SNRPA

small nuclear ribonucleoprotein polypeptide A, the group of U1 small nuclear ribonucleoprotein|RNA binding motif containing

Basic information

Region (hg38): 19:40750636-40765389

Links

ENSG00000077312 ∙ NCBI:6626 ∙ OMIM:182285 ∙ HGNC:11151 ∙ Uniprot:P09012 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AR

ClinVar

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

• Inborn genetic diseases (9 variants)
• Spliceosomepathy (3 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNRPA 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					1	1
missense		2	9	1		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	2	9	1	1

Variants in SNRPA

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

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

Position	Type	Phenotype	Significance	ClinVar
19-40757355-A-G		Spliceosomepathy	Likely benign (Nov 01, 2017)
19-40757356-T-C		Spliceosomepathy	Likely pathogenic (Nov 01, 2017)
19-40757358-T-A		Spliceosomepathy	Likely pathogenic (Nov 01, 2017)
19-40757398-G-A		not specified	Uncertain significance (Aug 28, 2023)
19-40757498-A-G		SNRPA-related disorder	Benign (Oct 22, 2019)
19-40757500-C-G		not specified	Uncertain significance (May 09, 2023)
19-40759451-C-T		SNRPA-related disorder	Benign/Likely benign (Mar 18, 2019)
19-40759474-T-C		not specified	Uncertain significance (Dec 19, 2023)
19-40759501-G-A		not specified	Uncertain significance (Mar 06, 2023)
19-40759506-C-T		not specified	Uncertain significance (Dec 07, 2021)
19-40759507-G-A		not specified	Uncertain significance (May 27, 2022)
19-40759540-C-T		not specified	Uncertain significance (Apr 12, 2023)
19-40759566-G-A		not specified	Uncertain significance (Mar 07, 2024)
19-40759570-G-T		not specified	Uncertain significance (Jan 30, 2024)
19-40759588-G-C		not specified	Uncertain significance (Sep 17, 2021)
19-40762911-C-T		not specified	Uncertain significance (Aug 21, 2023)
19-40762924-G-A		SNRPA-related disorder	Likely benign (Jun 06, 2019)
19-40762979-A-G		not specified	Uncertain significance (Dec 07, 2021)
19-40763590-T-G		not specified	Uncertain significance (Oct 10, 2023)
19-40764993-GTCGTTC-G		SNRPA-related disorder	Likely benign (Apr 30, 2019)
19-40765041-C-T		SNRPA-related disorder	Likely benign (Feb 20, 2019)
19-40765086-G-T		not specified	Uncertain significance (Feb 05, 2024)
19-40765137-C-T		SNRPA-related disorder	Likely benign (Feb 18, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNRPA	protein_coding	protein_coding	ENST00000243563	6	14753

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000281	0.557	125733	0	14	125747	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.75	116	183	0.635	0.0000112	1865
Missense in Polyphen		25	54.835	0.45591		585
Synonymous	-0.601	77	70.6	1.09	0.00000457	547
Loss of Function	0.681	8	10.4	0.772	4.39e-7	129

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000803	0.0000791
Middle Eastern	0.000110	0.000109
South Asian	0.0000655	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the spliceosomal U1 snRNP, which is essential for recognition of the pre-mRNA 5' splice-site and the subsequent assembly of the spliceosome. U1 snRNP is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. SNRPA binds stem loop II of U1 snRNA. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. May bind preferentially to the 5'-UGCAC-3' motif on RNAs. {ECO:0000269|PubMed:9848648}.
• Pathway: Spliceosome - Homo sapiens (human);mRNA Processing;spliceosomal assembly;Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.290

Intolerance Scores

• loftool: 0.485
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.26

Haploinsufficiency Scores

• pHI: 0.732
• hipred: Y
• hipred_score: 0.866
• ghis: 0.690

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.997

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Snrpa

Gene ontology

• Biological process: mRNA splicing, via spliceosome;regulation of mRNA polyadenylation
• Cellular component: nucleoplasm;spliceosomal complex;U1 snRNP
• Molecular function: RNA binding;protein binding;U1 snRNA binding;snRNA stem-loop binding;identical protein binding;U1 snRNP binding