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SRSF6

serine and arginine rich splicing factor 6, the group of RNA binding motif containing|Serine and arginine rich splicing factors

Basic information

Region (hg38): 20:43457892-43466046

Previous symbols: [ "SFRS6" ]

Links

ENSG00000124193NCBI:6431OMIM:601944HGNC:10788Uniprot:Q13247AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SRSF6 gene.

  • Inborn genetic diseases (12 variants)
  • not provided (3 variants)

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
clinvar
1
missense
11
clinvar
1
clinvar
12
nonsense
0
start loss
0
frameshift
1
clinvar
1
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
0
Total 0 0 12 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)2621929
20-43458481-T-G not specified Uncertain significance (Dec 03, 2021)2264195
20-43458482-C-T not specified Uncertain significance (Mar 08, 2024)3170279
20-43460026-C-T Benign (Jun 23, 2018)779389
20-43460064-AT-A Uncertain significance (Jul 01, 2019)872203
20-43460162-A-G not specified Uncertain significance (Dec 13, 2021)2266478
20-43460202-G-A not specified Uncertain significance (Feb 22, 2023)2455997
20-43460203-C-T Benign (Dec 31, 2019)731744
20-43460223-A-G not specified Uncertain significance (Dec 22, 2023)3170280
20-43460561-C-T not specified Uncertain significance (Aug 30, 2022)3170281
20-43460567-A-G not specified Uncertain significance (Apr 05, 2023)2516277
20-43460592-G-A not specified Uncertain significance (Mar 21, 2023)2537058
20-43460597-C-T not specified Uncertain significance (Feb 15, 2023)2454336
20-43460713-C-T not specified Uncertain significance (Apr 05, 2023)2533172
20-43460723-G-A not specified Uncertain significance (Mar 29, 2023)2531248
20-43460725-C-G not specified Uncertain significance (Dec 26, 2023)3170282
20-43460753-A-G not specified Uncertain significance (Feb 27, 2023)2469304
20-43460801-A-G not specified Likely benign (May 23, 2023)2514967
20-43460837-A-C not specified Uncertain significance (Dec 20, 2023)3170283
20-43460894-T-C not specified Uncertain significance (Feb 06, 2024)3170284
20-43461047-C-T not specified Uncertain significance (Oct 10, 2023)3170277
20-43461053-C-G not specified Uncertain significance (May 17, 2023)2547331
20-43461059-A-G not specified Uncertain significance (Dec 17, 2023)3170278

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SRSF6protein_codingprotein_codingENST00000244020 65678
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9110.0890125741051257460.0000199
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.101712170.7900.00001382178
Missense in Polyphen1662.8120.25473714
Synonymous-1.869070.21.280.00000354701
Loss of Function3.64321.00.1430.00000175189

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002900.0000290
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00003520.0000352
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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