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

ENSG00000116350 ∙ NCBI:6429 ∙ OMIM:601940 ∙ HGNC:10786 ∙ Uniprot:Q08170 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SRSF4 gene.

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			18	2		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	2	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)
1-29148528-G-A		not specified	Uncertain significance (Jun 07, 2023)
1-29148574-G-A		not specified	Uncertain significance (Dec 19, 2023)
1-29148594-G-A		not specified	Uncertain significance (Dec 16, 2023)
1-29148602-A-T		not specified	Uncertain significance (Dec 05, 2022)
1-29148709-T-C		not specified	Uncertain significance (May 24, 2023)
1-29148783-C-T		not specified	Uncertain significance (Aug 16, 2022)
1-29148964-C-T		not specified	Uncertain significance (Aug 12, 2021)
1-29149045-C-T		not specified	Uncertain significance (Dec 15, 2023)
1-29149050-T-C		not specified	Likely benign (Jan 25, 2023)
1-29149107-C-T		not specified	Likely benign (Jan 19, 2024)
1-29149155-C-T		not specified	Uncertain significance (Dec 19, 2023)
1-29149174-G-A		not specified	Uncertain significance (Jan 17, 2024)
1-29149180-G-A		not specified	Uncertain significance (Apr 13, 2022)
1-29149192-G-A		not specified	Uncertain significance (Sep 16, 2021)
1-29150145-C-T		not specified	Uncertain significance (Dec 15, 2023)
1-29150151-C-T		not specified	Uncertain significance (Oct 10, 2023)
1-29150188-G-A		not specified	Uncertain significance (Jul 25, 2023)
1-29154726-C-T		not specified	Uncertain significance (Dec 27, 2023)
1-29154736-T-C		not specified	Uncertain significance (Feb 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SRSF4	protein_coding	protein_coding	ENST00000373795	6	34245

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.867	0.133	125736	0	11	125747	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.40	205	327	0.627	0.0000223	3240
Missense in Polyphen		8	51.374	0.15572		535
Synonymous	-0.768	118	108	1.09	0.00000553	958
Loss of Function	3.81	4	24.2	0.165	0.00000185	253

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000667	0.0000667
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000890	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.0000368	0.0000327
Other	0.00	0.00

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

• 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

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

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