SF3A1

splicing factor 3a subunit 1, the group of SF3a complex|U2 small nuclear ribonucleoprotein

Basic information

Region (hg38): 22:30331987-30356919

Links

ENSG00000099995 ∙ NCBI:10291 ∙ OMIM:605595 ∙ HGNC:10765 ∙ Uniprot:Q15459 ∙ 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 SF3A1 gene.

• Inborn genetic diseases (10 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SF3A1 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	11	0	0

Variants in SF3A1

This is a list of pathogenic ClinVar variants found in the SF3A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-30337705-T-C		not specified	Uncertain significance (Oct 05, 2023)
22-30337750-T-C		not specified	Uncertain significance (Nov 28, 2023)
22-30337858-G-A		not specified	Uncertain significance (Aug 04, 2023)
22-30338829-C-T		not specified	Uncertain significance (Feb 27, 2023)
22-30338859-G-A		not specified	Uncertain significance (Nov 20, 2023)
22-30338880-T-C		not specified	Uncertain significance (Nov 08, 2022)
22-30338890-TG-T		Malignant lymphoma, large B-cell, diffuse	Pathogenic (Dec 04, 2023)
22-30338898-A-C		not specified	Uncertain significance (Mar 24, 2023)
22-30342201-T-G		not specified	Uncertain significance (Dec 27, 2023)
22-30342208-T-C		not specified	Uncertain significance (Aug 19, 2023)
22-30342843-T-G		not specified	Uncertain significance (Jun 03, 2022)
22-30342845-A-G		not specified	Uncertain significance (Dec 14, 2023)
22-30342861-C-A		not specified	Uncertain significance (Sep 17, 2021)
22-30344925-C-G			Benign (Dec 31, 2019)
22-30345009-T-C		not specified	Uncertain significance (Mar 01, 2023)
22-30346418-T-C		not specified	Uncertain significance (Jul 20, 2022)
22-30346479-T-A			Uncertain significance (Nov 01, 2022)
22-30353059-T-G		not specified	Uncertain significance (Dec 19, 2023)
22-30356755-G-A		not specified	Uncertain significance (Nov 06, 2023)
22-30356764-G-A		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SF3A1	protein_coding	protein_coding	ENST00000215793	16	24960

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.988	0.0125	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.16	203	452	0.449	0.0000256	5176
Missense in Polyphen		81	244.05	0.3319		2745
Synonymous	-0.293	177	172	1.03	0.0000102	1540
Loss of Function	4.96	6	39.7	0.151	0.00000205	451

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000298	0.0000298
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000573	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000635	0.0000615
Middle Eastern	0.0000573	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Subunit of the splicing factor SF3A required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA. May also be involved in the assembly of the 'E' complex.
• Pathway: Spliceosome - Homo sapiens (human);mRNA Processing;Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.210
• rvis_EVS: -0.78
• rvis_percentile_EVS: 12.77

Haploinsufficiency Scores

• pHI: 0.758
• hipred: Y
• hipred_score: 0.783
• ghis: 0.663

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.729

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sf3a1
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: mRNA 3'-splice site recognition;mRNA splicing, via spliceosome;mRNA processing
• Cellular component: nucleoplasm;spliceosomal complex;U2-type spliceosomal complex;U2 snRNP;nuclear speck;U2-type prespliceosome;catalytic step 2 spliceosome
• Molecular function: RNA binding;protein binding