SFSWAP

splicing factor SWAP

Basic information

Region (hg38): 12:131711080-131799738

Previous symbols: [ "SFRS8" ]

Links

ENSG00000061936 ∙ NCBI:6433 ∙ OMIM:601945 ∙ HGNC:10790 ∙ Uniprot:Q12872 ∙ 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 SFSWAP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SFSWAP 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				5		5
missense			47	4		51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	47	9	0

Variants in SFSWAP

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

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

Position	Type	Phenotype	Significance	ClinVar
12-131711254-G-C		not specified	Uncertain significance (Apr 29, 2024)
12-131711263-G-A		not specified	Uncertain significance (May 27, 2022)
12-131711288-A-C		not specified	Uncertain significance (Dec 28, 2022)
12-131711311-G-T		not specified	Uncertain significance (Aug 21, 2023)
12-131711312-G-A		not specified	Uncertain significance (Mar 21, 2024)
12-131711428-C-T		not specified	Uncertain significance (Sep 22, 2022)
12-131714136-G-A		not specified	Uncertain significance (May 15, 2024)
12-131714141-T-C		not specified	Uncertain significance (Jan 23, 2024)
12-131714163-C-T		not specified	Uncertain significance (Oct 29, 2021)
12-131714215-C-G		not specified	Uncertain significance (May 05, 2023)
12-131714896-A-C		not specified	Uncertain significance (May 05, 2023)
12-131719498-G-A			Likely benign (Nov 01, 2022)
12-131719519-G-A		not specified	Uncertain significance (Nov 21, 2023)
12-131725528-C-T		not specified	Uncertain significance (Nov 17, 2022)
12-131725559-A-G		not specified	Uncertain significance (Feb 23, 2023)
12-131726961-A-G		not specified	Uncertain significance (Apr 19, 2024)
12-131728380-G-A		not specified	Uncertain significance (Mar 04, 2024)
12-131728420-C-T		not specified	Uncertain significance (Jun 10, 2022)
12-131728426-A-G		not specified	Uncertain significance (Feb 05, 2024)
12-131753227-C-T		not specified	Uncertain significance (Mar 21, 2024)
12-131753246-T-A		not specified	Uncertain significance (Apr 22, 2024)
12-131753273-C-T		not specified	Uncertain significance (Nov 07, 2022)
12-131753274-C-T			Likely benign (Apr 01, 2022)
12-131753306-C-T		not specified	Uncertain significance (Dec 20, 2023)
12-131753342-C-T		not specified	Uncertain significance (Sep 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SFSWAP	protein_coding	protein_coding	ENST00000541286	19	88657

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000778	125743	0	3	125746	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.80	439	638	0.688	0.0000412	6480
Missense in Polyphen		102	208.31	0.48965		2193
Synonymous	-0.546	286	275	1.04	0.0000201	2022
Loss of Function	5.89	3	46.2	0.0649	0.00000220	591

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000184	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role as an alternative splicing regulator. Regulate its own expression at the level of RNA processing. Also regulates the splicing of fibronectin and CD45 genes. May act, at least in part, by interaction with other R/S-containing splicing factors. Represses the splicing of MAPT/Tau exon 10. {ECO:0000269|PubMed:8940107}.
• Pathway: mRNA Processing (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• rvis_EVS: -0.96
• rvis_percentile_EVS: 9

Haploinsufficiency Scores

• pHI: 0.191
• hipred: Y
• hipred_score: 0.673
• ghis: 0.583

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sfswap
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hearing/vestibular/ear phenotype

Gene ontology

• Biological process: alternative mRNA splicing, via spliceosome;mRNA 5'-splice site recognition;negative regulation of mRNA splicing, via spliceosome
• Cellular component: nucleus
• Molecular function: RNA binding;protein binding