SF3A3

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

Basic information

Region (hg38): 1:37956974-37990075

Links

ENSG00000183431 ∙ NCBI:10946 ∙ OMIM:605596 ∙ HGNC:10767 ∙ Uniprot:Q12874 ∙ 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 SF3A3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SF3A3 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			12	1		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	0

Variants in SF3A3

This is a list of pathogenic ClinVar variants found in the SF3A3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-37969716-T-C		not specified	Uncertain significance (Jan 06, 2023)
1-37976886-C-T		not specified	Uncertain significance (Jul 17, 2023)
1-37978722-C-G		not specified	Uncertain significance (Dec 06, 2021)
1-37979511-G-T		not specified	Uncertain significance (Apr 28, 2022)
1-37979526-G-C		not specified	Uncertain significance (Jun 18, 2024)
1-37980610-C-A		not specified	Likely benign (Jan 02, 2024)
1-37984206-T-C		not specified	Uncertain significance (Mar 16, 2022)
1-37984221-T-C		not specified	Uncertain significance (Aug 08, 2022)
1-37984733-C-T		not specified	Uncertain significance (Aug 02, 2022)
1-37984779-T-G		not specified	Uncertain significance (Nov 06, 2023)
1-37987658-T-C		not specified	Uncertain significance (Dec 30, 2023)
1-37987791-T-C		not specified	Uncertain significance (Apr 13, 2022)
1-37987808-C-G		not specified	Uncertain significance (Apr 07, 2023)
1-37989579-T-C		not specified	Uncertain significance (Apr 07, 2022)
1-37989958-G-A		not specified	Uncertain significance (Jun 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SF3A3	protein_coding	protein_coding	ENST00000373019	17	33947

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000318	125729	0	2	125731	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.62	99	265	0.374	0.0000130	3300
Missense in Polyphen		13	86.696	0.14995		1082
Synonymous	0.224	90	92.7	0.970	0.00000435	864
Loss of Function	5.70	1	39.8	0.0251	0.00000236	435

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	0.0000925	0.0000924
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: 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);Exercise-induced Circadian Regulation;mRNA Processing;Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.0899

Intolerance Scores

• loftool: 0.0425
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

• pHI: 0.354
• hipred: Y
• hipred_score: 0.748
• ghis: 0.608

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: K
• 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: Sf3a3

Zebrafish Information Network

• Gene name: sf3a3
• Affected structure: ventral wall of dorsal aorta
• Phenotype tag: abnormal
• Phenotype quality: absent

Gene ontology

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