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Intellectual disability

Gene: RNU4ATAC

Amber List (moderate evidence)
RNU4ATAC (RNA, U4atac small nuclear (U12-dependent splicing))
EnsemblGeneIds (GRCh38): ENSG00000264229
EnsemblGeneIds (GRCh37): ENSG00000264229
OMIM: 601428, Gene2Phenotype
RNU4ATAC is in 16 panels

4 reviews

Ida Ertmanska (Genomics England Curator)

Green List (high evidence)

PMID: 41864208 Johnson et al., 2026
Identified 19 individuals with early-onset diabetes (diagnosed <5 years) and additional clinical features who had biallelic pathogenic variants in the novel disease gene RNU6ATAC (n=7) or in RNU4ATAC (n=12). 12/19 had additional immune features of immune dysregulation.
Around 60% of patients also had microcephaly and developmental delay.

Among the 12 families with biallelic RNU4ATAC variants, the variants reported were: n.13C>T, n.16G>A, n.17G>A, n.36T>G, n.36T>C, n.51G>A, n.46G>A, n.48G>A, n.55G>A (recurrent in 5 individuals), n.60G>A.

PMID: 36802443 Khatri et al., 2023
5 patients from 4 unrelated families with biallelic RNU4ATAC variants and Joubert-syndrome-like features of ciliopathy. 4/5 patients had developmental and/or psychomotor delay. Variants detected: P1 & P2 were homozygous for n.16G>A, P3 was comp het for n.[16G>A];[51G>A], and sibs P4 and P5 harboured n.[16G>A];[33C>G] variants.

PMID: 29391254 Heremans et al., 2018
3 patients from 2 unrelated kindreds harboring compound heterozygous or homozygous stem II variants in RNU4ATAC. All patients have a common phenotype of moderate psychomotor delay and autism spectrum disorder, retinal dystrophy with hypovascularization, severe growth retardation, spondyloepiphysial dysplasia with irregularly shaped vertebral bodies with platyspondyly and flattened proximal femoral epiphyses, pruritic ichthyosis-like skin rash, brachydactyly, hyperlaxity, hypotonia, and hepatosplenomegaly.
All 3 patients have hypogammaglobulinemia and B-cell lymphopenia, and they experienced recurrent viral infections, necessitating immunoglobulin substitution therapy.

RNU4ATAC has been linked to several phenotypes in OMIM: Lowry-Wood syndrome, 226960; Microcephalic osteodysplastic primordial dwarfism, type I, 210710; Roifman syndrome, 616651. All three disease entities have clinical overlap, with most common features being epiphyseal dysplasia with intellectual disability, microcephaly, immunodeficiency, and/or retinal anomalies. OMIM accessed on 29th Dec 2025.
Created: 29 Apr 2026, 4:18 p.m. | Last Modified: 29 Apr 2026, 4:18 p.m.
Panel Version: 9.400

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
RNU4ATAC spectrum disorder, MONDO:0100558

Publications

Created: 29 Apr 2026, 4:18 p.m.
Last Modified: 29 Apr 2026, 4:18 p.m.
Panel version: 9.400

Helen Brittain (Genomics England Curator)

Comment when marking as ready: Majority of reported cases fit into the MOPD spectrum, with variable effects on learning / development. In view of the universal short stature and microcephaly, this presentation is likely to lead to the diagnosis, rather than ID.
Created: 21 Dec 2017, 2:14 p.m.
Comment on list classification: Majority of reported cases fit into the MOPD spectrum, with variable effects on learning / development. In view of the universal short stature and microcephaly, this presentation is likely to lead to the diagnosis, rather than ID.
Created: 21 Dec 2017, 2:13 p.m.
Created: 21 Dec 2017, 2:13 p.m.

Panel version: Imported from Intellectual disability update Dec 2017 panel version 0.95

Louise Daugherty (Genomics England Curator)

added tag locus-type-rna-small-nuclear.
Created: 9 Aug 2017, 2:06 p.m.
Comment on list classification: This gene is from an expert list and needs further assessment by the Genomics England curation team to assess inclusion and pertinence to this panel.
Created: 20 Jul 2017, 1:34 p.m.
Created: 9 Aug 2017, 2:06 p.m.

Panel version: 1.354

BRIDGE consortium (NIHRBR-RD)

Green List (high evidence)

This is a pertinent gene from the NIHR BioResource - Rare Diseases Study (NIHRBR-RD) BRIDGE Study : SPEED (Specialist Pathology: Evaluating Exomes in Diagnostics) which covers epilepsies, movement and microcephaly disorders, this gene is on the SPEED_NEURO_20170705 gene list. Evidences used for SPEED NEURO gene list: in_ddg2p_20141118_conf;in_ddg2p_20141118_conf;in_ddg2p_201507;in_ddg2p_201507_conf;in_ddg2p_2_4_2017;in_ddg2p_2_4_2017_conf;in_omim_20150205_microcephaly . Main mutation mechanism : Uncertain
Created: 27 Jul 2017, 8:16 p.m.
Evidences key, gene present in following gene lists and main mutation mechanism : ddg2p_20141118; ddg2p_20141118_conf; ddg2p_201507; ddg2p_201507_conf; omim_20150205_microcephaly; neuro_20160418_strict; Uncertain. This is a pertinent gene from the BRIDGE Study : SPEED (Specialist Pathology: Evaluating Exomes in Diagnostics) which covers epilepsies, movement and microcephaly disorders, this gene comes from the SPEED_NEURO_v3.0_20170404 gene list. The following experts from the BRIDGE consortium NIHRBR-RD contributed to this panel: - Professor F. Lucy Raymond, Cambridge Institute for Medical Research, University of Cambridge - Manju Kurian, Paediatric neurologist, Great Ormond Street Hosptial - Keren Carss, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Alba Sanchis-Juan, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Marie Erwood NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Louise Daugherty, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust
Created: 19 Jul 2017, 1:17 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Publications

Created: 2 Aug 2017, 10:12 p.m.

Panel version: 1.354

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
  • Expert Review Amber
Phenotypes
  • Lowry-Wood syndrome, OMIM:226960
  • Microcephalic osteodysplastic primordial dwarfism, type I, OMIM:210710
  • Roifman syndrome, OMIM:616651
Tags
locus-type-rna-small-nuclear Q2_26_promote_green
OMIM
601428
Clinvar variants
Variants in RNU4ATAC
Penetrance
Complete
Panels with this gene

History Filter Activity

29 Apr 2026, Gel status: 2

Added Tag

Ida Ertmanska (Genomics England Curator)

Tag Q2_26_promote_green tag was added to gene: RNU4ATAC.

24 Apr 2024, Gel status: 2

Set Phenotypes

Arina Puzriakova (Genomics England Curator)

Phenotypes for gene: RNU4ATAC were changed from Gene2Phenotype confirmed gene with ID HPO to Lowry-Wood syndrome, OMIM:226960; Microcephalic osteodysplastic primordial dwarfism, type I, OMIM:210710; Roifman syndrome, OMIM:616651

12 Mar 2018, Gel status: 2

Panel promoted to version 2.0

Ellen McDonagh (Genomics England Curator)

12.03.2018: Due to major updates completed (Phase 1, 2 and 3), this panel was promoted to Version 2 in order to reflect the major updates since November 2017 which have resulted in reviews for 836 genes added by Genomics England Curators and the Clinical Team, 130 new Green genes added to the interpretation pipeline (from 751 to 881 Green genes), and the gene total has increased from 1879 to 1927.

20 Jul 2017, Gel status: 2

Gene classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

This gene has been classified as Amber List (Moderate Evidence).

19 Jul 2017, Gel status: 0

Added New Source

BRIDGE consortium (NIHRBR-RD)

RNU4ATAC was added to Intellectual disabilitypanel. Sources: BRIDGE study SPEED NEURO Tier1 Gene

19 Jul 2017, Gel status: 0

Created

BRIDGE consortium (NIHRBR-RD)

RNU4ATAC was created by BRIDGE