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GeneBe

SF3A2

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

Basic information

Region (hg38): 19:2236823-2248655

Links

ENSG00000104897NCBI:8175OMIM:600796HGNC:10766Uniprot:Q15428AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SF3A2 gene.

  • Inborn genetic diseases (17 variants)

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
17
clinvar
17
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 17 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)2613922
19-2243491-G-A not specified Uncertain significance (Jan 09, 2024)3160806
19-2246771-C-T not specified Uncertain significance (Aug 12, 2021)2357106
19-2247623-G-T not specified Uncertain significance (Oct 06, 2021)2371058
19-2247804-C-T not specified Uncertain significance (Oct 22, 2021)2345815
19-2247816-G-C not specified Uncertain significance (May 17, 2023)2547479
19-2247858-C-G not specified Uncertain significance (Feb 27, 2023)2489554
19-2247888-C-T not specified Uncertain significance (Sep 14, 2022)2311826
19-2247948-C-T not specified Uncertain significance (Dec 01, 2022)2209710
19-2247975-C-T not specified Uncertain significance (Mar 31, 2022)2281059
19-2248094-G-A not specified Uncertain significance (Dec 11, 2023)3160807
19-2248100-C-A not specified Uncertain significance (Jun 30, 2023)2594237
19-2248211-G-A not specified Uncertain significance (Oct 05, 2023)3160802
19-2248218-G-C not specified Uncertain significance (Dec 14, 2023)3160803
19-2248232-G-A not specified Uncertain significance (Dec 15, 2023)3160804
19-2248299-C-A not specified Uncertain significance (May 30, 2023)2552762
19-2248312-C-A not specified Uncertain significance (Jul 19, 2023)2613261
19-2248314-C-T not specified Uncertain significance (Dec 01, 2022)2331403
19-2248385-C-A not specified Uncertain significance (Jan 05, 2022)2270484
19-2248398-C-T not specified Uncertain significance (Jan 23, 2023)2471261
19-2248401-C-T not specified Uncertain significance (Feb 13, 2023)2471488
19-2248423-G-C not specified Uncertain significance (Nov 21, 2023)3160805
19-2248449-C-G not specified Uncertain significance (Sep 27, 2022)2313780

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SF3A2protein_codingprotein_codingENST00000221494 812159
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.8830.117118157011181580.00000423
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.611352520.5370.00001612924
Missense in Polyphen1168.6410.16025724
Synonymous-1.901311061.240.000007651012
Loss of Function3.21215.80.1277.53e-7179

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000009050.00000905
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);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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sf3a2
Phenotype

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