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SRSF2

serine and arginine rich splicing factor 2, the group of RNA binding motif containing|Serine and arginine rich splicing factors|MicroRNA protein coding host genes

Basic information

Region (hg38): 17:76734114-76737333

Previous symbols: [ "SFRS2" ]

Links

ENSG00000161547NCBI:6427OMIM:600813HGNC:10783Uniprot:Q01130AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SRSF2 gene.

  • Inborn genetic diseases (4 variants)
  • not provided (3 variants)
  • Acute megakaryoblastic leukemia in down syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SRSF2 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
2
clinvar
2
missense
1
clinvar
4
clinvar
5
nonsense
0
start loss
0
frameshift
0
inframe indel
1
clinvar
1
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 1 5 2 0

Highest pathogenic variant AF is 0.0000789

Variants in SRSF2

This is a list of pathogenic ClinVar variants found in the SRSF2 region.

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

Position Type Phenotype Significance ClinVar
17-76736270-C-A not specified Uncertain significance (Feb 15, 2023)2464223
17-76736271-G-C not specified Uncertain significance (Apr 12, 2023)2536561
17-76736271-GGGACCT-G Uncertain significance (Jan 19, 2017)423166
17-76736297-G-C not specified Uncertain significance (Sep 06, 2022)2310902
17-76736323-C-T Likely benign (Mar 01, 2023)2648319
17-76736844-G-A not specified Uncertain significance (Oct 03, 2022)2374008
17-76736877-G-A Atypical chronic myeloid leukemia, BCR-ABL1 negative • Acute myeloid leukemia Pathogenic (Jun 08, 2023)2504111
17-76736877-G-C Acute megakaryoblastic leukemia in down syndrome Likely pathogenic (Sep 01, 2020)998075
17-76736978-G-A Likely benign (Feb 01, 2023)2648320
17-76737017-G-A SRSF2-related disorder Benign (May 03, 2022)3058855

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SRSF2protein_codingprotein_codingENST00000392485 23260
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.4790.500120664011206650.00000414
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.71551480.3730.000006911378
Missense in Polyphen533.8340.14778318
Synonymous-2.398662.01.390.00000283512
Loss of Function1.8615.840.1712.66e-760

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)0.000009290.00000929
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Necessary for the splicing of pre-mRNA. It is required for formation of the earliest ATP-dependent splicing complex and interacts with spliceosomal components bound to both the 5'- and 3'-splice sites during spliceosome assembly. It also is required for ATP-dependent interactions of both U1 and U2 snRNPs with pre- mRNA. Interacts with other spliceosomal components, via the RS domains, to form a bridge between the 5'- and 3'-splice site binding components, U1 snRNP and U2AF. Binds to purine-rich RNA sequences, either 5'-AGSAGAGTA-3' (S=C or G) or 5'-GTTCGAGTA-3'. Can bind to beta-globin mRNA and commit it to the splicing pathway. The phosphorylated form (by SRPK2) is required for cellular apoptosis in response to cisplatin treatment. {ECO:0000269|PubMed:19592491, ECO:0000269|PubMed:21157427}.;
Pathway
Spliceosome - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);mRNA Processing;Gene expression (Transcription);spliceosomal assembly;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
0.116

Intolerance Scores

loftool
rvis_EVS
-0.25
rvis_percentile_EVS
35.42

Haploinsufficiency Scores

pHI
0.531
hipred
Y
hipred_score
0.624
ghis
0.711

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.539

Mouse Genome Informatics

Gene name
Srsf2
Phenotype
mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); immune system phenotype; endocrine/exocrine gland phenotype; cellular phenotype; muscle phenotype;

Gene ontology

Biological process
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;mRNA cis splicing, via spliceosome;negative regulation of nucleic acid-templated transcription
Cellular component
nucleus;nucleoplasm;cytoplasm;cytosol;PML body;nuclear speck
Molecular function
transcription corepressor activity;RNA binding;protein binding