SF3A2
Basic information
Region (hg38): 19:2236824-2248655
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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) | ||
19-2248110-C-T | not specified | Uncertain significance (Jun 13, 2024) | ||
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:
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:
- 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
- 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