SWAP70

protein-coding

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

Gene summary

Enables cadherin binding activity. Predicted to be involved in regulation of small GTPase mediated signal transduction. Predicted to act upstream of or within isotype switching. Located in actin cytoskeleton; cytoplasm; and plasma membrane. Is active in postsynapse. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_015055.4

Inheritance

—

ClinVar variants

U:55B:2

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.27

Max pathogenic AF

—

Genomic locus

chr11:9,664,077-9,752,993

External References & Databases

Ensembl (ENSG00000133789)

Transcript & Mutation Effects

hg38 • Region Span ~88.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SWAP70 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 55

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015055.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			54 clinvar	2 clinvar		56
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	55	2	0	57

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015055.4	RefSeq	NP_055870.2	12	MANE Select
ENST00000318950.11	Ensembl	ENSP00000315630.6	12	MANE Select
NM_001297714.2	RefSeq	NP_001284643.1	11	Standard
ENST00000447399.6	Ensembl	ENSP00000399056.2	11	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
swap70b	Danio rerio	Structure: oligodendrocyte Quality: decreased amount abnormal

Gene / Model

Organism

Observed Phenotype

swap70b

Danio rerio

Structure: oligodendrocyte

Quality: decreased amount

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

Molecular Function

DNA binding
calcium ion binding
protein binding
ATP binding
cadherin binding

Cellular Component

nucleus
cytoplasm
cytoskeleton
plasma membrane
lamellipodium

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000318950
Coding exons: 12
Length: 88915
Individuals with no LoFs: 125729
Homozygous LoFs: 0
Heterozygous LoFs: 17
Defined: 125746
p: 0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.83	208	297	0.701	0.0000156	3870
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000059	0.000058	rare
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.000054	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000054	0.000053	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.744

Gene Damage Prediction

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