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SRSF9

serine and arginine rich splicing factor 9, the group of RNA binding motif containing|Serine and arginine rich splicing factors

Basic information

Region (hg38): 12:120461671-120495946

Previous symbols: [ "SFRS9" ]

Links

ENSG00000111786NCBI:8683OMIM:601943HGNC:10791Uniprot:Q13242AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SRSF9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SRSF9 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
5
clinvar
5
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 5 0 1

Variants in SRSF9

This is a list of pathogenic ClinVar variants found in the SRSF9 region.

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

Position Type Phenotype Significance ClinVar
12-120462041-A-T not specified Uncertain significance (Jun 27, 2022)2368718
12-120462080-C-T not specified Uncertain significance (Mar 23, 2023)2570423
12-120464084-G-A not specified Uncertain significance (Feb 23, 2023)2488369
12-120465781-T-C Benign (Dec 18, 2018)708410
12-120469438-G-A not specified Uncertain significance (Dec 13, 2022)2334149
12-120469494-C-G not specified Uncertain significance (Jun 05, 2023)2556420

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SRSF9protein_codingprotein_codingENST00000229390 48126
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.6390.360125735041257390.0000159
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.53551390.3960.000007911405
Missense in Polyphen745.1390.15508489
Synonymous-1.596449.71.290.00000240435
Loss of Function2.66211.90.1687.56e-7123

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)0.00003880.0000352
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Plays a role in constitutive splicing and can modulate the selection of alternative splice sites. Represses the splicing of MAPT/Tau exon 10. {ECO:0000269|PubMed:10196175, ECO:0000269|PubMed:11875052, ECO:0000269|PubMed:12024014, ECO:0000269|PubMed:12604611, ECO:0000269|PubMed:15009090, ECO:0000269|PubMed:15009664, ECO:0000269|PubMed:15695522, ECO:0000269|PubMed:7556075}.;
Pathway
Spliceosome - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);miR-targeted genes in adipocytes - TarBase;miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;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
0.149

Intolerance Scores

loftool
rvis_EVS
-0.05
rvis_percentile_EVS
49.76

Haploinsufficiency Scores

pHI
0.630
hipred
Y
hipred_score
0.831
ghis
0.491

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
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Srsf9
Phenotype

Gene ontology

Biological process
regulation of alternative mRNA splicing, via spliceosome;mRNA splicing, via spliceosome;mRNA splice site selection;mRNA processing;RNA export from nucleus;mRNA export from nucleus;response to toxic substance;mRNA 3'-end processing;response to alkaloid;mRNA cis splicing, via spliceosome;negative regulation of mRNA splicing, via spliceosome
Cellular component
nucleoplasm;nucleolus;nuclear speck
Molecular function
RNA binding;protein binding;protein domain specific binding