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GeneBe

SFSWAP

splicing factor SWAP

Basic information

Region (hg38): 12:131711080-131799738

Previous symbols: [ "SFRS8" ]

Links

ENSG00000061936NCBI:6433OMIM:601945HGNC:10790Uniprot:Q12872AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
5
missense
47
clinvar
4
clinvar
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
12-131711263-G-A not specified Uncertain significance (May 27, 2022)2292973
12-131711288-A-C not specified Uncertain significance (Dec 28, 2022)2340042
12-131711311-G-T not specified Uncertain significance (Aug 21, 2023)2620099
12-131711428-C-T not specified Uncertain significance (Sep 22, 2022)2312779
12-131714141-T-C not specified Uncertain significance (Jan 23, 2024)3160936
12-131714163-C-T not specified Uncertain significance (Oct 29, 2021)2257919
12-131714215-C-G not specified Uncertain significance (May 05, 2023)2543941
12-131714896-A-C not specified Uncertain significance (May 05, 2023)2544014
12-131719498-G-A Likely benign (Nov 01, 2022)2643601
12-131719519-G-A not specified Uncertain significance (Nov 21, 2023)3160937
12-131725528-C-T not specified Uncertain significance (Nov 17, 2022)2384476
12-131725559-A-G not specified Uncertain significance (Feb 23, 2023)2488602
12-131728380-G-A not specified Uncertain significance (Mar 04, 2024)3160920
12-131728420-C-T not specified Uncertain significance (Jun 10, 2022)2295371
12-131728426-A-G not specified Uncertain significance (Feb 05, 2024)3160921
12-131753273-C-T not specified Uncertain significance (Nov 07, 2022)2363200
12-131753274-C-T Likely benign (Apr 01, 2022)2643602
12-131753306-C-T not specified Uncertain significance (Dec 20, 2023)3160922
12-131753342-C-T not specified Uncertain significance (Sep 29, 2022)3160923
12-131754411-G-A not specified Likely benign (Dec 17, 2023)3160924
12-131754446-C-T Likely benign (Jun 01, 2022)2643603
12-131755413-G-C not specified Uncertain significance (May 03, 2023)2542630
12-131755443-G-A Likely benign (Jun 01, 2022)2643604
12-131755468-G-A not specified Uncertain significance (Nov 09, 2021)3160925
12-131756501-C-A not specified Uncertain significance (May 23, 2023)2509735

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SFSWAPprotein_codingprotein_codingENST00000541286 1988657
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.00000778125743031257460.0000119
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.804396380.6880.00004126480
Missense in Polyphen102208.310.489652193
Synonymous-0.5462862751.040.00002012022
Loss of Function5.89346.20.06490.00000220591

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.00001840.0000176
Middle Eastern0.00005440.0000544
South Asian0.000.00
Other0.000.00

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

loftool
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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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