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SRSF1

serine and arginine rich splicing factor 1, the group of RNA binding motif containing|Serine and arginine rich splicing factors

Basic information

Region (hg38): 17:58000918-58007346

Previous symbols: [ "SFRS1" ]

Links

ENSG00000136450NCBI:6426OMIM:600812HGNC:10780Uniprot:Q07955AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Neurodevelopmental disorder with dysmorphic facies and behavioral abnormalitiesADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Musculoskeletal; Neurologic37071997

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SRSF1 gene.

  • Neurodevelopmental delay;Intellectual disability (9 variants)
  • Neurodevelopmental disorder with dysmorphic facies and behavioral abnormalities (5 variants)
  • Intellectual disability;Neurodevelopmental delay (4 variants)
  • not provided (3 variants)
  • Inborn genetic diseases (1 variants)
  • Autism spectrum disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SRSF1 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
4
clinvar
4
clinvar
8
nonsense
3
clinvar
1
clinvar
4
start loss
0
frameshift
3
clinvar
3
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 10 0 5 0 0

Variants in SRSF1

This is a list of pathogenic ClinVar variants found in the SRSF1 region.

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

Position Type Phenotype Significance ClinVar
17-58005420-G-A Inborn genetic diseases Uncertain significance (Feb 28, 2023)2490509
17-58005551-CT-C Neurodevelopmental delay;Intellectual disability Pathogenic (Feb 15, 2023)2429788
17-58005573-C-CT Intellectual disability;Neurodevelopmental delay • Neurodevelopmental disorder with dysmorphic facies and behavioral abnormalities Pathogenic (Feb 15, 2023)2429782
17-58005805-T-C Neurodevelopmental delay;Intellectual disability Uncertain significance (Feb 15, 2023)2429785
17-58005875-C-T Intellectual disability;Neurodevelopmental delay • Neurodevelopmental disorder with dysmorphic facies and behavioral abnormalities Pathogenic (Feb 15, 2023)2429781
17-58005893-G-A Inborn genetic diseases Uncertain significance (Mar 12, 2024)3170251
17-58006343-CAG-C Neurodevelopmental delay;Intellectual disability Pathogenic (Feb 15, 2023)2429775
17-58006433-G-A Uncertain significance (Oct 21, 2016)488950
17-58006471-A-C Intellectual disability;Neurodevelopmental delay • Neurodevelopmental disorder with dysmorphic facies and behavioral abnormalities Pathogenic (Feb 15, 2023)2429778
17-58006491-A-C Neurodevelopmental delay;Intellectual disability Pathogenic (Feb 15, 2023)2429777
17-58006513-G-A Inborn genetic diseases Uncertain significance (Mar 11, 2024)3170250
17-58006514-C-T Neurodevelopmental delay;Intellectual disability Pathogenic (Feb 15, 2023)2429776
17-58007008-C-T Neurodevelopmental delay;Intellectual disability Uncertain significance (Feb 16, 2023)2429779
17-58007019-C-A Intellectual disability;Neurodevelopmental delay • Neurodevelopmental disorder with dysmorphic facies and behavioral abnormalities Pathogenic (Feb 15, 2023)2429786
17-58007041-C-A Neurodevelopmental delay;Intellectual disability Pathogenic (Feb 15, 2023)2429787
17-58007056-G-A Neurodevelopmental delay;Intellectual disability Pathogenic (Feb 15, 2023)2429784
17-58007067-G-A Neurodevelopmental disorder with dysmorphic facies and behavioral abnormalities • Neurodevelopmental delay;Intellectual disability Conflicting classifications of pathogenicity (Feb 15, 2023)1331676
17-58007068-G-A Autism spectrum disorder Uncertain significance (Aug 16, 2021)2429912

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SRSF1protein_codingprotein_codingENST00000258962 43987
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9830.017300000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.96221650.1330.000008781585
Missense in Polyphen143.2960.023097478
Synonymous-0.2545956.61.040.00000260527
Loss of Function3.26012.40.006.87e-7124

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)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Plays a role in preventing exon skipping, ensuring the accuracy of splicing and regulating alternative splicing. 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. Can stimulate binding of U1 snRNP to a 5'-splice site-containing pre-mRNA. Binds to purine-rich RNA sequences, either the octamer, 5'-RGAAGAAC-3' (r=A or G) or the decamers, AGGACAGAGC/AGGACGAAGC. Binds preferentially to the 5'- CGAGGCG-3' motif in vitro. Three copies of the octamer constitute a powerful splicing enhancer in vitro, the ASF/SF2 splicing enhancer (ASE) which can specifically activate ASE-dependent splicing. Isoform ASF-2 and isoform ASF-3 act as splicing repressors. May function as export adapter involved in mRNA nuclear export through the TAP/NXF1 pathway. {ECO:0000269|PubMed:8139654}.;
Pathway
IL-17 signaling pathway - Homo sapiens (human);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
0.0447

Intolerance Scores

loftool
rvis_EVS
-0.01
rvis_percentile_EVS
52.85

Haploinsufficiency Scores

pHI
0.851
hipred
Y
hipred_score
0.748
ghis
0.660

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
Srsf1
Phenotype
cellular phenotype; muscle phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye 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); 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);

Gene ontology

Biological process
alternative mRNA splicing, via spliceosome;regulation of alternative mRNA splicing, via spliceosome;mRNA 5'-splice site recognition;mRNA splicing, via spliceosome;in utero embryonic development;mRNA splice site selection;mRNA processing;RNA export from nucleus;mRNA export from nucleus;mRNA 3'-end processing;positive regulation of RNA splicing;mRNA cis splicing, via spliceosome;oligodendrocyte differentiation;cardiac muscle contraction;liver regeneration
Cellular component
nucleus;nucleoplasm;cytoplasm;nuclear speck;exon-exon junction complex;catalytic step 2 spliceosome
Molecular function
RNA binding;mRNA binding;protein binding;protein kinase B binding;DNA topoisomerase binding;RS domain binding