RNU4ATAC

Summary

RNU4ATAC (RNA, U4atac small nuclear, HGNC:34016) is a small nuclear RNA gene on chromosome 2q14.2.

The small nuclear RNA (snRNA) encoded by this gene is part of the U12-dependent minor spliceosome complex. In addition to the encoded RNA, this ribonucleoprotein complex consists of U11, U12, U5, and U6atac snRNAs. The U12-dependent spliceosome acts on approximately 700 specific introns in the human genome. Defects in this gene are a cause of microcephalic osteodysplastic primordial dwarfism type 1 (MOPD).

Source: NCBI Gene 100151683 — RefSeq curated summary.

At a glance

• Gene type: non-coding (snRNA) — no protein product; not a drug target. Variant/disease associations are omitted (they would be positional, from an overlapping protein-coding gene).

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34016
Approved symbol	RNU4ATAC
Name	RNA, U4atac small nuclear
Location	2q14.2
Locus type	RNA, small nuclear
Status	Approved
Aliases	RNU4ATAC1, U4atac
Ensembl gene	ENSG00000264229
Ensembl biotype	snRNA
OMIM	601428
Entrez	100151683
RNAcentral	URS000075ADBA — ncRNA, 130 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 snRNA

ENST00000580972

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000580972 — 1 exons

Exon	Start	End
ENSE00003649349	121530880	121531009

Expression profiles

Bgee: expression breadth ubiquitous, 116 present calls, max score 99.10.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 47.2417 / max 3735.5050, expressed in 1763 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
22339	47.2417	1763

Top tissues by expression

116 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	99.10	gold quality
sural nerve	UBERON:0015488	98.68	gold quality
calcaneal tendon	UBERON:0003701	98.58	gold quality
adrenal tissue	UBERON:0018303	98.46	gold quality
granulocyte	CL:0000094	95.12	gold quality
corpus callosum	UBERON:0002336	94.11	gold quality
monocyte	CL:0000576	93.00	gold quality
hindlimb stylopod muscle	UBERON:0004252	90.37	gold quality
bone marrow	UBERON:0002371	88.48	gold quality
skeletal muscle tissue	UBERON:0001134	84.32	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	83.60	gold quality
mucosa of transverse colon	UBERON:0004991	83.24	gold quality
liver	UBERON:0002107	82.28	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	81.08	gold quality
left uterine tube	UBERON:0001303	81.02	gold quality
lymph node	UBERON:0000029	79.94	gold quality
blood	UBERON:0000178	79.40	gold quality
omental fat pad	UBERON:0010414	79.32	gold quality
adipose tissue	UBERON:0001013	78.96	gold quality
subcutaneous adipose tissue	UBERON:0002190	78.72	gold quality
muscle of leg	UBERON:0001383	78.46	gold quality
stomach	UBERON:0000945	78.36	gold quality
kidney	UBERON:0002113	78.11	gold quality
skin of abdomen	UBERON:0001416	78.10	gold quality
Ammon’s horn	UBERON:0001954	78.00	gold quality
ectocervix	UBERON:0012249	77.87	gold quality
substantia nigra	UBERON:0002038	77.49	gold quality
hypothalamus	UBERON:0001898	77.30	gold quality
right lobe of liver	UBERON:0001114	77.09	gold quality
tibial artery	UBERON:0007610	77.01	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	10.51

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 16)

• findings show gene encoding U4atac snRNA is mutated in individuals with MOPD I; mutations (30G>A, 51G>A, 55G>A, and 111G>A) associated with MOPD I cause defective U12-dependent splicing (PMID:21474760)
• identified 4 point mutations in U4atac snRNA component of minor spliceosome in patients with TALS; minor intron splicing was affected in cell lines from TALS; findings demonstrate crucial role of U4atac snRNA in early development and postnatal survival (PMID:21474761)
• the clinical and molecular data for 17 cases of Microcephalic osteodysplastic primordial dwarfism type I, including 15 previously unreported cases, all carrying biallelic mutations in the RNU4ATAC gene (PMID:21815888)
• Oro-dental anomalies, pigmentary disorder and vasculopathy are found in MOPD1 patients. (PMID:21990275)
• Mutations in the RNU4ATAC gene cause microcephalic osteodysplastic primordial dwarfism type I. These findings expand the mutational and phenotypic spectrum of this syndrome. (PMID:22581640)
• Mutation in RNU4ATAC is associated with microcephalic osteodysplastic primordial dwarfism type I. (PMID:23794361)
• This report establishes a mechanistic basis for MOPD I disease and show that the inefficient splicing of genes containing U12-dependent introns in patient cells is due to defects in minor tri-snRNP formation, and the MOPD I-associated RNU4ATAC mutations can affect multiple facets of minor snRNA function. (PMID:24865609)
• Mutations in the noncoding RNU4ATAC cause Roifman Syndrome by disrupting minor intron splicing. (PMID:26522830)
• We report here four foetuses and four unrelated patients with RNU4ATAC mutations. We provide antenatal descriptions of this rare syndrome including unusual features found in two twin foetuses with compound heterozygosity for two rare mutations who presented with mild intrauterine growth retardation and atypical dysmorphic facial features. (PMID:27040866)
• report on a novel 5.8 Mb deletion of 2q14.1q14.3 identified by array comparative genomic hybridization in a fetus with severe intrauterine growth retardation and partial agenesis of the corpus callosum. (PMID:27346851)
• This report expands the phenotypic spectrum for biallelic RNU4ATAC disorder causing variants and is the first to establish the genetic cause for Lowry Wood syndrome (PMID:29265708)
• the identification of a novel RNU4ATAC variant within the mutational hotspot for MOPD1-causative variants further strengthens the critical role of the 5’ stem-loop structure of U4atac in health and disease. Finally, this analysis enabled us to provide prenatal diagnosis and genetic counselling for the mother’s third pregnancy, the first report of its kind in the context of inherited RNU4ATAC variants. (PMID:29370840)
• this study shows the immunologic and hematologic systems of 3 patients with Roifman syndrome from 2 unrelated kindreds bearing RNU4ATAC variants (PMID:29391254)
• We are thus confirming that RNU4ATAC is the gene responsible for LWS and provide a genotype-phenotype correlation analysis (PMID:30368667)
• Whole genome sequencing identifies pathogenic RNU4ATAC variants in a child with recurrent encephalitis, microcephaly, and normal stature. (PMID:34405953)
• Deep phenotypic characterization of the retinal dystrophy in patients with RNU4ATAC-associated Roifman syndrome. (PMID:37225827)

Cross-species orthologs

0 orthologs

Protein

Non-coding RNA — no protein product; not a drug target.

Function

No curated pathway, Gene-Ontology, or interaction data.

Disease & clinical

No curated disease, variant, or cancer-driver associations.

Drugs & pharmacology

No drug or pharmacology data — not an established drug target.