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SRSF4

serine and arginine rich splicing factor 4, the group of RNA binding motif containing|Serine and arginine rich splicing factors

Basic information

Region (hg38): 1:29147742-29181900

Previous symbols: [ "SFRS4" ]

Links

ENSG00000116350NCBI:6429OMIM:601940HGNC:10786Uniprot:Q08170AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SRSF4 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 SRSF4 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
8
clinvar
1
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 8 1 0

Variants in SRSF4

This is a list of pathogenic ClinVar variants found in the SRSF4 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
1-29148447-G-C not specified Uncertain significance (Dec 19, 2023)3170262
1-29148528-G-A not specified Uncertain significance (Jun 07, 2023)2558549
1-29148574-G-A not specified Uncertain significance (Dec 19, 2023)3170261
1-29148594-G-A not specified Uncertain significance (Dec 16, 2023)3170260
1-29148602-A-T not specified Uncertain significance (Dec 05, 2022)2370180
1-29148709-T-C not specified Uncertain significance (May 24, 2023)2525385
1-29148783-C-T not specified Uncertain significance (Aug 16, 2022)2344840
1-29148964-C-T not specified Uncertain significance (Aug 12, 2021)3170270
1-29149045-C-T not specified Uncertain significance (Dec 15, 2023)3170269
1-29149050-T-C not specified Likely benign (Jan 25, 2023)2479111
1-29149107-C-T not specified Likely benign (Jan 19, 2024)3170268
1-29149155-C-T not specified Uncertain significance (Dec 19, 2023)3170267
1-29149174-G-A not specified Uncertain significance (Jan 17, 2024)3170266
1-29149180-G-A not specified Uncertain significance (Apr 13, 2022)2374112
1-29149192-G-A not specified Uncertain significance (Sep 16, 2021)2384464
1-29150145-C-T not specified Uncertain significance (Dec 15, 2023)3170265
1-29150151-C-T not specified Uncertain significance (Oct 10, 2023)3170264
1-29150188-G-A not specified Uncertain significance (Jul 25, 2023)2602284
1-29154726-C-T not specified Uncertain significance (Dec 27, 2023)3170263
1-29154736-T-C not specified Uncertain significance (Feb 27, 2023)2489746

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SRSF4protein_codingprotein_codingENST00000373795 634245
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.8670.1331257360111257470.0000437
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.402053270.6270.00002233240
Missense in Polyphen851.3740.15572535
Synonymous-0.7681181081.090.00000553958
Loss of Function3.81424.20.1650.00000185253

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006670.0000667
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00008900.0000703
Middle Eastern0.000.00
South Asian0.00003680.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Plays a role in alternative splice site selection during pre-mRNA splicing. Represses the splicing of MAPT/Tau exon 10. {ECO:0000269|PubMed:15009664}.;
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;mRNA 3,-end processing;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

pRec
0.129

Intolerance Scores

loftool
rvis_EVS
0.06
rvis_percentile_EVS
58.85

Haploinsufficiency Scores

pHI
0.923
hipred
Y
hipred_score
0.783
ghis
0.581

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.539

Gene Damage Prediction

AllRecessiveDominant
MendelianHighHighHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh

Mouse Genome Informatics

Gene name
Srsf4
Phenotype
homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); pigmentation phenotype;

Gene ontology

Biological process
RNA splicing, via transesterification reactions;regulation of alternative mRNA splicing, via spliceosome;mRNA splicing, via spliceosome;mRNA processing;RNA export from nucleus;mRNA export from nucleus;RNA splicing;mRNA 3'-end processing;response to insulin;mRNA cis splicing, via spliceosome;negative regulation of mRNA splicing, via spliceosome
Cellular component
nucleus;nucleoplasm;nuclear speck
Molecular function
RNA binding;protein binding;sequence-specific mRNA binding