ReNU Syndrome: RNU4-2-Related Neurodevelopmental Disorder

Literature and regulatory information updated: 6 October 2026.

0. Initial Reference Table

1. Introduction

ReNU syndrome is one of the commonest monogenic causes of neurodevelopmental disorder and results from variants in a gene that does not encode protein and measures only 145 nucleotides. This combination explains why it remained hidden during the decade in which exome sequencing became the main diagnostic tool: exome capture probes were designed for coding regions and do not include RNU4-2. The syndrome's name derives from the gene symbol, RNU4-2 [1, 7].

The discovery was independently published by two groups in 2024, both using genome sequencing data from the British 100,000 Genomes Project. Greene and colleagues, in a Bayesian rare variant association analysis of 41,132 non-coding genes, compared 5,529 unrelated intellectual disability cases and 46,401 controls; RNU4-2 was by far the most strongly associated gene, with 47 cases carrying variants in two contiguous regions and replication in three additional collections, totalling 73 unrelated cases [9]. Chen and colleagues identified a recurrent single-base insertion, n.64_65insT, de novo in 38 trio probands, delineated a population variation-depleted 18-base-pair critical region and assembled 115 affected individuals, 77.4% with the same insertion [7].

Both foundational studies showed that RNU4-2 explained a proportion of cases similar to the commonest classic genes. In 100,000 Genomes, RNU4-2 was the commonest aetiology among 9,112 cases with neurodevelopmental abnormalities (46 cases, 0.50%); in the UK National Health Service Genomic Medicine Service (GMS), which performs less prior genetic screening, it was second, with 21 of 5,527 cases (0.38%), immediately after MECP2 (24 cases) [9]. Chen and colleagues estimated that critical-region variants explain approximately 0.4% of all neurodevelopmental disorders, assuming a prior diagnostic yield of 40% in the starting cohort [7].

Knowledge expanded rapidly between 2025 and 2026. A French and international cohort of 150 individuals established a correlation between the affected structural domain and severity, described a splicing signature and methylation episignature, and implicated the U5 snRNA genes RNU5B-1 and RNU5A-1 [8]. Subsequent descriptions included dominant and recessive RNU2-2 disorders [11–15], a recessive form of RNU4-2 itself with characteristic white matter abnormalities [16], a functional map of all gene variants through saturation genome editing [6], and RNU4-2 and U6 snRNA gene variants causing non-syndromic retinitis pigmentosa [17]. GeneReviews devoted a chapter to the syndrome in May 2026, with data from more than 200 individuals, although substantial overlap exists between Chen's and Greene's participants [1]. This article treats ReNU syndrome as the principal entity and presents other snRNA diseases as needed for differential diagnosis and variant interpretation.

Locally available reference books were published between 2017 and 2022 and do not address RNU4-2. However, they contain the historical model of snRNA diseases, recessive RNU4ATAC spliceosomopathies, which remain relevant to understanding the mechanism and differential diagnosis [18–20]. The foundational clinical source is therefore the 2026 GeneReviews, supplemented by primary articles and subsequent reports.

2. Molecular Genetics and Pathophysiology

2.1. The major spliceosome and U4 snRNA

Pre-messenger RNA splicing removes introns and joins exons. The major spliceosome processes more than 99% of U2-type introns, with GU–AG dinucleotides, and consists of five small nuclear ribonucleoproteins (snRNPs), each with its snRNA (U1, U2, U4, U5 and U6), and approximately 100 proteins [8, 9]. The minor spliceosome, responsible for less than 1% of introns, uses its own snRNAs, including U4atac, encoded by RNU4ATAC, and U12, encoded by RNU12 [11].

U4 forms an extensive RNA duplex with U6, incorporated into the U4/U6.U5 tri-snRNP. In this configuration, U4 maintains U6 in an inactive conformation and positions the U6 ACAGAGA sequence, which will pair with the intron's 5′ donor splice site (5′SS). Spliceosome activation requires unwinding of the U4/U6 duplex by BRR2 helicase, encoded by SNRNP200; the central U4 region, where ReNU syndrome variants cluster, is loaded into this helicase's active site [7, 9]. U4 nucleotides 62 to 79 include stem I (n.62), the T-loop or quasi-pseudoknot (n.63–67), the RBM42 protein interaction region (n.68–70) and stem III, which pairs with U6 (n.72–79) [8, 9].

2.2. The RNU4-2 gene and RNU4-1 paralogue

The human genome contains many U4 genes and pseudogenes, but only RNU4-2 and RNU4-1, adjacent at 12q24.23, are substantially expressed in the brain. They differ at only four positions (n.37, n.88, n.99 and n.113). RNU4-2 is expressed in the prefrontal cortex at consistently higher levels than RNU4-1 throughout development, and surrounding chromatin is more accessible in the foetal brain, supporting its role as the principal U4 source in nervous tissue [4, 7, 17]. RNU4-1 tolerates more population variation (cumulative variant allele frequency 20.4% versus 1.2% in RNU4-2, gnomAD v4.1) and shows no variant enrichment in patients [7, 17].

Gene length varies with annotation. The MANE Select RefSeq transcript NR_003137.3 has 145 nucleotides; the GENCODE transcript initially used by Chen and colleagues had 141, lacking nucleotides 142–145, which are present in mature RNA and cortical RNA reads. Critical-region variant numbering is identical in both annotations and RefSeq versions .2 and .3 [5–7].

2.3. Critical regions and variant spectrum

Syndrome-associated variants cluster in two adjacent regions: n.62–70, around the quasi-pseudoknot, and n.73–79, in stem III [1, 9]. Together they span 18 nucleotides (chr12:120,291,825–120,291,842, GRCh38), a region in which only 26% of all possible single-nucleotide variants are observed in UK Biobank, compared with a median of 78% elsewhere in the gene [7]. Saturation genome editing of 539 variants in HAP1 cells redefined this region at nucleotide resolution: two segments of 9 nucleotides (n.62–70, including insertions at n.61_62) and 4 nucleotides (n.75–78). Within them, 85.4% of tested variants reduced cellular fitness, compared with 17.4% elsewhere in the gene; all 18 known syndrome variants fell below the depletion threshold [6].

The n.64_65insT insertion predominates in the spectrum. It was observed in 33 families in Greene's discovery cohort [9], in 89 of 115 individuals (77.4%) in Chen's series [7], and in 106 of 150 (71%) in Nava's cohort, where seven other variants recurred: n.76C>T (10 patients), n.66A>G (5), n.67A>G (5), n.65A>G (3), n.77_78insT (3), n.70T>C (2) and n.72_73del (2) [8]. The insertion occurs after a four-thymine sequence on the transcribed strand, arguing against the usual sequencing error mechanism of polymerase slippage; call quality was confirmed through read inspection, Sanger sequencing and long-read sequencing [7]. Single-base insertions in the critical region were found in 54 of 8,841 probands with undiagnosed neurodevelopmental disorder (0.61%) and 2 of 490,132 UK Biobank participants (odds ratio 1,531; 95% confidence interval 404–16,384) [7].

Table 2.1 lists the most frequently cited variants, with genomic correspondence obtained using VariantValidator and ClinVar classification at the consultation date. Conversions were not calculated manually: the gene is on the negative strand, so a thymine insertion in the transcript corresponds to an adenine insertion in the reference genome [5, 21].

Table sources: [5, 7–9, 17, 21].

Interpretation outside the critical region requires caution. Low-penetrance variants have been described outside it, and GeneReviews states that, up to 2026, there is no evidence that variants outside the two regions cause highly penetrant dominant disease [1]. Two 5′ stem-loop variants (n.30A>T and n.43_44insT), inherited from unaffected mothers, were initially proposed as causing ReNU syndrome [22]. Saturation editing and the recessive series located them in the k-turn region associated with recessive disease, and n.43_44insT was subsequently observed in compound heterozygosity with a stem II variant; the authors consider involvement in recessive disease more likely [6, 16]. The gene has a high mutation rate, common to snRNA genes, and rare variants unrelated to phenotype will arise by chance in every patient cohort [6, 7].

2.4. Mechanism: altered 5′ donor splice site selection

Quasi-pseudoknot and stem III variants appear to destabilise U4/U6 duplex organisation within the tri-snRNP and positioning of the U6 ACAGAGA sequence. In blood from five patients, Chen and colleagues observed more aberrant splicing events than in 378 controls (mean 21.6 versus 4.5), with the largest effect on increased use of unannotated 5′ donor splice sites (8.8 versus 0.7 events). Twelve events were shared by at least two patients and none by controls; positions +3, +4 and +5 of sites with increased usage, which pair directly with ACAGAGA, departed from consensus [7]. In lymphocyte cultures from 19 patients, Nava and colleagues identified 111 5′SS events separating patients from controls and severe from mild phenotypes; most represented a shift between existing isoforms rather than activation of new cryptic sites, and 30% of events altered the reading frame. Affected genes included KMT2A, KMT2C, KMT2D and KDM6A, chromatin regulators associated with neurodevelopmental syndromes [8].

The same cohort described a blood DNA methylation episignature with 147 differentially methylated positions, distinct from KMT2A and KMT2D episignatures; cross-validation sensitivity was 0.91 (31/35), 1.00 (24/24) in n.64_65insT carriers, and specificity 0.98 (44/45) [8]. GeneReviews emphasises that the identified splicing events are modest and neuronal transcriptomic studies do not yet exist; the mechanism suggests aberrant splicing but is not fully characterised [1]. RNU4-2 levels are not reduced in the dominant syndrome, distinguishing its dominant effect on function from the loss of expression observed in recessive forms [16].

2.5. Maternal bias, insertion recurrence and mosaicism

In all 54 individuals in whom parental origin was determined in Chen's series, the variant was on the maternal allele, contrary to the usual paternal bias of de novo mutations [7]. In Nava's cohort, 47 of 51 phased variants were maternal, including all 38 n.64_65insT insertions; the four paternal variants comprised two likely pathogenic variants (n.62T>C and n.68A>C) and two of uncertain significance [8]. Hypotheses include negative selection in the male germline if U4 is critical in spermatogenesis, and imprinting effects. High n.64_65insT recurrence was not associated with maternal age (mean 30.2 versus 29.7 years) and may reflect a high local mutation rate, structural sequence propensity or selection in the female germline [6, 7]. Maternal mosaicism (n.65A>G, with 8 of 62 alternative reads) was documented in a phenotypically unaffected parent [7, 9].

2.6. Allelic RNU4-2 disorders

RNU4-2 exemplifies pleiotropy in which variant position defines the disease. Table 2.2 summarises the three allelic entities.

Table sources: [1, 3, 6, 16, 17].

The recessive form was discovered because variants depleted in saturation editing outside the critical region, almost always present heterozygously in the population, were found homozygously or in compound heterozygosity in 20 individuals with neurodevelopmental disorder, without any case with another phenotype; the expanded group assembled 38 individuals [6, 16]. Five of the 13 recessive variants have exact pathogenic equivalents in RNU4ATAC, linking this form to recessive minor spliceosome spliceosomopathies [6]. A Japanese series also identified four individuals from two families with biallelic variants in stem II, the k-turn and Sm site, with milder delay and intellectual disability and no extracerebral involvement [23]. Retinitis pigmentosa was identified in 41 individuals from 15 families; the two RNU4-2 variants and two recurrent insertions in U6 paralogues (RNU6-1, RNU6-2, RNU6-8 and RNU6-9) may explain up to approximately 1.4% of undiagnosed retinitis pigmentosa cases [17, 24].

2.7. Other major spliceosome snRNA genes

RNU2-2, previously annotated as the pseudogene RNU2-2P, has 191 nucleotides, differs from canonical RNU2-1 at eight positions (all between n.108 and n.191) and occupies a unique locus at 11q12.3, within a WDR74 5′ untranslated exon. It is expressed in blood at levels comparable to RNU2-1 and incorporated into the spliceosome [4, 11]. Two distinct conditions are associated with this gene. The dominant form results from recurrent de novo variants at positions 4 (U6 interaction domain) and 35 (GUAGUA branch point recognition sequence), particularly n.4G>A and n.35A>G, and corresponds in OMIM to developmental and epileptic encephalopathy 119 (DEE119, 621304); the recessive form results from dispersed biallelic variants destabilising U2-2 stems and binding domains and reducing pathogenic allele expression by more than 90% [3, 11, 12, 14]. The transcript cited in the literature is ENST00000410396.1; the consulted VariantValidator had no RefSeq or MANE transcript for this gene [5, 13].

U5 snRNA is predominantly encoded by RNU5A-1 and RNU5B-1 in the brain. De novo variants clustered in U5 5′ loop I, which pairs with the exon adjacent to the 5′SS, were described in 17 patients with neurodevelopmental disorder in the RNU5B-1 critical region (chr15:65,304,713–65,304,720, GRCh38; NR_002757.3), with recurrent n.39C>G, n.42_43insA and n.44A>G; the entity was registered in OMIM as neurodevelopmental disorder with seizures and joint laxity (NEDSJL, 621302) [3, 8, 13]. RNU5A-1 was considered a strong candidate [8]. These entities belong to the group of snRNA disorders and are treated as differential diagnoses in section 6.

2.8. Historical model: minor spliceosome spliceosomopathies

Before 2024, the only known snRNA diseases involved the minor spliceosome and were recessive. RNU4ATAC, at 2q14.2, encodes U4atac of the U12-dependent spliceosome; biallelic variants cause microcephalic osteodysplastic primordial dwarfism types 1 and 3 (Taybi-Linder syndrome), Roifman syndrome and Lowry-Wood syndrome [18, 19, 25]. RNU12 causes early-onset cerebellar ataxia and CDAGS syndrome [11]. These diseases involve minor intron retention in blood cells and fibroblasts, whereas splicing defects in dominant major spliceosome forms are subtle [11]. GeneGuidance records the RNU4ATAC founder variant n.51G>A in the Amish population and the recommendation for immunological assessment before live vaccines, aspects that do not apply to ReNU syndrome [24].

3. Clinical Spectrum and Manifestations by System

3.1. Frequencies and limitations of cohort comparisons

Table 3.1 compares the three series with detailed clinical data. Denominators vary because not all items were assessed in all patients, and cohorts were identified through genome reanalysis in genetics services, favouring more severe phenotypes and paediatric ages. Median ages were 10 years (2–38) in Chen's series and 9 years (4 months to 45 years) in Nava's [7, 8].

Table sources: [1, 7, 8].

3.2. Prenatal and neonatal period

Approximately one-third of patients have a history of intrauterine growth restriction, frequently without postnatal catch-up [1]. In Nava's cohort, 60% of fetuses with n.64_65insT had prenatal findings, predominantly growth restriction (30%) and brain abnormalities (33%), with ventriculomegaly in 19.5%; 62% had two or more signs [8]. Reduced fetal movements and breech presentation are among the suggestive findings [1]. In the neonatal period, hypotonia (71%) and feeding difficulties (57%) predominate [8].

3.3. Development, language and behaviour

All patients have some degree of global delay. Independent walking is acquired, on average, at around 3 years (13 months to 12 years); approximately 15% never walk, and 10% walk at the usual age. The gait is frequently wide-based or ataxic, and most young adults need help with dressing and other activities of daily living [1]. Approximately 60% have no verbal language, 23% use a few words and 15% speak in sentences; comprehension appears more preserved than expression, and communicative intent is strong, with alternative methods used [1, 26]. Global regression has not been described with n.64_65insT; one patient with n.66A>G had neurological regression following a viral infection, associated with intractable epilepsy, at 2 years and 10 months [1, 27].

Autism and midline stereotypies reminiscent of Rett syndrome occurred in 84% of n.64_65insT carriers in Nava's series [8]. Frustration associated with communication difficulties, changes in routine and anxiety-provoking situations may manifest as self-injury or aggression (15%), and sleep disturbances, described in 15–45%, include difficulty falling asleep, fragmented sleep, night terrors and obstructive sleep apnoea [1]. Carers describe the children as happy and affectionate, with a fondness for music and water [1]. A longitudinal study of two patients highlighted persistent attention deficits and autism spectrum disorder, social anxiety and self-injury in adolescence in one of them [28].

3.4. Neurology and epilepsy

Approximately 55% of patients develop epilepsy, and a further 10% have at least one seizure. Onset ranges from the neonatal period to 13 years (median close to 3 years), with infantile epileptic spasms, febrile seizures, generalised tonic-clonic seizures, absences and focal seizures [1]. Among 143 individuals, up to 30% had status epilepticus and approximately 15% refractory epilepsy [1, 8]. A retrospective European series of 10 patients from six tertiary centres found a mean onset at 2.8 ± 2.1 years, predominance of focal seizures with impaired awareness and observable manifestations, peaking between 6 and 11 years, predominantly frontoparietal epileptiform activity and no structural epileptogenic lesions; five patients became seizure-free with medication [29].

MRI is abnormal in 85% of patients. The most frequent findings are ventriculomegaly and dysgenesis of the corpus callosum, which is short and thin, sometimes lacking a rostrum; less frequent findings include reduced white matter volume, delayed myelination, non-specific white matter abnormalities, abnormalities of the gyral pattern and periventricular heterotopias. Two patients with intracranial arterial tortuosity have been described [1]. Hypotonia tends to improve over time [1].

3.5. Growth and feeding

Microcephaly is congenital in up to 30% and develops after birth in a further 40%. Approximately 60% meet the criteria for short stature (at least 2 standard deviations below the mean), with a proportionate, slender build [1]. Feeding difficulties may persist throughout life: hypotonia and poor sucking in the newborn, gastro-oesophageal reflux, difficulty with texture transitions in childhood, drooling due to facial hypotonia, and constipation [1]. In a Swedish series of 11 patients, parents described the first year as the most difficult period because of feeding difficulties and poor weight gain; in several patients, feeding problems and seizures improved with age [30].

3.6. Bone and skeleton

Clubfoot and hip dysplasia may be evident in the neonatal period; scoliosis, kyphosis and pectus carinatum may develop later, alongside joint hypermobility and flat feet [1]. In adolescence and early adulthood, 25–40% of patients have low bone mineral density or low-impact fractures; five infants had unexpected fractures in the first year of life, and asymptomatic vertebral fractures have been described in an adolescent [1, 31]. A review of 173 assessed patients found bone abnormalities in 72 (42%): fractures in 26%, osteoporosis in 17%, osteopenia in 16% and low mineral density in 9% [31]. A 19-year-old adult had a spontaneous humeral fracture at 16 years, a low-impact fibular fracture at 8, and Z-scores of −1.9 at the lumbar spine, −3.5 at the femoral neck and −3.7 at the total femur, with elevated bone turnover markers and exclusion of secondary causes [32]. The pathophysiology is unknown; increased bone turnover has been proposed [1].

3.7. Eyes, hearing and other systems

Strabismus, nystagmus and refractive errors are common; Chen described optic nerve hypoplasia and/or cortical blindness in approximately 20% and one case of suspected cone-rod dystrophy, and Nava described retinopathy in seven patients [1]. Hearing loss, when present, is predominantly conductive due to recurrent otitis media [1]. Endocrine problems include hypothyroidism, sometimes neonatal, growth hormone deficiency and panhypopituitarism [1].

Multicystic dysplastic kidney, hydronephrosis, pyelectasis, vesicoureteric reflux, nephrocalcinosis and stones have been described in the kidney and urinary tract [1]. A girl with n.64_65insT had isolated proteinuria from 3 months, with minimal change disease on biopsy, no response to prednisone, and nephrotic-range proteinuria with normal renal function at 16 years; the authors suggest screening for proteinuria during surveillance, on the basis of a single case [33]. Cryptorchidism and inguinal hernia occur in boys. Dental abnormalities include malocclusion, widely spaced teeth, caries, hypomineralisation, enamel hypoplasia and early tooth eruption or loss [1]. Cardiac abnormalities include atrial and ventricular septal defects, a bicuspid aortic valve and mitral regurgitation, and some patients had supraventricular or sinus tachycardia [1]. Skin findings include acrocyanosis or vasomotor disturbances, hypohidrosis, dry skin, keratosis pilaris, haemangiomas, hirsutism and café-au-lait spots; 13 patients had blood count abnormalities [1, 8]. Two Japanese patients with n.64_65insT were initially investigated for mitochondrial disease and had reduced oxygen consumption in fibroblasts, a finding the authors interpret as an expansion of the spectrum [34].

3.8. Dysmorphology

The face becomes more characteristic with age: a myopathic face, deep-set eyes, epicanthus, a prominent nasal bridge with a broad base, anteverted nostrils, a short philtrum, an open, tented mouth with thick lips, downturned corners and eversion of the lower lip, a high palate, a large or protruding tongue, full cheeks and large, cupped ears; a triangular face develops later [1, 7]. Hooded upper eyelids, a tented philtrum and profuse drooling have been consistently described in Spanish and Japanese series [26, 35]. A combination of a tented upper lip with an exaggerated Cupid's bow, an everted lower lip and a horizontally oriented philtrum has been proposed as a clinical clue [36]. In Nava's study, dysmorphism in n.64_65insT carriers suggested Pitt-Hopkins syndrome [8]. Published photographs of patients are available in Figure 3 of Chen et al. and Figure 4 of Nava et al. [7, 8]. In Rosenblum's series, two of four patients were identified through targeted sequencing prompted solely by facial resemblance to the first case [37].

3.9. Genotype-phenotype correlation

Variants in the quasi-pseudoknot, T-loop and RBM42 region are associated with severe or profound intellectual disability, absent or minimal language and a median walking age of 30 months; stem III variants, including n.76C>T, are associated with fewer neonatal and MRI findings, less severe disability, more expressive language and a median walking age of 19 months [1]. In the principal component analysis of 143 patients, 121 of 123 carriers of T-loop and RBM42-region variants fell within the severe cluster, and 12 of 19 carriers of stem III variants within the mild cluster [8]. All 10 n.76C>T carriers walked, four at the usual age, and all spoke, six in simple sentences and four with normal language; six had medication-controlled fever-sensitive generalised epilepsy and four an isolated febrile seizure [8]. Saturation editing added nuance: two T-loop variants, n.63T>C and n.65A>G, showed moderate depletion, and their carriers clustered with mild phenotypes; strong depletion was associated with severe delay (73.3% versus 5.9%), severe intellectual disability (76.6% versus 5.9%) and absent or minimal language (92.8% versus 5.6%), without a difference in seizure frequency [6]. No relevant differences between sexes were observed [7].

4. Clinical Recognition and Red Flags

4.1. When to suspect the condition

There are no consensus clinical criteria. GeneReviews proposes considering the syndrome in developmental delay or moderate to severe intellectual disability associated with early childhood manifestations: intrauterine growth restriction, reduced fetal movements or breech presentation; generalised neonatal hypotonia; congenital or acquired microcephaly; weight and height below the 10th centile; feeding difficulties; epilepsy of variable types; autism, midline stereotypies or sleep disturbance; and bone involvement (clubfoot, hip dysplasia, hyperlaxity, osteopenia or low-impact fractures) [1]. On MRI, dysgenesis of the corpus callosum, which is short and thin, and ventriculomegaly strengthen suspicion; the family history predominantly involves an isolated case [1].

4.2. Clues warranting targeted testing

Table sources: [1, 7, 8, 31, 33, 34, 38].

4.3. Clinical red flags during follow-up

Status epilepticus, which affected up to 30% of patients with epilepsy, requires a written rescue plan and carer education [1]. Pain on moving a limb, refusal to bear weight or deformity after minimal trauma should raise suspicion of a fracture, including in infants; vertebral fractures may be asymptomatic [1, 31]. Coughing during feeding, recurrent respiratory infections or poor weight gain suggest dysphagia and aspiration [1]. Abdominal pain should prompt ultrasound to exclude stones or nephrocalcinosis [1]. Snoring, respiratory pauses and fragmented sleep warrant investigation for obstructive apnoea [1]. Palpitations or tachycardia should be assessed, given the reports of arrhythmias [1]. Loss of skills is not the usual course and should prompt investigation for uncontrolled seizures, intercurrent illness or an alternative diagnosis [1, 27].

5. Diagnosis: Criteria, Tests and Algorithms

5.1. Confirmation criterion

The diagnosis is established in a proband with suggestive findings and a heterozygous pathogenic or likely pathogenic RNU4-2 variant. Under the American College of Medical Genetics and Genomics and Association for Molecular Pathology (ACMG/AMP) standards, both categories are diagnostic; a variant of uncertain significance neither confirms nor excludes the syndrome [1, 39]. There is no routine biochemical biomarker.

5.2. Test selection and limitations

RNU4-2 is not included in commercial exome capture kits. In the Deciphering Developmental Disorders cohort, 3,408 of 13,450 exomes (25.3%) had at least one read at the n.64_65insT position, and the maximum was five reads, below heterozygous calling thresholds; of 22 insertion carriers with both exome and genome sequencing, only two had one exome read, and this showed the reference sequence [7]. Exome sensitivity for this variant is therefore very low, and any call obtained from off-target reads requires independent confirmation [7]. GeneReviews concludes that a negative exome does not exclude the syndrome and that genome sequencing is the comprehensive test that allows confirmation [1].

Table sources: [1, 6–8, 40].

The value of genome sequencing and reanalysis has been documented in several settings. In 95 Japanese patients with a negative exome, genome sequencing found de novo n.64_65insT in five (5.3%) [36]; in another Japanese series, four of 93 exome-negative cases (4.3%) had RNU4-2 variants [27]. In an Italian undiagnosed diseases programme, reanalysis and targeted sequencing found causal variants in 11 of 375 patients (2.93%) [41]. Reanalysis of genomes from 1,578 unresolved Japanese probands identified pathogenic snRNA gene variants (RNU4-2, RNU2-2, RNU5B-1 and RNU4ATAC) in 19 (1.2%), and the same group showed that adding probes for 50 snRNA genes to the exome design detects these variants [40]. In a Belgian national prospective randomised trial involving 567 individuals with a developmental disorder, genome sequencing had a yield of 39.8% versus 30% for exome sequencing combined with microarray; subsequent targeted RNU4-2 reanalysis added one diagnosis among inconclusive genomes [42].

General recommendations support this choice. The 2021 ACMG guideline strongly recommends exome or genome sequencing as a first- or second-line test in paediatric patients with congenital abnormalities, developmental delay or intellectual disability [43]. The American Academy of Pediatrics (AAP) 2025 clinical report proposes selecting the test according to the phenotype when recognisable and, otherwise, an agnostic approach guided by diagnostic yield [44]. For ReNU syndrome, these recommendations imply that the choice between exome and genome sequencing is not immaterial: only genome sequencing or targeted testing covers the gene. The 2017 edition of the Oxford Desk Reference recommended exome sequencing after microarray and exclusion of recognisable syndromes; this sequence, predating the discovery of RNU4-2, should be read as historical [45].

5.3. Variant interpretation in a non-coding gene

The report should state the gene, versioned transcript (NR_003137.3), non-coding HGVS nomenclature (prefix “n.”), GRCh38 genomic coordinate, zygosity, parental origin when studied, ACMG/AMP classification and method limitations [5, 39]. The ACMG/AMP standards were devised for coding genes; an international panel published recommendations in 2022 for adapting the criteria to variants in non-coding regions [46]. In Nava's cohort, the criteria used were PS2 or PM6 for de novo variants, supporting-level PM2 for variants absent or very rare in gnomAD, PM1 for the critical region, supporting or moderate PS4 according to the number of patients (applied only to n.64_65insT), and PS3 when RNA or methylation studies supported pathogenicity [8]. In silico predictors have limited value: in saturation editing, the area under the ROC curve was 0.93 for the functional score and 0.65 for CADD, and a CADD threshold capturing all syndrome variants would classify 56.4% of variants observed in the population as deleterious [6]. Saturation editing data were calibrated to provide strong PS3 or strong BS3 evidence only within the critical region; outside it, they should not be used as evidence of pathogenicity for dominant disease, and the authors suggest only supporting evidence for depleted variants in the recessive context [6, 16].

Three technical aspects merit attention. First, homology between RNU4-2, RNU4-1 and pseudogenes, as well as between U2 and U6 paralogues, may generate misalignments; retinitis pigmentosa studies used paralogue-specific Sanger sequencing [6, 24]. Second, transcript numbering differs between RefSeq and Ensembl for some snRNA genes, so the transcript used should always be included in the report [8]. Third, n.76C>T occurs once in gnomAD and was transmitted by an affected mother, and a variant at the same position (n.76C>G) was observed in an individual without a neurodevelopmental disorder; population frequency should be interpreted in light of the expressivity of stem III variants [9].

5.4. Practical algorithm

Table sources: [1, 6–8, 38].

In a retrospective Chinese study of 148 fetuses with central nervous system abnormalities and non-diagnostic karyotyping, microarray and exome sequencing, Sanger sequencing found de novo n.64_65insT in two (1.35%), both with microcephaly; in one, the diagnosis allowed an inherited duplication of uncertain significance at Xp22.13 to be excluded as the cause [38]. A heterozygous deletion encompassing RNU4-2 and RNU4-1 was described in a fetus with urogenital and anorectal malformations, a mechanism distinct from that of critical-region point variants [47].

5.5. Assessment after diagnosis

Table 5.3 summarises the assessments recommended by GeneReviews if not performed during the investigation [1].

6. Differential Diagnosis

6.1. Clinical differential diagnosis

The ReNU syndrome phenotype overlaps with several neurodevelopmental disorders featuring absent language, a happy temperament and epilepsy. Table 6.1 reproduces the entities listed by GeneReviews with their distinguishing features [1].

6.2. Other snRNA diseases

Table 6.2 compares ReNU syndrome with the other snRNA diseases. Relative frequencies derive from genome cohorts in the United Kingdom and France and are not population prevalences [8, 11, 12, 15–17, 25].

Additional table sources: [13, 18, 19, 24, 48–50].

The distinction between ReNU and dominant ReNU2 has practical implications. In the 25 cases in the original RNU2-2 description, all had prominent epilepsy, usually from the first months, severe and drug-resistant, with a progressive and frequently severe phenotype; hyperventilation and severe global delay were the phenotypic terms distinguishing these patients from RNU4-2 variant carriers [11]. In an Australian series of 672 unexplained epileptic encephalopathies, RNU2-2 variants explained 0.6%, with status epilepticus in all five patients, sleep-activated multifocal discharges, hippocampal sclerosis in three and obstructive sleep apnoea in three [48]. In the recessive form, a Swedish series of 14 individuals described severe to profound intellectual disability, inability to walk or communicate, hyperkinesia and refractory epilepsy with spasms and tonic seizures, and showed splicing abnormalities in fibroblasts not detectable in blood [50]. In recessive RNU2-2, the ratio of U2-2 to U2-1 levels in blood discriminated cases from controls and is proposed as a biomarker [12, 14].

6.3. Differential diagnosis with primordial dwarfism

Microcephaly and short stature in ReNU syndrome are generally moderate, without radiological skeletal dysplasia. In microcephalic osteodysplastic primordial dwarfism type 1/3, caused by RNU4ATAC, head circumference and height are often below −4 standard deviations, with dolichocephalic microcephaly, alopecia, dry skin, prominent eyes, short long bones without metaphyseal widening, short ilia and markedly delayed ossification, with cortical malformations and death usually before 2 years [18–20]. In type 2, due to PCNT variants, development is relatively preserved, and there is a risk of moyamoya and insulin resistance [20]. These conditions should be considered when growth restriction is extreme or skeletal dysplasia is present.

7. Treatments and Risk Management Strategies

7.1. Organisation of care

There are no published clinical guidelines for ReNU syndrome; GeneReviews recommendations are based on the authors' personal experience [1]. The aim is to improve quality of life, maximise function and reduce complications through multidisciplinary care, coordinating appointments, equipment, medicines and social support [1]. The 2025 international conference organised by families identified early recognition, optimisation of clinical care, family experience, clarification of the mechanism, acquisition of natural history data with validated endpoints, and therapeutic development as priorities [51].

Table sources: [1].

7.2. Epilepsy

Treatment follows the general principles of childhood epilepsy, with a rescue plan for prolonged seizures given the frequency of status epilepticus [1]. In the European series of 10 patients, neurologists considered valproate the most effective drug, followed by levetiracetam, clobazam, lamotrigine and phenytoin; this was a retrospective assessment without controlled comparison [29]. In girls and women of reproductive potential, the European Union contraindicates valproate unless the conditions of a pregnancy prevention programme are fulfilled [52]. Antiepileptic drug doses are not presented in this article because there is no syndrome-specific regimen; doses follow each drug's label.

7.3. Drooling and sleep: drugs indicated in neurological paediatric populations

Glycopyrronium is an anticholinergic authorised for severe chronic drooling in children with neurological disease, and prolonged-release melatonin has European authorisation for insomnia in children with autism or neurogenetic disorders. Neither medicine has been studied specifically in ReNU syndrome. Use falls within the population described in the label when the child meets the age and neurological disease criteria, but efficacy data are extrapolated from other diseases [53–55].

Table sources: [53–55].

The most common adverse effects of glycopyrrolate in the US controlled trial were dry mouth and vomiting (40% each), constipation (35%), flushing and nasal congestion (30% each) [53]. In the European label, irritability, flushing, nasal congestion, reduced bronchial secretions, dry mouth and constipation are very common [54].

7.4. Bone health

GeneReviews recommends optimising physical activity, calcium and vitamin D, considering supplementation and limiting drugs with a negative effect on bone, such as corticosteroids; it records bisphosphonate use with an unknown long-term response [1]. No bisphosphonate has an approved indication for ReNU syndrome. In the report by Holling and colleagues, the adolescent received intravenous neridronate 2 mg/kg every 3 months for 3 years, from 16 to 19 years, with good tolerability, an initial increase followed by stabilisation of mineral density and no new vertebral fractures, although he had patellar and humeral fractures after falls at 19 years [31]. Zoledronic acid was indicated in the adult described by Peñafiel-Sam and colleagues [32]. These approaches are case reports and off-label use; the cited dose is that of the report, not a routine recommendation.

7.5. Research, trials and developments over the past 12 months

Table sources: [1, 6, 10, 12, 16, 17, 56, 57].

None of these elements yet constitutes clinical evidence of efficacy. The July 2026 announcement describes a preclinical programme, without published human data, without a regulatory application and without orphan drug status identified in the sources consulted; there is therefore no table of pivotal trials or regulatory authorisation for specific therapy [10, 56]. The oligonucleotide's allele specificity, if demonstrated, will apply only to n.64_65insT carriers [10]. Therapeutic strategies for U4/U6 retinitis pigmentosa have been discussed on the basis of previous studies of spliceosome genetics in yeast, also without clinical data [58].

7.6. Special populations and situations

There are no published data on pregnancy in women with the syndrome, which is rare because of phenotype severity with T-loop variants; the reported transmission involved parents with stem III variants and a mild phenotype [1, 8]. For procedures involving anaesthesia, hypotonia, dysphagia, aspiration risk and obstructive apnoea warrant prior assessment; no specific anaesthetic recommendations were found in the sources. Paediatric glycopyrronium use below 3 years and Slenyto® use below 2 years are off-label [53–55]. Transition to adult care should begin at around 10 years [1].

8. Reproductive Options and Family Counselling

8.1. Risk to relatives

Almost all patients have a de novo variant. n.64_65insT was de novo in every patient whose parents were tested, and there is a strong bias towards maternal origin [1]. Two families with vertical transmission have been described: n.76C>T transmitted by an affected mother and n.72_73del transmitted by an affected father, both with milder phenotypes [1, 8, 9]. Parental testing is recommended [1].

Table sources: [1, 7, 9].

8.2. Reproductive options

Once the variant is identified, prenatal diagnosis and preimplantation genetic testing are possible [1]. The ideal time to discuss risk and options is before pregnancy. Given the risk of gonadal mosaicism, prenatal testing may be offered even when the variant was not detected in the parents, explaining that the risk is low and the decision personal [1]. Fetal genome sequencing or targeted RNU4-2 testing is of interest when ultrasound shows growth restriction, ventriculomegaly or a corpus callosum abnormality without a diagnosis after exome sequencing [8, 38].

8.3. Counselling in related forms

Counselling should distinguish the dominant syndrome from recessive forms. In recessive RNU2-2, frequently involving an inherited variant in trans with a de novo variant, recurrence risk to siblings may reach 25% when both are inherited, and preconception or prenatal diagnosis is possible; prevalence will probably be greater in cultures with consanguineous marriages [12, 15]. In recessive RNU4-2, seven patients with homozygous variants had consanguineous parents [16]. Allelic retinitis pigmentosa has incomplete penetrance, with obligate carriers without visual symptoms [17].

8.4. Information for the family

Diagnosis allows the diagnostic odyssey to be brought to an end, the expected course to be explained and bone, epilepsy and feeding surveillance to be organised. It does not allow precise prediction of language or independence in an individual child, although variant location provides guidance: stem III variants are associated with a better walking and language prognosis [1, 8]. Parents described strong social connection and affection and considered the first year the most difficult period [30].

9. Special Considerations: Population Diversity and Epidemiology

9.1. What the frequencies measure

Published proportions measure the fraction of diagnoses in cohorts of patients with neurodevelopmental disorders, frequently already subjected to previous tests, rather than prevalence in the general population. Table 9.1 brings together the available data by cohort.

The highest proportions occur in cohorts already filtered by a negative exome or phenotype, explaining the difference from the 0.4–0.7% in large cohorts not selected by phenotype. The lower proportion in the consanguineous subgroup of the international biobank reflects the greater contribution of recessive diseases in this group rather than a lower frequency of the dominant syndrome [60]. In autism cohorts without selection for severe disability, the frequency was approximately tenfold lower [7].

9.2. Prevalence estimates

GeneReviews estimated prevalence by comparison with MECP2-associated Rett syndrome, with a worldwide prevalence of approximately 7.1 per 100,000 females: in the British GMS, ReNU syndrome had 87.5% of the frequency of Rett syndrome, which, assuming similar life expectancy, gives approximately 7.1 × 0.5 × 0.875 = 3.1 per 100,000 people of any age and sex. Using childhood intellectual disability as the comparator, the estimate was slightly above 3.5 per 100,000 children [1]. These are indirect estimates, dependent on assumptions about life expectancy and ascertainment bias. Announcements and articles referring to approximately 100,000 affected people worldwide present a projection rather than a count [6, 10].

9.3. Sex, ancestry and founder populations

There were no relevant differences between sexes in the principal series (21 females and 28 males in Chen; 74 females and 69 males with clinical data in Nava) [7, 8]. Recurrence of n.64_65insT was observed in European, North American, Korean, Japanese, Chinese and Middle Eastern cohorts, indicating a recurrent mutational event rather than a founder effect [7, 36, 38, 59, 60]. No founder effect for ReNU syndrome was identified in the sources consulted; the founder effect described within the snRNA disease family is the RNU4ATAC n.51G>A variant in the Amish population [24]. Recessive RNU4-2 and RNU2-2 forms will be relatively more frequent in populations with high consanguinity [12, 16].

The sources consulted did not include specific data from Portugal or Brazil on ReNU syndrome; absence from the sources does not demonstrate that there are no patients or studies in those countries. Lack of diagnoses in many adults with intellectual disability who have never undergone genomic testing suggests underdiagnosis in all regions [1].

9.4. European networks and resources for families

In the European Union, the relevant European Reference Network for syndromic intellectual disability and rare malformation syndromes is ERN ITHACA, and for epilepsy with a rare cause, ERN EpiCARE; the search performed identified no ReNU-specific document from these networks. GeneReviews lists the Asociación Síndrome de ReNU (Spain), Association Française du Syndrome ReNU (France), Erfocentrum (the Netherlands), ReNU Syndrome United and the British organisation Unique [1]. Families affected by the RNU2-2-related form have created their own foundation (ReNU2) [12]. Mount Sinai in New York maintains a multidisciplinary clinical RNUopathy programme and the INDEED natural history and laboratory research study [57]. The Simons Searchlight registry includes RNU4-2 among eligible conditions [56].

10. Illustrative Clinical Case

10.1. Published case: severe osteoporosis leading to diagnosis

Holling and colleagues from Hamburg described a 16-year-old boy with an undiagnosed neurodevelopmental disorder, intellectual disability, microcephaly and epilepsy, referred to a specialist bone disease clinic by his orthopaedic surgeon because of worsening genu valgum and gait abnormalities despite previous guided growth procedures [31]. He had a history of small fractures of the hands and fingers and a proximal humeral fracture. Lateral spinal assessment revealed multiple previously undiagnosed thoracic and lumbar fractures. Densitometry showed Z-scores of −3.9 at the left hip, −4.9 at the right hip, −4.7 at the lumbar spine and −3.0 at the height-adjusted spine. High-resolution peripheral computed tomography of the tibia showed trabecular mass and cortical thickness reduced to approximately 25% and 22% of values in age- and sex-matched controls. Bone formation and resorption markers were at the upper limit of normal, calcium and phosphate were normal, and hyponatraemia and low creatinine were present. A tibial bone biopsy obtained during removal of guided growth plates showed increased erosion surfaces and more osteoclasts and osteoblasts than in a control, consistent with activated remodelling [31]. Clinical, radiological and histological images are in Figure 1 of the article.

Before molecular diagnosis, intravenous neridronate 2 mg/kg every 3 months was initiated and was well tolerated. Trio exome sequencing, analysing approximately 20,000 coding genes under recessive, dominant de novo and X-linked models, found no explanatory variant. Sanger sequencing of RNU4-2, prompted by the fact that RNA genes are not captured by exome sequencing, identified the heterozygous NR_003137.3:n.64_65insT variant, absent in both parents [31]. Treatment lasted 3 years and was stopped at 19 years after growth plate closure. Mineral density initially increased and stabilised, without new vertebral fractures, but the patient sustained a patellar fracture after a fall at 19 years and a proximal humeral fracture 8 weeks later. A structured muscle training programme was not feasible, and epileptic seizures were not fully controlled despite several treatments [31]. The course of mineral density, laboratory parameters and the electropherogram of the de novo variant are in Figure 2 of the article.

10.2. Lessons

The case offers three lessons. First, a negative trio exome does not exclude the syndrome, and targeted RNU4-2 testing ended a 16-year diagnostic odyssey [1, 31]. Second, vertebral fractures may be asymptomatic, supporting the recommendation for densitometry from 3 years and a lateral thoracolumbar radiograph [1]. Third, the choice of neridronate and its dose reflect one centre's practice, by analogy with other bone fragility diseases, rather than a general recommendation: the authors advocate intravenous bisphosphonates in children and adolescents with a neurodevelopmental disorder and osteoporosis, but long-term efficacy in ReNU syndrome is not established [1, 31]. The article itself describes the biopsy as tibial in the case description and as iliac crest in the discussion; the case description is followed here.

11. Prognosis and Long-Term Follow-up

11.1. Course and survival

Whether life expectancy is reduced is unknown. Patients with n.64_65insT are alive at 45 years and in their late fourth decade, and a 47-year-old patient with n.70T>C has been described, demonstrating survival into adulthood; the slightly higher prevalence estimate in children is consistent with some reduction in life expectancy but does not prove it [1]. A Swedish series described an age-dependent trajectory: feeding difficulties, hypotonia, deceleration of head growth and visual abnormalities in infancy; gait abnormalities, autistic behaviour and seizure onset in early childhood; persistence of severe language limitation and orthopaedic complications later [30]. Hypotonia tends to improve, epilepsy is mostly controlled with medication, and bone involvement becomes more relevant in adolescence and young adulthood [1, 29]. Most young adults need support with activities of daily living [1].

11.2. Recommended surveillance

Table source: [1].

Proteinuria surveillance was suggested on the basis of a single case and is not included in GeneReviews recommendations [33]. Substances affecting bone health, such as corticosteroids, should be avoided or limited [1].

11.3. Transition and adult life

Transition planning should begin at around 10 years, following the model of transitions in paediatric epilepsy, and incorporate decisions on support in adult life, guardianship, respite care and, when necessary, palliative care [1]. Underdiagnosis in adults with intellectual disability who have never undergone genome sequencing warrants considering testing in adult clinics [1].

11.4. Reassessment of genetic information

Classification of rare variants outside the critical region changes as functional data and recessive cohorts emerge; a variant of uncertain significance should be reviewed periodically [6, 16]. Negative genomes generated before 2024 should be reanalysed for RNU4-2, RNU2-2 and RNU5B-1 [36, 40, 42].

12. Summary and Final Considerations

ReNU syndrome is a dominant neurodevelopmental disorder caused by de novo variants, almost always maternal, in a region of approximately 18 nucleotides of RNU4-2, the non-coding gene for U4 snRNA of the major spliceosome. The n.64_65insT insertion (NR_003137.3) explains 70–77% of cases. The syndrome accounts for 0.4–0.7% of undiagnosed neurodevelopmental disorders in large genome cohorts and has an estimated prevalence of approximately 3 per 100,000 people [1, 7, 9].

The clinical picture combines moderate to severe intellectual disability, absent or minimal language, microcephaly, neonatal hypotonia, feeding difficulties, short stature, epilepsy with a risk of status epilepticus, autism and stereotypies, ventriculomegaly and a thin corpus callosum, bone fragility, ocular abnormalities and a recognisable facial appearance. Stem III variants such as n.76C>T are associated with milder phenotypes and explain the rare cases of parental transmission [1, 8].

Exome sequencing does not cover the gene. Confirmation requires genome sequencing or targeted Sanger sequencing, and all negative genomes predating 2024 warrant reanalysis. Interpretation of variants outside the critical region should consider recessive RNU4-2 and RNU2-2 forms, allelic retinitis pigmentosa variants and saturation editing functional data [1, 6, 7, 16, 17].

Management is symptomatic and multidisciplinary, with particular attention to epilepsy, feeding, bone health, vision and augmentative communication. The only specific therapeutic programme identified is an antisense oligonucleotide targeting n.64_65insT, in the preclinical phase since July 2026. Genetic counselling should explain the low but non-zero recurrence risk due to mosaicism and the possibility of prenatal diagnosis [1, 10].

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