who meet the criteria remain undiagnosed even with whole genome sequencing [1, 26].

5.7. Report, variants of uncertain significance and segregation

The report should state the gene, the transcript and version (NM_000503.6 for EYA1 and NM_005982.4 for SIX1), the variant in HGVS, the zygosity and the class according to the ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology) standards, ideally with the specification of the ClinGen hearing loss working group, which the Japanese national cohort and that of Masuda applied [8, 25, 50]. For CNV, the description should follow ISCN, as in rsa 8q13.3(EYA1 exons 10–18)×1 [50]. A VUS in EYA1 or SIX1 neither establishes nor excludes the diagnosis [1]. Family segregation, confirmed de novo occurrence and functional splicing studies allow reclassification: the Danish deep intronic variant moved from VUS to likely pathogenic with the minigene and cosegregation, applying the ClinGen recommendations for splicing variants, and the fetal variant c.640-15G>A followed the same path [49, 68]. In a Brazilian patient, the in-frame deletion c.1558_1575del p.(Val520_Asn525del) remained a VUS (PM2, PM4, PP4), and the decision to regard the case as solved was based on clinical correlation [73]. A SIX5 variant should not be reported as the explanation of the phenotype [1, 12]. Without a molecular diagnosis, the ACMG recommends genetics follow-up every 3 years for reinterpretation and new tests, and GeneReviews recommends storing the proband's DNA [1, 32].

5.8. Prenatal and preimplantation diagnosis

Once the familial alteration has been identified, prenatal diagnosis and preimplantation genetic testing (PGT) are possible, but intrafamilial variability makes it impossible to predict the manifestations and severity in a carrier fetus [1]. Without a molecular diagnosis, these options are limited, as highlighted by the Danish family who waited six years for identification of the variant [49]. In an at-risk fetus, ultrasound at 16–17 weeks assesses significant renal malformations and oligohydramnios [1]. The kidneys are visible on ultrasound at 11–12 weeks, but not all phenotypes are detectable so early, which justifies serial scans in at-risk pregnancies [38]. In the presence of a fetal renal anomaly, karyotype or microarray is indicated if there is bilateral renal involvement or another finding, and DNA from the fetus and parents should be stored [86]. Fetal exome sequencing has identified EYA1 variants in fetuses with urinary, cardiac or facial anomalies, including de novo cases [68, 85].

5.9. Practical algorithm

6. Differential Diagnosis

6.1. Comparative table

OMIM lists more than 700 entries for syndromic deafness; the spectrum is easily recognised in a large family, but is difficult to distinguish in an isolated case or a small family [1]. In the GeneReviews “Genetic Hearing Loss Overview”, the spectrum is the second most common cause of autosomal dominant syndromic deafness, after Waardenburg syndrome [94]. In the table, AD denotes autosomal dominant and AR autosomal recessive inheritance.

6.2. Main differential diagnoses

Townes-Brocks syndrome shares the ear anomalies, deafness and renal anomalies, but is distinguished by the thumb malformations, imperforate anus and heart disease [1, 95]. In the Japanese series of Unzaki, 2 of the 26 families with an identified cause had SALL1 variants, and patients with a spectrum-like phenotype, bilateral sensorineural deafness and external ear anomalies with a SALL1 variant have been described [4, 80]. Branchio-oculo-facial syndrome also has cervical anomalies, nasolacrimal duct stenosis, deafness, prehelical pits, malformed pinnae and renal anomalies, but the cervical and infra-auricular skin lesions, the lip pseudocleft and the ocular anomalies distinguish it; the two conditions are not allelic [97, 98].

Alport syndrome is the most important renal differential, because it also combines deafness and progressive kidney disease. In the case in section 10, deafness, visual loss and proteinuria led to consideration of Alport, which was ruled out by the absence of typical ocular lesions, normal expression of collagen IV α3, α4 and α5 in the glomerular basement membrane and by exome sequencing; thin basement membrane nephropathy and oligomeganephronia were also excluded [60]. In the Greek-Cypriot family, the absence of significant proteinuria and the presence of operated branchial clefts helped to distinguish the two diseases [83]. Pendred syndrome shares the enlarged vestibular aqueduct, cochlear hypoplasia and fluctuating and progressive deafness, but has no external or middle ear malformations or fistulae, and goitre appears at puberty [1, 34]. PAX2-related disease is distinguished by the optic nerve anomaly, and the 17q12 deletion by diabetes, cystic kidneys and neurodevelopmental disorders [99, 100].

The oculo-auriculo-vertebral spectrum is unilateral or asymmetric and has tags along the line between the tragus and the oral commissure, whereas in the branchio-oto-renal spectrum preauricular pits and cervical fistulae predominate [39, 59]. Even so, the branchio-oto-renal spectrum may show mild facial asymmetry and hemifacial microsomia, and a complex rearrangement involving SIX1 has been described in an individual with overlap of the two phenotypes [1, 34]. In the child with microtia and ear anomalies, molecular analysis is indicated when Townes-Brocks, the branchio-oto-renal spectrum or Treacher Collins is suspected, and renal ultrasound should be requested unless there is a clear diagnosis of Treacher Collins [39, 59].

6.3. Congenital anomalies of the kidney and urinary tract

CAKUT accounts for 20–30% of all congenital malformations, with a prevalence of 3–6 per 1000 births; it is the predominant group among children in the ERKNet ERKReg registry and the cause of about 30% of paediatric kidney failure in the 2016 registry of the European Society for Paediatric Nephrology (ESPN) and the European Renal Association (ERA) [38]. Unilateral renal agenesis occurs in 0.15 per 1000 newborns and bilateral agenesis in 0.12 per 1000, with a male predominance (2.45:1) [37]. Monogenic forms account for 10–15% of cases, and PAX2, HNF1B and EYA1 are the most frequent genes among more than 50; known pathogenic CNV were found in 4.1% of 2824 cases, and novel CNV in a further 2% [38]. In a microarray study of 522 children with renal agenesis, hypoplasia or dysplasia, 10.5% had a genomic disorder not suspected clinically, and half the pathogenic CNV had been inherited from an apparently unaffected parent [37]. In patients with renal agenesis, hypoplasia or dysplasia, a molecular diagnosis is possible in up to 15–20%, and 5–10% have variants in PAX2, HNF1B, DSTYK, SALL1, SIX1 or EYA1 [37]. In fetal or neonatal renal agenesis or dysplasia, looking for pits, fistulae and familial deafness and renal ultrasound in the parents make it possible to distinguish the branchio-oto-renal spectrum from isolated CAKUT [86]. About one-third of patients with unilateral renal agenesis or multicystic dysplastic kidney have contralateral VUR or pelviureteric junction obstruction [38].

7. Treatments and Risk Management Strategies

7.1. Principles and organisation of care

There is no consensus clinical practice guideline specific to the spectrum; the GeneReviews recommendations are based on the authors' experience, and the others come from general documents on hearing loss (ACMG 2022, JCIH 2019) and chronic kidney disease (KDIGO 2024 and the European Renal Best Practice, ERBP, commentary), from systematic reviews and from case series [1, 32, 34, 87, 91]. There is no pharmacological therapy directed at the cause; treatment is organ-directed and requires a team with otorhinolaryngology, audiology, speech and language therapy, nephrology, urology, medical genetics and genetic counselling [1, 9]. The ACMG recommends referral to a multidisciplinary centre that also includes early intervention and family support [32]. All children with hearing loss should be enrolled in an appropriate educational programme, and early identification and intervention are decisive for speech and language; late identification is associated with poorer reading, communication and speech [1, 94].

7.2. Assessment after diagnosis

Table sources: [1, 4, 91].

7.3. Hearing rehabilitation

Hearing aids are the first step in mild to moderate sensorineural or mixed loss and should be fitted before any definitive treatment in prelingual children [1, 4]. In the Japanese national survey, 80% of patients (40 of 50) were successful with hearing aids, and 8 of 10 in another series [34]. The only contraindication to hearing aids and cochlear implantation is aplasia of the cochlear nerve [1].

A bone conduction device (BAHA, bone-anchored hearing aid) is an option in canal atresia or when the middle ear is abnormal and the Jahrsdoerfer score is low [4]. In the systematic review, the two patients described benefited; a Japanese child with canal atresia, the sister of another affected child, had a good result with a transcutaneous bone conduction device, and in the Japanese national cohort some patients received a BAHA after middle ear surgery without sufficient improvement [25, 34, 101].

Canaloplasty may be considered in canal atresia or stenosis when the middle ear is functional, but associated anomalies, such as the facial nerve overlying the oval window, may prevent a good result; thin-slice CT of the temporal bones in the axial and coronal planes is needed before surgery [1, 4]. The results of middle ear surgery (ossiculoplasty, stapedotomy, stapedectomy, tympanoplasty) are, as a rule, poor. In the systematic review, there was benefit in only 11 of the 30 middle ear procedures with a reported outcome, with isolated successes (for example, closure of the air-bone gap from 55 to 15 dB two years after mastoidectomy with a neo-oval window) and failures in series of stapedectomies, Teflon interpositions and ossiculoplasties [34]. In the Japanese national cohort, only 3 of 13 operated patients improved, and the authors advise against middle ear surgery in conductive or mixed loss [25]. In a Korean series of 18 patients from 12 families, the air-bone gap improved by a mean of 20.5 dB in ears without an enlarged vestibular aqueduct and did not change or worsened (+0.8 dB) in ears with an enlarged aqueduct, even after adjustment; the authors conclude that surgery is not always contraindicated, but that an enlarged aqueduct, which acts as a “third window”, predicts failure [102]. Multiple ossicular malformations, such as an irregular stapes angle or a thickened long process, make prosthesis fixation difficult, and congenital cholesteatoma, described in the spectrum, requires cautious surgery because of the frequency of complications in malformed ears [25].

Cochlear implantation is indicated in severe to profound bilateral sensorineural loss and when hearing aids give insufficient benefit [1, 103]. Inner ear malformations do not exclude it, but require preoperative imaging and planning: CT estimates the electrode insertion depth in cochlear hypoplasia, rotation of the cochlea may require a more anterosuperior cochleostomy and an enlarged vestibular aqueduct increases the risk of perilymph outflow (gusher) [1, 34]. In the systematic review, the five patients described with an implant benefited, including a 50-year-old man with thresholds of 40 dB or less between 250 and 2000 Hz; in the Japanese survey, surgery, including implantation, was successful in 7 of 11 patients (64%) [34]. The first adult with bilateral implants and objective results before and after performed comparably to nonsyndromic adults with normal anatomy [103]. In the Chinese series with cochlear nerve deficiency, two implanted patients had, at 12 months, mean thresholds of 40 dB HL and word recognition of 80–90%, and a child with bilateral cochlear nerve deficiency, without cortical potentials before implantation, showed cortical potentials and mismatch negativity (MMN) 9 months later [22]. In that series, ears without cochlear nerve deficiency reached with hearing aids a mean threshold of 36.3 ± 11.4 dB HL, and ears with deficiency a threshold of 45.8 ± 34.0 dB HL [22].

7.4. Branchial and lacrimal anomalies

Second arch cysts and fistulae can be monitored if asymptomatic; infection is treated with antibiotics, and excision is indicated if there is recurrent infection, symptomatic discharge or cosmetic reasons [1, 4]. Complete resection of the tract minimises recurrence [1]. In a 20-year-old Chinese woman with bilateral preauricular and cervical fistulae and intermittent discharge since birth, bilateral fistulectomies had not recurred at 6 months [104]. In the case in section 10, the patient had repeated discharge from the branchial fistula and required incision and drainage of an abscess of the preauricular fistula [60]. Epiphora due to aplasia or hypoplasia of the nasolacrimal duct should be looked for at each visit and referred to ophthalmology [1, 4].

7.5. Kidney and urinary tract

Early referral to paediatric nephrology is recommended in all patients with a renal anomaly [1, 4]. Pelviureteric junction obstruction is corrected surgically, usually by pyeloplasty, and VUR is treated with antibiotic prophylaxis and/or surgical correction [1]. The sources consulted contain no prophylaxis regimen specific to the spectrum; VUR, which affects about 1% of live births, is as a rule asymptomatic and self-limiting, medical and surgical treatments have similar efficacy, high-grade reflux and scarring at birth are the poor prognostic factors, and neonatal management is controversial and should be led by an experienced paediatrician [37]. Unilateral renal agenesis and dysplasia require follow-up with monitoring of proteinuria, arterial hypertension and infections [4].

In chronic kidney disease, the aims are to slow progression, control hypertension and treat proteinuria, under the guidance of the nephrologist [1]. ARBs have been used as nephroprotective agents in patients with proteinuria: the Japanese man with FSGS kept stable renal function for 11 years, and in the case in section 10 the urinary albumin/creatinine ratio (ACR) fell from 133.16 to 73.23 mg/g in three years [60, 82]. This use follows the general principles of chronic kidney disease and not an approved indication for the spectrum; the sources consulted give no doses, which should follow the SmPC of the chosen drug and the KDIGO paediatric or adult recommendations. After starting ACE inhibitors (angiotensin-converting enzyme inhibitors), ARBs or other haemodynamically active therapies, KDIGO 2024 regards initial falls in eGFR of 10–30% as usual and reversible, not warranting discontinuation, and recommends assessment if the fall exceeds 30% [91, 92]. In stages G3 to G5, KDIGO recommends (grade 1A) calculating the risk of kidney failure with a validated equation (KFRE, Kidney Failure Risk Equation): a 5-year risk of 3–5% justifies referral to nephrology, a 2-year risk above 10% multidisciplinary care and above 40% preparation for kidney replacement therapy [91]. In children and young people with kidney failure, a genetic cause is more likely, and a genetic diagnosis may avoid renal biopsy [91].

Immunosuppression has no demonstrated efficacy in the glomerular disease of the spectrum. In one of the children in the Lin series, with immune complex-mediated glomerulonephritis, there was no response to corticosteroids or immunosuppressants [72]. In the child with EYA1 c.1050+5G>A and steroid-resistant proteinuria, the urinary protein/creatinine ratio improved with tacrolimus, used off-label and with no dose given in the abstract; podocytes derived from the patient's induced pluripotent stem cells (iPSC) showed increased motility and cytoskeletal rearrangement, and dexamethasone did not protect them from puromycin aminonucleoside injury in vitro [71]. These data from one case and a cell model do not justify the routine use of immunosuppressants. In end-stage chronic kidney disease, kidney replacement therapy (haemodialysis, peritoneal dialysis or kidney transplantation) is indicated [1, 4]. Bilateral renal agenesis is lethal [4, 54].

7.6. Drugs and regulatory status

A search of ClinicalTrials.gov on 10 October 2026, with the terms “branchio-oto-renal”, “branchiootorenal syndrome”, “EYA1”, “branchio-otic syndrome” and “Melnick-Fraser”, found no registered study; GeneReviews also points to the EU Clinical Trials Register and acknowledges that there may be no trials for the disease [1, 33]. The absence of registrations does not prove that no research is under way.

7.7. Intervention studies and limits of the evidence

Table sources: [22, 25, 34, 60, 71, 82, 102]. There is no randomised trial in the spectrum, and all intervention data come from retrospective series, isolated cases and reviews of published cases, with publication bias towards successes and failures, no control group and heterogeneous outcome measures [9, 34]. The percentages from the different series cannot be compared with one another, because selection, ear anatomy and techniques differ. Renal outcomes on ARBs concern isolated cases and a reduction in albuminuria, not a demonstrated effect on progression to end-stage chronic kidney disease.

7.8. Developments in the last twelve months

None of these publications is a clinical trial, a regulatory opinion or an authorisation. CRISPR genome editing to correct complex EYA1 structural variants has been used only experimentally [26]. The GeneReviews “Genetic Hearing Loss Overview” mentions intracochlear gene therapy as a general possibility for hearing intervention, with no data for the spectrum [94].

7.9. Agents and exposures to avoid

Environmental exposures that cause hearing loss should be avoided, especially repeated overexposure to noise in mild to moderate loss; mobile phones allow headphone volume to be limited to 75 dB [1]. Anecdotal reports that increased intracranial pressure in an enlarged vestibular aqueduct may trigger drops in hearing led some authors to advise against weightlifting and contact sports, but there is no evidence that avoiding these activities reduces progression; families should be informed of the possible association between an enlarged aqueduct and hearing loss after head injury and decide for themselves [1]. In CAKUT, drugs that may compromise renal function or that require normal renal physiology, such as some antibiotics and analgesics, should be used with caution and at doses adjusted to eGFR [1].

7.10. Pregnancy, lactation, perioperative care and transition

A pregnant woman with the spectrum and known renal involvement should be followed in maternal-fetal medicine [1]. ACE inhibitors and ARBs should be reviewed before conception, because fetal exposure to ACE inhibitors produces a phenocopy of renal tubular dysgenesis [86]. The sources consulted describe no specific data on lactation in the spectrum.

In the perioperative setting, retrognathia may cause breathing difficulty and a short or cleft palate feeding difficulties, which should be anticipated in anaesthesia [1]. Middle ear surgery and cochlear implantation require prior CT because of the aberrant position of the facial nerve, the ossicular malformations and the risk of gusher [1, 25, 34]. Perioperative drug doses should be adjusted to renal function [1].

Transition to adult care coincides with the period of greatest renal risk: in the Greek-Cypriot family, three of the four patients who reached end-stage chronic kidney disease were 14 or 17 years old, and KDIGO 2024 recommends more frequent monitoring during pubertal growth, because the renal reserve may be exhausted in adolescence or early adulthood [83, 91]. Transition should include transfer to adult nephrology, continuity of audiological follow-up and genetic counselling directed at the young person themselves (section 8) [1].

7.11. Guideline recommendations and divergences

8. Reproductive Options and Family Counselling

8.1. Inheritance and recurrence risks

The spectrum is transmitted in an autosomal dominant manner, and each child of an affected individual has a 50% probability of inheriting the variant [1]. Most diagnosed patients have an affected parent, although the case may appear isolated because the signs in relatives were not recognised [1]. Among patients with a molecular diagnosis, 10–20% have a de novo variant in EYA1 or SIX1 [1]. In a hearing loss panel applied without phenotype-based exclusions, de novo variants occurred in 10% of trios with segregation, which shows that the absence of a family history does not rule out a dominant cause [105]. The observed proportion depends on recruitment: in the Japanese national cohort, among 133 patients with a known family history, 60.4% had evident autosomal dominant inheritance and 18.3% were sporadic cases, whereas in a Chinese tertiary referral series the variants were de novo in 4 of 8 families [22, 25]. A 2026 review states that more than 90% of patients have an affected parent, a figure that does not match that of GeneReviews [1, 4].

Germline mosaicism has been documented: two Japanese sisters with branchio-otic syndrome and the same EYA1 variant were born to unaffected parents, and haplotype analysis confirmed parentage [101]. The empirical risks of nonsyndromic renal agenesis do not apply when the spectrum has been diagnosed [1, 37].

Expressivity is unpredictable within the same family, and the 50% risk refers to the variant and not to a specific phenotype [1]. The next child may have a different and more severe renal phenotype than that of the parent or sibling, including bilateral renal agenesis [1, 38]. Fraser estimated that the offspring of affected individuals with pits or fistulae had about an 80% probability of deafness and that the risk of severe renal malformation was probably low, an estimate made before molecular diagnosis [41]. Incomplete penetrance, as with the deletion of exons 12 to 18 present in the asymptomatic father and brother of a Chinese proband, means that a relative should not be excluded on the basis of a normal examination alone when molecular testing is possible [22].

8.2. Assessment of parents and at-risk relatives

In an apparently isolated case, the parents should be assessed. If the proband's variant is known, targeted molecular testing is performed, with a method capable of detecting the type of alteration found (MLPA, microarray or whole genome sequencing when it is a CNV or structural rearrangement) [1]. Without a molecular diagnosis, the parents are examined for hearing loss, preauricular pits, lacrimal duct stenosis, branchial fistulae or cysts and renal anomalies [1]. In bilateral renal agenesis or dysgenesis, 9% of first-degree relatives had asymptomatic renal malformations, which supports renal ultrasound in the parents before counselling on recurrence [54, 86, 106].

Asymptomatic at-risk relatives should be assessed because the otological and renal anomalies are treatable or progressive: molecular testing when the familial variant is known; otherwise, complete physical examination with hearing assessment and renal imaging and function [1]. In a relative of an affected individual, a single major criterion is sufficient for the clinical diagnosis [1, 47]. Assessment includes minors, because early detection of deafness and kidney disease has therapeutic consequences in childhood; testing an at-risk child does not raise the issue of predictive testing for diseases with no possible intervention [1, 94].

8.3. Reproductive options

The ideal time to discuss the risk and the options for prenatal diagnosis or PGT is before pregnancy, and counselling should be offered to affected or at-risk young adults [1]. With the familial variant identified, prenatal diagnosis and PGT are possible, but do not allow severity to be predicted; perspectives on their use differ and the decision is personal [1]. Preimplantation diagnosis with NGS has been applied effectively in families with genetic deafness [26]. Without a molecular diagnosis, the options are limited to ultrasound; Fraser already regarded the offspring of affected individuals as eligible for prenatal diagnosis of renal dysplasia [28, 49]. Ultrasound at 16–17 weeks assesses significant renal malformations and oligohydramnios, and the kidneys are visible from 11–12 weeks, although not all phenotypes are detectable so early [1, 38]. In the Chinese fetus with c.640-15G>A, the pregnancy was terminated at the parents' request after counselling; the authors could not exclude parental gonadal mosaicism [68].

8.4. Content of counselling

Counselling should address the nature of the spectrum and its variability, even within the family, the 50% risk and the residual risk of gonadal mosaicism, the need for hearing and renal assessment of all at-risk relatives, the reproductive options and their limits, storage of the proband's DNA when there is no molecular diagnosis and periodic reassessment when testing is negative [1, 32]. Results should be communicated in a genetic counselling consultation, including the risks to relatives [32]. When the diagnosis rests on a VUS, as with the in-frame deletion described in a Brazilian patient, the result should not be used for predictive testing or prenatal diagnosis until reclassification [1, 73].

9. Special Considerations: Population Diversity and Epidemiology

9.1. Prevalence and what each figure measures

There are no large-scale population prevalence studies [1]. The estimate of about 1/40,000, repeated by the Smith text, NORD (National Organization for Rare Disorders) and Orphanet (2.5/100,000, classified as validated, with worldwide and Canadian values), derives from a single Montreal study published in 1980, in which 19 of 421 white children in schools for the deaf had preauricular pits and the spectrum was confirmed in 4 of the 9 families studied [2, 3, 28, 107]. That study measures the proportion of cases in a selected population of children with profound deafness (about 2%) and not the prevalence in the general population; the extrapolation to 1/40,000 is an order of magnitude [9, 28]. NORD states that the spectrum accounts for 2–3% of children with profound deafness and that both sexes are equally affected [107].

The proportion of 58 in 8032 corresponds to 0.72% of all those tested; GeneReviews describes it as a proportion of patients with a genetic diagnosis, which would give 1.7% (58 in 3376) [1]. The spectrum is the second most common cause of autosomal dominant syndromic deafness [94]. The ACMG states that about 30% of genetic deafness is syndromic and that Pendred, Usher, Waardenburg and branchio-oto-renal syndromes account for substantial percentages in some populations [32].

9.2. Geography, ancestry and gene distribution

In the United States, the largest series come from the University of Iowa and Boys Town: Orten studied 435 families, with detection of EYA1 variants in 31% of those meeting the criteria, and Kochhar found SIX1 variants in 4% of 247 families [61, 69]. In Europe, the French (140 patients from 124 families), Dutch (32 patients from 6 families) and Danish series show a predominance of EYA1 and a contribution of SIX1 of 2–4.5% in Western series [26, 27, 49, 76]. A three-generation Greek-Cypriot family documents the renal natural history [83].

In East Asia, the contribution of SIX1 is greater: 17.9% of probands tested in the Japanese national cohort and 35% of families in the Korean cohort [25, 26]. In Japan, EYA1 explained 66.7% of probands tested, and the earlier national review had found an EYA1 variant in 11 of 12 families [25]. None of the Japanese and Korean cohorts found SIX5 variants, unlike some older Western series [25, 26, 50]. Families have been described in China, including the family with the ANLN variant, and in Tunisia, with a SIX1 variant and an exclusively auditory and auricular phenotype [3, 70]. The sources consulted describe no founder variants; EYA1 variants are mostly private, and the documented recurrences (SIX1 c.328C>T in five unrelated families, EYA1 c.1081C>T in patients of various origins, HERV-mediated 8q13.2-q13.3 deletion) result from mutational hotspots and not from a demonstrated founder effect [22, 60, 61, 63, 69].

In Brazil, a large family with branchio-otic syndrome, without renal anomaly, had a 71.8 kb duplication of exons 4 to 10 of EYA1, and a cohort of 99 probands with deafness, tested with a 218-gene panel after exclusion of GJB2, GJB6 and the mitochondrial variant MT-RNR1 NC_012920.1:m.1555A>G and without ear malformations on imaging, included one patient with branchio-otic syndrome type 1 and the EYA1 deletion c.1558_1575del, with bilateral profound postlingual deafness and dominant inheritance [67, 73]. The sources consulted contain no data from Portugal, which does not demonstrate that none exist.

9.3. Special populations

In pregnancy, a patient with renal involvement needs maternal-fetal follow-up, and the fetus has a 50% risk of inheriting the variant [1]. Adolescents and young adults concentrate the risk of progression to end-stage chronic kidney disease [83, 91]. Adults may be diagnosed late, on the basis of chronic kidney disease or worsening deafness, and in 7.1% of Japanese patients symptoms were noticed after 19 years of age [25, 60, 82]. Patients followed only in otorhinolaryngology may have renal anomalies that have never been investigated, and only about 8.7% of published studies on the spectrum appeared in nephrology journals [25, 60].

9.4. European Reference Networks and patient associations

ERKNet (European Rare Kidney Disease Reference Network), one of the 24 European Reference Networks, has working groups dedicated to congenital malformations and ciliopathies, obstructive uropathies and paediatric chronic kidney disease, dialysis and transplantation, and maintains the ERKReg registry [35, 38]. ERN CRANIO, with 36 member hospitals in 15 countries of the European Union and the European Economic Area, covers craniofacial anomalies and ear, nose and throat disorders and is the relevant network for the otological and branchial component [36]. The CAKUT, urinary tract infection and bladder dysfunction working group of the European Society for Paediatric Nephrology (ESPN) collaborates with ERKNet and maintains the EURECA registry of familial CAKUT [109].

No patient association specific to the spectrum was identified. GeneReviews and NORD list general organisations: GARD (Genetic and Rare Diseases Information Center), NORD, American Society for Deaf Children, BabyHearing.org (from the National Institute on Deafness and Other Communication Disorders, NIDCD), Children's Craniofacial Association, Face Equality International, Kidney Foundation of Canada, National Association of the Deaf, National Kidney Foundation, American Kidney Fund, Let Them Hear Foundation and American Academy of Audiology [1, 107]. In the United Kingdom, the Oxford Desk Reference lists Contact a Family and, for families facing oligohydramnios, ARC (Antenatal Results and Choices) [39, 86]. The MORL laboratory of the University of Iowa accepts cases without an identified variant for comprehensive hearing loss testing [1]. The sources consulted identify no specific resources in Portugal or Brazil.

10. Illustrative Clinical Case

Yang and colleagues, from the Third Xiangya Hospital (China), published in November 2025 the case of an 18-year-old man who attended a clinic for acne and in whom stage 2 chronic kidney disease with proteinuria, without haematuria or oedema, was discovered incidentally [60]. Blood pressure was 115/65 mmHg, height 175 cm and weight 60 kg. Examination showed bilateral preauricular and branchial fistulae, with serous discharge from the right branchial fistula (figure 1 of the article: https://pmc.ncbi.nlm.nih.gov/articles/PMC12752338/figure/Fig1/). The patient had a history of repeated discharge from the branchial fistula and of drainage of an infection; he had been born at term weighing 2.9 kg without perinatal complications, had had deafness since about 10 years of age and visual loss since 17. There was no family history of fistulae, deafness, visual loss or kidney disease [60].

Investigations showed creatinine 121 µmol/L (reference 59–104), urea 5.96 mmol/L, uric acid 661 µmol/L (reference 208–428), eGFR 81.38 mL/min/1.73 m², ACR 133.16 mg/g, serum albumin 48 g/L and haemoglobin 144 g/L; immunoglobulins, complement (C3 0.72 g/L; C4 0.12 g/L), autoantibodies and serology were normal or negative [60]. Ultrasound showed small kidneys, the left measuring 79 × 32 mm (−2.07 and −3.00 standard deviations) and the right 97 × 40 mm (−0.79 and −2.00 standard deviations), with normal echogenicity and flow. Audiometry revealed bilateral mixed deafness, with an Ad tympanogram on the left and B on the right. Ophthalmological examination showed only a refractive error, without anterior lenticonus, posterior subcapsular cataract, posterior polymorphous dystrophy or retinal flecks, and MRI of the internal auditory canals showed submucosal cysts of the maxillary sinuses [60].

Biopsy of the right kidney included 15 glomeruli, 7 enlarged (180–280 µm) and 4 with mesangial cellular and matrix proliferation, tubular dilatation with loss of the brush border in some tubules and mild fibrosis. Electron microscopy showed focal thinning of the glomerular basement membrane (160–380 nm) with segmental wrinkling and segmental foot process effacement, without deposits (figure 3 of the article: https://pmc.ncbi.nlm.nih.gov/articles/PMC12752338/figure/Fig3/), and immunofluorescence was weakly positive for IgM and C3. Expression of collagen IV α3, α4 and α5 in the basement membrane was normal [60]. Exome sequencing identified no variants in COL4A3, COL4A4 or COL4A5 and revealed the heterozygous variant NM_000503.6:c.1081C>T p.(Arg361Ter) in EYA1, absent from both parents, classified as pathogenic according to the ACMG standards [60]. The same variant is registered in ClinVar as pathogenic, without conflicts, and had previously been described in two patients with renal impairment and in a Chinese family with branchio-otic syndrome, which illustrates the variability associated with a single truncating variant [22, 58, 60].

The authors ruled out Alport syndrome (no typical ocular lesions, normal collagen IV, negative exome), oligomeganephronia (normal birth weight and glomerular number) and thin basement membrane nephropathy (non-uniform thinning, absence of isolated haematuria, presence of extrarenal signs) [60]. The patient started an ARB as a nephroprotective agent and a urate-lowering agent, with six-monthly follow-up. The ACR fell from 133.16 mg/g in July 2022 to 73.23 mg/g in June 2025; in November 2024 incision and drainage of an abscess of the left preauricular fistula was required. At the last assessment, in June 2025, blood pressure was between 100–120/65–75 mmHg, creatinine between 109 and 130 µmol/L and ACR between 73.23 and 92.31 mg/g [60].

The case shows that the spectrum can reach adulthood undiagnosed despite cervical fistulae with repeated infections and deafness since childhood, and that kidney disease can present with hypoplasia and glomerular changes and not only with an obvious structural malformation [60]. The authors acknowledge that glomerular hypertrophy may be compensatory for atrophy of the left kidney and recommend, in patients with ear and branchial arch anomalies, even without renal symptoms, assessment of renal function and imaging of the urinary tract [60]. Renal biopsy followed by exome sequencing reflects this patient's diagnostic pathway and not the usual approach: with fistulae, pits and mixed deafness, a clinical diagnosis by the Chang criteria and targeted genetic testing with CNV analysis can precede biopsy, which KDIGO accepts may be avoided when there is a genetic diagnosis [1, 91]. The use of the ARB is extrapolated from the general principles of chronic kidney disease, without a trial in the spectrum [91].

11. Prognosis and Long-Term Follow-up

11.1. Hearing prognosis

Hearing loss is stable in about 70% of families and progressive in about 30%, with an enlarged vestibular aqueduct as the main marker of progression and fluctuation [1, 76]. In the Japanese national cohort, 43.0% of patients reported progression, and 7.1% noticed the first symptoms in adulthood [25]. With appropriate rehabilitation, the functional prognosis is favourable in most: 80% of Japanese patients were successful with hearing aids, and the cochlear implants described provided benefit even with inner ear malformations [34, 103]. Cochlear nerve deficiency, present in 38.5% of patients in a series with EYA1, affects the outcome of hearing aids and implantation, and aplasia of the nerve contraindicates both [1, 22, 87]. Middle ear surgery rarely improves hearing durably [25, 34].

11.2. Renal prognosis

The vital and renal prognosis is determined by CAKUT and glomerular disease. Bilateral renal agenesis is lethal in the fetal or neonatal period [1, 4]. Fraser estimated severe renal dysplasia in about 6% of heterozygotes, and the Smith text reports chronic kidney failure in about 6% of patients [3, 28]. In the Greek-Cypriot family followed for 27 years, 4 of the 10 affected individuals reached end-stage chronic kidney disease at 14, 17, 17 and 36 years of age [83]. Proteinuria and glomerulosclerosis can lead to progression even without severe malformation, and cases with late diagnosis show that kidney disease can progress without symptoms for years [1, 60, 72]. The sources consulted describe no cohorts with systematic renal follow-up from birth, so there is no validated estimate of the lifetime risk of end-stage chronic kidney disease; nor are there data on life expectancy in patients without severe kidney disease. Data on treated disease are limited to cases with stable renal function for 3 to 11 years on an ARB [60, 82].

11.3. Surveillance

The renal intervals apply to the patient with or without a known structural anomaly, because glomerular disease may appear late, as in the mother and brother of the proband with EYA1 c.1050+5G>A, who developed proteinuria and a decline in GFR over 8 years without an initial structural anomaly [22, 71]. During pubertal growth, renal monitoring should be more frequent [91]. Regular follow-up involves otorhinolaryngology, audiology, speech and language therapy, nephrology and urology, and genetics remains involved as long as there is no molecular diagnosis [1, 32].

12. Summary and Final Considerations

The branchio-oto-renal spectrum is an autosomal dominant disorder of the development of the ear, the second pharyngeal arch derivatives and the kidney, caused by loss of function of EYA1 or by SIX1 variants, the two components of a transcriptional complex that coordinates the organogenesis of these tissues. The distinction between branchio-oto-renal and branchio-otic syndrome depends solely on the presence of a renal anomaly and has no nosological value, because both occur in the same family. SIX5, which still appears in OMIM and Orphanet, was disputed by ClinGen in 2018 and withdrawn by GeneReviews in 2025, and a variant in this gene should not be accepted as the cause.

Hearing loss, present in more than 90% of patients, is mixed, conductive or sensorineural depending on the malformed region, and progresses in about one-third, especially with an enlarged vestibular aqueduct. Preauricular pits and cervical fistulae or cysts are the signs that most guide the diagnosis and best predict a positive genetic result, and a cochlear turn alignment ratio below 0.476 on CT or MRI is practically diagnostic of the EYA1-related spectrum. Renal anomalies, from 15% to 67% depending on the recruitment of the series, range from minor dysplasia to lethal bilateral agenesis, and glomerular disease with proteinuria may lead to end-stage chronic kidney disease in adolescence or young adulthood, sometimes in patients diagnosed only at that stage.

Genetic testing must include deletion and duplication analysis of EYA1, which account for about one-fifth of variants; whole genome sequencing identifies cryptic inversions, balanced rearrangements and deep intronic variants, and raises the yield to about 90% in patients who meet the criteria. There is no specific drug and no registered clinical trial. Treatment is based on early hearing rehabilitation with hearing aids, bone conduction devices or cochlear implants, excision of symptomatic fistulae, urological correction and nephroprotection, and middle ear surgery has limited results, especially with an enlarged vestibular aqueduct. Hearing and renal surveillance should be maintained throughout life and intensified in adolescence.

Genetic counselling should explain the 50% risk to offspring, the residual risk of about 1% from gonadal mosaicism when the parents are not carriers and the impossibility of predicting severity, even within the family. All at-risk relatives should have hearing and renal assessment or targeted testing, because the manifestations are treatable. The epidemiological data rest on a 1980 study and hospital series, and cohorts with systematic renal follow-up that would allow the lifetime risk of kidney failure to be estimated are lacking.

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