SNRPA1

small nuclear ribonucleoprotein polypeptide A', the group of U2 small nuclear ribonucleoprotein

Basic information

Region (hg38): 15:101281510-101295282

Links

ENSG00000131876 ∙ NCBI:6627 ∙ OMIM:603521 ∙ HGNC:11152 ∙ Uniprot:P09661 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SNRPA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNRPA1 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in SNRPA1

This is a list of pathogenic ClinVar variants found in the SNRPA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-101281746-T-C		not specified	Uncertain significance (Oct 12, 2022)
15-101284976-G-A		not specified	Uncertain significance (Mar 11, 2024)
15-101284978-T-C		not specified	Uncertain significance (Oct 06, 2023)
15-101285757-C-G		not specified	Uncertain significance (Jul 21, 2022)
15-101286969-A-G		not specified	Uncertain significance (Aug 21, 2023)
15-101287689-G-C		not specified	Uncertain significance (Dec 05, 2022)
15-101291970-C-T		not specified	Uncertain significance (Aug 15, 2023)
15-101292003-G-C		not specified	Uncertain significance (Jul 13, 2022)
15-101293054-T-A		not specified	Uncertain significance (Dec 14, 2023)
15-101293096-C-G		not specified	Uncertain significance (Apr 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNRPA1	protein_coding	protein_coding	ENST00000254193	9	13773

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.990	0.0102	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.87	75	137	0.549	0.00000726	1641
Missense in Polyphen		26	46.815	0.55538		611
Synonymous	-0.677	60	53.7	1.12	0.00000293	503
Loss of Function	3.44	0	13.8	0.00	6.77e-7	181

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in pre-mRNA splicing as component of the spliceosome (PubMed:11991638, PubMed:28502770, PubMed:28781166, PubMed:28076346, PubMed:27035939). Associated with sn-RNP U2, where it contributes to the binding of stem loop IV of U2 snRNA (PubMed:9716128, PubMed:27035939). {ECO:0000269|PubMed:11991638, ECO:0000269|PubMed:27035939, ECO:0000269|PubMed:28076346, ECO:0000269|PubMed:28502770, ECO:0000269|PubMed:28781166, ECO:0000269|PubMed:9716128}.
• Pathway: Spliceosome - Homo sapiens (human);Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation;mRNA Processing;spliceosomal assembly;Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.136

Intolerance Scores

• rvis_EVS: 0.3
• rvis_percentile_EVS: 72.01

Haploinsufficiency Scores

• pHI: 0.835
• hipred: Y
• hipred_score: 0.774
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.993

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snrpa1

Gene ontology

• Biological process: mRNA splicing, via spliceosome;spermatogenesis;RNA splicing;interleukin-12-mediated signaling pathway
• Cellular component: nucleus;nucleoplasm;spliceosomal complex;U2 snRNP;nuclear body;nuclear speck;small nuclear ribonucleoprotein complex;U2-type precatalytic spliceosome;U2-type catalytic step 2 spliceosome;catalytic step 2 spliceosome
• Molecular function: RNA binding;protein binding;U2 snRNA binding