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GeneBe

SF3A3

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

Basic information

Region (hg38): 1:37956974-37990075

Links

ENSG00000183431NCBI:10946OMIM:605596HGNC:10767Uniprot:Q12874AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SF3A3 gene.

  • Inborn genetic diseases (9 variants)

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
9
clinvar
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 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)2474239
1-37976886-C-T not specified Uncertain significance (Jul 17, 2023)2612295
1-37978722-C-G not specified Uncertain significance (Dec 06, 2021)2370153
1-37979511-G-T not specified Uncertain significance (Apr 28, 2022)2227764
1-37980610-C-A not specified Likely benign (Jan 02, 2024)3160811
1-37984206-T-C not specified Uncertain significance (Mar 16, 2022)2278691
1-37984221-T-C not specified Uncertain significance (Aug 08, 2022)2305952
1-37984733-C-T not specified Uncertain significance (Aug 02, 2022)3160810
1-37984779-T-G not specified Uncertain significance (Nov 06, 2023)3160809
1-37987658-T-C not specified Uncertain significance (Dec 30, 2023)3160808
1-37987791-T-C not specified Uncertain significance (Apr 13, 2022)2283705
1-37987808-C-G not specified Uncertain significance (Apr 07, 2023)2534143
1-37989579-T-C not specified Uncertain significance (Apr 07, 2022)2216662

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SF3A3protein_codingprotein_codingENST00000373019 1733947
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.00000318125729021257310.00000795
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.62992650.3740.00001303300
Missense in Polyphen1386.6960.149951082
Synonymous0.2249092.70.9700.00000435864
Loss of Function5.70139.80.02510.00000236435

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00009250.0000924
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sf3a3
Phenotype

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