RNU4-2:n.64_65insT

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Nomenclaturen.64_65insTchr12:120,291,840NR_003137.3MANE|ClinVar #3068742

TypesnRNA variant

InheritanceAutosomal dominant

gnomAD

Absent

Not observed in gnomAD

CADD

20.9

Where it sitsReNU critical region · T-loop

In the ReNU critical region (T-loop) — a de novo heterozygous change here causes ReNU syndrome.?

Function score?-1.23strongly depletedPS3 · functional

Cell fitness in haploid HAP1 cells · De Jonghe et al. 2026, Supplementary Table 1 (CC BY 4.0) · reported in ReNU syndrome

ReNU & the snRNA disorders — where this sits on U4/U6, features, counselling →

Tutor Research

ClinVarPathogenic

VCV003068742

Review: criteria provided, multiple submitters, no conflictsSubmitters: 24view ↗Last evaluated: 2026/08/07 00:00

not provided[MedGen]

Multiple congenital anomalies/dysmorphic syndrome-intellectual disability[MedGen][Orphanet][MONDO]

RNU4-2-associated neurodevelopmental disorder

Neurodevelopmental disorder with hypotonia, brain anomalies, distinctive facies, and absent language[OMIM][MedGen][Orphanet][MONDO]

Protein-structure analyses omitted

RNU4-2 is a non-coding RNA (snRNA) gene with no protein product, so the lollipop plot, 3D structure, and structural constraint views don't apply to this variant.

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	0	10	0	10
Likely Pathogenic	0	0	24	0	24
VUS	0	0	35	0	35
Likely Benign	0	0	20	0	20
Benign	0	0	1	0	1
Conflicting	—				2
Total	0	0	90	0	92

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

5 pathogenic / likely-pathogenic (of 6) ClinVar copy-number / structural variants overlap RNU4-2 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →