RNU4ATAC

RNA, U4atac small nuclear, the group of Small nuclear RNAs|Minor spliceosome

Basic information

Region (hg38): 2:121530881-121531007

Links

ENSG00000264229 ∙ NCBI:100151683 ∙ OMIM:601428 ∙ HGNC:34016 ∙ ∙ ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• microcephalic osteodysplastic primordial dwarfism type I (Definitive), mode of inheritance: AR
• microcephalic osteodysplastic primordial dwarfism type I (Moderate), mode of inheritance: AR
• Roifman syndrome (Moderate), mode of inheritance: AR
• Lowry-Wood syndrome (Limited), mode of inheritance: AR
• Roifman syndrome (Definitive), mode of inheritance: AR
• microcephalic osteodysplastic primordial dwarfism type I (Strong), mode of inheritance: AR
• Roifman syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Roifman syndrome	AR	Allergy/Immunology/Infectious	Among other features, individuals with Roifman syndrome have been described with antibody deficiency and recurrent and severe infections, and awareness may allow preventive measures and early and aggressive treatment of infections	Allergy/Immunology/Infectious; Craniofacial; Dermatologic; Musculoskeletal; Neurologic; Ophthalmologic; Renal	934161; 984702; 9800907; 10189087; 12571786; 21474760; 21474761; 22581640; 25735804; 26522830; 29265708; 30368667

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RNU4ATAC gene.

• not provided (202 variants)
• Osteodysplastic primordial dwarfism, type 1 (16 variants)
• Roifman syndrome (15 variants)
• Lowry-Wood syndrome (8 variants)
• RNU4ATAC-related condition (6 variants)
• Osteodysplastic primordial dwarfism, type 1;Roifman syndrome;Lowry-Wood syndrome (3 variants)
• RNU4ATAC-related spliceosomopathies (2 variants)
• Intellectual disability;Short stature (2 variants)
• Lowry-Wood syndrome;Roifman syndrome;Osteodysplastic primordial dwarfism, type 1 (2 variants)
• Spondyloepiphyseal dysplasia congenita (2 variants)
• not specified (1 variants)
• Microcephaly;Cardiomyopathy;Short stature;Craniosynostosis syndrome;Neurodevelopmental delay (1 variants)
• Roifman syndrome;Osteodysplastic primordial dwarfism, type 1;Lowry-Wood syndrome (1 variants)
• Osteodysplastic primordial dwarfism, type 1;Lowry-Wood syndrome (1 variants)
• Lowry-Wood syndrome;Osteodysplastic primordial dwarfism, type 1;Roifman syndrome (1 variants)
• Roifman syndrome;Lowry-Wood syndrome;Osteodysplastic primordial dwarfism, type 1 (1 variants)
• Lowry-Wood syndrome;Osteodysplastic primordial dwarfism, type 1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNU4ATAC gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			3			3
splice region						0
non coding	8	16	168	10	5	207
Total	8	16	171	10	5

Highest pathogenic variant AF is 0.0000920

Variants in RNU4ATAC

This is a list of pathogenic ClinVar variants found in the RNU4ATAC region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-121530882-C-G			Uncertain significance (Jun 08, 2022)
2-121530882-C-T			Uncertain significance (Jan 25, 2024)
2-121530883-C-T			Uncertain significance (Oct 18, 2022)
2-121530884-A-C		Lowry-Wood syndrome	Uncertain significance (Jun 01, 2020)
2-121530884-A-G			Uncertain significance (Jan 29, 2024)
2-121530884-A-T			Uncertain significance (May 30, 2022)
2-121530885-T-C		RNU4ATAC-related spliceosomopathies	Conflicting classifications of pathogenicity (Jun 19, 2022)
2-121530885-TC-AT			Uncertain significance (Jan 17, 2024)
2-121530886-C-T			Uncertain significance (Oct 24, 2022)
2-121530887-C-A		Lowry-Wood syndrome	Likely pathogenic (Jul 16, 2018)
2-121530887-C-G		Roifman syndrome	Conflicting classifications of pathogenicity (May 02, 2023)
2-121530887-C-T		Roifman syndrome • Neurodevelopmental delay;Short stature;Cardiomyopathy;Craniosynostosis syndrome;Microcephaly • not specified • Spondyloepiphyseal dysplasia congenita • RNU4ATAC-related disorder	Conflicting classifications of pathogenicity (Jan 31, 2024)
2-121530889-T-C			Uncertain significance (Jan 20, 2022)
2-121530889-TTTC-T			Uncertain significance (Nov 03, 2021)
2-121530890-T-C			Uncertain significance (Dec 26, 2023)
2-121530890-T-G			Uncertain significance (Feb 03, 2021)
2-121530890-T-TA			Uncertain significance (Oct 19, 2022)
2-121530891-T-A			Uncertain significance (Jul 06, 2022)
2-121530891-T-C			Uncertain significance (Jun 03, 2022)
2-121530891-T-G			Uncertain significance (May 09, 2022)
2-121530892-C-G			Conflicting classifications of pathogenicity (Apr 15, 2024)
2-121530892-C-T		Roifman syndrome • Osteodysplastic primordial dwarfism, type 1;Lowry-Wood syndrome;Roifman syndrome • CLASP1-related disorder	Pathogenic (Jun 01, 2024)
2-121530893-T-C			Uncertain significance (Sep 25, 2022)
2-121530894-T-C			Uncertain significance (Sep 09, 2022)
2-121530894-T-G			Uncertain significance (Jul 25, 2022)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

• Pathway: RNA polymerase II transcribes snRNA genes;Gene expression (Transcription);RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription (Consensus)

Essentials

• gene_indispensability_pred: E
• gene_indispensability_score: 0.912