SF3A2

splicing factor 3a subunit 2, the group of SF3a complex|U2 small nuclear ribonucleoprotein

Basic information

Region (hg38): 19:2236823-2248655

Links

ENSG00000104897 ∙ NCBI:8175 ∙ OMIM:600796 ∙ HGNC:10766 ∙ Uniprot:Q15428 ∙ 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 SF3A2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SF3A2 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			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	0

Variants in SF3A2

This is a list of pathogenic ClinVar variants found in the SF3A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-2243479-G-A		not specified	Uncertain significance (Jul 25, 2023)
19-2243491-G-A		not specified	Uncertain significance (Jan 09, 2024)
19-2246771-C-T		not specified	Uncertain significance (Aug 12, 2021)
19-2247623-G-T		not specified	Uncertain significance (Oct 06, 2021)
19-2247804-C-T		not specified	Uncertain significance (Oct 22, 2021)
19-2247816-G-C		not specified	Uncertain significance (May 17, 2023)
19-2247858-C-G		not specified	Uncertain significance (Feb 27, 2023)
19-2247888-C-T		not specified	Uncertain significance (Sep 14, 2022)
19-2247948-C-T		not specified	Uncertain significance (Dec 01, 2022)
19-2247975-C-T		not specified	Uncertain significance (Mar 31, 2022)
19-2248094-G-A		not specified	Uncertain significance (Dec 11, 2023)
19-2248100-C-A		not specified	Uncertain significance (Jun 30, 2023)
19-2248211-G-A		not specified	Uncertain significance (Oct 05, 2023)
19-2248218-G-C		not specified	Uncertain significance (Dec 14, 2023)
19-2248232-G-A		not specified	Uncertain significance (Dec 15, 2023)
19-2248299-C-A		not specified	Uncertain significance (May 30, 2023)
19-2248312-C-A		not specified	Uncertain significance (Jul 19, 2023)
19-2248314-C-T		not specified	Uncertain significance (Dec 01, 2022)
19-2248385-C-A		not specified	Uncertain significance (Jan 05, 2022)
19-2248398-C-T		not specified	Uncertain significance (Jan 23, 2023)
19-2248401-C-T		not specified	Uncertain significance (Feb 13, 2023)
19-2248423-G-C		not specified	Uncertain significance (Nov 21, 2023)
19-2248449-C-G		not specified	Uncertain significance (Sep 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SF3A2	protein_coding	protein_coding	ENST00000221494	8	12159

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.883	0.117	118157	0	1	118158	0.00000423

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.61	135	252	0.537	0.0000161	2924
Missense in Polyphen		11	68.641	0.16025		724
Synonymous	-1.90	131	106	1.24	0.00000765	1012
Loss of Function	3.21	2	15.8	0.127	7.53e-7	179

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)	0.00000905	0.00000905
Middle Eastern	0.00	0.00
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: 0.137

Haploinsufficiency Scores

• pHI: 0.229
• hipred: Y
• hipred_score: 0.831
• ghis: 0.580

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.970

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sf3a2

Gene ontology

• Biological process: spliceosomal complex assembly;mRNA 3'-splice site recognition;mRNA splicing, via spliceosome;mRNA processing;RNA splicing;positive regulation of neuron projection development
• Cellular component: nucleoplasm;spliceosomal complex;U2 snRNP;nuclear speck;small nuclear ribonucleoprotein complex;U2-type prespliceosome;catalytic step 2 spliceosome
• Molecular function: RNA binding;protein binding;zinc ion binding