SRSF6

serine and arginine rich splicing factor 6, the group of RNA binding motif containing|Serine and arginine rich splicing factors

Basic information

Region (hg38): 20:43457892-43466046

Previous symbols: [ "SFRS6" ]

Links

ENSG00000124193 ∙ NCBI:6431 ∙ OMIM:601944 ∙ HGNC:10788 ∙ Uniprot:Q13247 ∙ 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 SRSF6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SRSF6 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	1
missense			19	1		20
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	20	1	1

Variants in SRSF6

This is a list of pathogenic ClinVar variants found in the SRSF6 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-43458050-T-C		not specified	Uncertain significance (Sep 13, 2023)
20-43458481-T-G		not specified	Uncertain significance (Dec 03, 2021)
20-43458482-C-T		not specified	Uncertain significance (Mar 08, 2024)
20-43460026-C-T			Benign (Jun 23, 2018)
20-43460064-AT-A			Uncertain significance (Jul 01, 2019)
20-43460162-A-G		not specified	Uncertain significance (Dec 13, 2021)
20-43460202-G-A		not specified	Uncertain significance (Feb 22, 2023)
20-43460203-C-T			Benign (Dec 31, 2019)
20-43460223-A-G		not specified	Uncertain significance (Dec 22, 2023)
20-43460561-C-T		not specified	Uncertain significance (Aug 30, 2022)
20-43460567-A-G		not specified	Uncertain significance (Apr 05, 2023)
20-43460592-G-A		not specified	Uncertain significance (Mar 21, 2023)
20-43460597-C-T		not specified	Uncertain significance (Feb 15, 2023)
20-43460713-C-T		not specified	Uncertain significance (Apr 05, 2023)
20-43460723-G-A		not specified	Uncertain significance (Mar 29, 2023)
20-43460725-C-G		not specified	Uncertain significance (Dec 26, 2023)
20-43460753-A-G		not specified	Uncertain significance (Feb 27, 2023)
20-43460801-A-G		not specified	Likely benign (May 23, 2023)
20-43460837-A-C		not specified	Uncertain significance (Dec 20, 2023)
20-43460894-T-C		not specified	Uncertain significance (Feb 06, 2024)
20-43461047-C-T		not specified	Uncertain significance (Oct 10, 2023)
20-43461053-C-G		not specified	Uncertain significance (May 17, 2023)
20-43461059-A-G		not specified	Uncertain significance (Dec 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SRSF6	protein_coding	protein_coding	ENST00000244020	6	5678

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.911	0.0890	125741	0	5	125746	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	171	217	0.790	0.0000138	2178
Missense in Polyphen		16	62.812	0.25473		714
Synonymous	-1.86	90	70.2	1.28	0.00000354	701
Loss of Function	3.64	3	21.0	0.143	0.00000175	189

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in constitutive splicing and modulates the selection of alternative splice sites. Plays a role in the alternative splicing of MAPT/Tau exon 10. Binds to alternative exons of TNC pre-mRNA and promotes the expression of alternatively spliced TNC. Plays a role in wound healing and in the regulation of keratinocyte differentiation and proliferation via its role in alternative splicing. {ECO:0000269|PubMed:12549914, ECO:0000269|PubMed:15009664, ECO:0000269|PubMed:22767602, ECO:0000269|PubMed:24440982}.
• 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 - 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: 0.114

Intolerance Scores

• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.31

Haploinsufficiency Scores

• pHI: 0.0856
• hipred: Y
• hipred_score: 0.783
• ghis: 0.621

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Srsf6

Gene ontology

• Biological process: alternative mRNA splicing, via spliceosome;regulation of alternative mRNA splicing, via spliceosome;mRNA splicing, via spliceosome;mRNA splice site selection;RNA export from nucleus;mRNA export from nucleus;regulation of keratinocyte proliferation;mRNA 3'-end processing;response to insulin;mRNA cis splicing, via spliceosome;negative regulation of keratinocyte differentiation;negative regulation of mRNA splicing, via spliceosome;positive regulation of epithelial cell proliferation involved in lung morphogenesis;negative regulation of cell death;regulation of wound healing;negative regulation of type B pancreatic cell apoptotic process
• Cellular component: nucleoplasm;nuclear speck
• Molecular function: RNA binding;protein binding;pre-mRNA binding