SWAP70

switching B cell complex subunit SWAP70, the group of EF-hand domain containing|Minor histocompatibility antigens|Pleckstrin homology domain containing

Basic information

Region (hg38): 11:9664077-9752993

Links

ENSG00000133789

∙ NCBI:23075 ∙ OMIM:604762 ∙ HGNC:17070 ∙ Uniprot:Q9UH65 ∙ 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 SWAP70 gene.

not_specified (42 variants)
EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SWAP70 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015055.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			41 clinvar	2 clinvar		43
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	41	2	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SWAP70	protein_coding	protein_coding	ENST00000318950	12	88915

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0496	0.950	125729	0	17	125746	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.83	208	297	0.701	0.0000156	3870
Missense in Polyphen		52	96.737	0.53754		1212
Synonymous	0.989	92	105	0.877	0.00000513	991
Loss of Function	3.91	9	33.3	0.270	0.00000158	413

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000182	0.000182
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.0000544	0.0000544
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000537	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Phosphatidylinositol 3,4,5-trisphosphate-dependent guanine nucleotide exchange factor (GEF) which, independently of RAS, transduces signals from tyrosine kinase receptors to RAC. It also mediates signaling of membrane ruffling. Regulates the actin cytoskeleton as an effector or adapter protein in response to agonist stimulated phosphatidylinositol (3,4)-bisphosphate production and cell protrusion (By similarity). {ECO:0000250, ECO:0000269|PubMed:10681448, ECO:0000269|PubMed:12925760}.;

Intolerance Scores

loftool: 0.402
rvis_EVS: -0.51
rvis_percentile_EVS: 21.41

Haploinsufficiency Scores

pHI
hipred: Y
hipred_score: 0.506
ghis: 0.594

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.744

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Swap70
Phenotype: cellular phenotype; immune system phenotype; hematopoietic system phenotype;

Zebrafish Information Network

Gene name: swap70b
Affected structure: oligodendrocyte
Phenotype tag: abnormal
Phenotype quality: decreased amount

Gene ontology

Biological process: positive regulation of cytosolic calcium ion concentration;negative regulation of actin filament depolymerization;positive regulation of actin filament bundle assembly;regulation of protein localization;negative regulation of cell-cell adhesion mediated by integrin;isotype switching;actin filament bundle assembly;positive regulation of mast cell chemotaxis;negative regulation of peptidyl-serine dephosphorylation
Cellular component: nucleus;cytoplasm;cytoskeleton;plasma membrane;lamellipodium
Molecular function: DNA binding;calcium ion binding;protein binding;ATP binding;cadherin binding