SRSF6
Basic information
Region (hg38): 20:43457892-43466046
Previous symbols: [ "SFRS6" ]
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 SRSF6 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 | 1 | |||||
missense | 19 | 20 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region ? | 1 | 1 | ||||
non coding ? | 0 | |||||
Total | 0 | 0 | 20 | 1 | 1 |
Variants in SRSF6
This is a list of pathogenic ClinVar variants found in the SRSF6 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
20-43458050-T-C | not specified | Uncertain significance (Sep 13, 2023) | ||
20-43458481-T-G | not specified | Uncertain significance (Dec 03, 2021) | ||
20-43458482-C-T | not specified | Uncertain significance (Mar 08, 2024) | ||
20-43460026-C-T | Benign (Jun 23, 2018) | |||
20-43460064-AT-A | Uncertain significance (Jul 01, 2019) | |||
20-43460162-A-G | not specified | Uncertain significance (Dec 13, 2021) | ||
20-43460201-C-T | not specified | Uncertain significance (Mar 15, 2024) | ||
20-43460202-G-A | not specified | Uncertain significance (Feb 22, 2023) | ||
20-43460203-C-T | Benign (Dec 31, 2019) | |||
20-43460223-A-G | not specified | Uncertain significance (Dec 22, 2023) | ||
20-43460561-C-T | not specified | Uncertain significance (Aug 30, 2022) | ||
20-43460567-A-G | not specified | Uncertain significance (Apr 05, 2023) | ||
20-43460592-G-A | not specified | Uncertain significance (Mar 21, 2023) | ||
20-43460597-C-T | not specified | Uncertain significance (Feb 15, 2023) | ||
20-43460713-C-T | not specified | Uncertain significance (Apr 05, 2023) | ||
20-43460723-G-A | not specified | Uncertain significance (Mar 29, 2023) | ||
20-43460725-C-G | not specified | Uncertain significance (Dec 26, 2023) | ||
20-43460726-G-A | not specified | Uncertain significance (Jun 10, 2024) | ||
20-43460753-A-G | not specified | Uncertain significance (Feb 27, 2023) | ||
20-43460792-G-A | not specified | Uncertain significance (Apr 09, 2024) | ||
20-43460801-A-G | not specified | Likely benign (May 23, 2023) | ||
20-43460837-A-C | not specified | Uncertain significance (Dec 20, 2023) | ||
20-43460894-T-C | not specified | Uncertain significance (Feb 06, 2024) | ||
20-43461047-C-T | not specified | Uncertain significance (Oct 10, 2023) | ||
20-43461053-C-G | not specified | Uncertain significance (May 17, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SRSF6 | protein_coding | protein_coding | ENST00000244020 | 6 | 5678 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.911 | 0.0890 | 125741 | 0 | 5 | 125746 | 0.0000199 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.10 | 171 | 217 | 0.790 | 0.0000138 | 2178 |
Missense in Polyphen | 16 | 62.812 | 0.25473 | 714 | ||
Synonymous | -1.86 | 90 | 70.2 | 1.28 | 0.00000354 | 701 |
Loss of Function | 3.64 | 3 | 21.0 | 0.143 | 0.00000175 | 189 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000290 | 0.0000290 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000352 | 0.0000352 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Plays a role in constitutive splicing and modulates the selection of alternative splice sites. Plays a role in the alternative splicing of MAPT/Tau exon 10. Binds to alternative exons of TNC pre-mRNA and promotes the expression of alternatively spliced TNC. Plays a role in wound healing and in the regulation of keratinocyte differentiation and proliferation via its role in alternative splicing. {ECO:0000269|PubMed:12549914, ECO:0000269|PubMed:15009664, ECO:0000269|PubMed:22767602, ECO:0000269|PubMed:24440982}.;
- Pathway
- Spliceosome - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);mRNA Processing;Gene expression (Transcription);RNA Polymerase II Transcription;Metabolism of RNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;mRNA Splicing - Major Pathway;Transport of Mature mRNA derived from an Intron-Containing Transcript;mRNA Splicing - Minor Pathway;mRNA Splicing;mRNA 3,-end processing;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Recessive Scores
- pRec
- 0.114
Intolerance Scores
- loftool
- rvis_EVS
- -0.56
- rvis_percentile_EVS
- 19.31
Haploinsufficiency Scores
- pHI
- 0.0856
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.621
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.539
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Srsf6
- Phenotype
Gene ontology
- Biological process
- alternative mRNA splicing, via spliceosome;regulation of alternative mRNA splicing, via spliceosome;mRNA splicing, via spliceosome;mRNA splice site selection;RNA export from nucleus;mRNA export from nucleus;regulation of keratinocyte proliferation;mRNA 3'-end processing;response to insulin;mRNA cis splicing, via spliceosome;negative regulation of keratinocyte differentiation;negative regulation of mRNA splicing, via spliceosome;positive regulation of epithelial cell proliferation involved in lung morphogenesis;negative regulation of cell death;regulation of wound healing;negative regulation of type B pancreatic cell apoptotic process
- Cellular component
- nucleoplasm;nuclear speck
- Molecular function
- RNA binding;protein binding;pre-mRNA binding