GAPT

protein-coding

GRB2 binding adaptor protein, transmembrane

Gene summary

Predicted to be involved in B cell homeostasis and B cell proliferation involved in immune response. Located in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C5orf29

MANE transcript

NM_001304431.2

Inheritance

—

ClinVar variants

U:22B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr5:58,491,435-58,497,090

External References & Databases

Ensembl (ENSG00000175857)

Transcript & Mutation Effects

hg38 • Region Span ~5.7 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 GAPT variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 25

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001304431.2. 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					1 clinvar	1
missense			22 clinvar	3 clinvar	1 clinvar	26
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	22	3	2	27

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001304431.2	RefSeq	NP_001291360.1	1	MANE Select
ENST00000502276.6	Ensembl	ENSP00000423113.2	1	MANE Select
NM_001304428.2	RefSeq	NP_001291357.1	1	Standard
NM_001304429.2	RefSeq	NP_001291358.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

TYROBP Causal Network

Biological Process

B cell homeostasis
B cell proliferation involved in immune response
immunoglobulin production involved in immunoglobulin mediated immune response

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000396776
Coding exons: 1
Length: 5656
Individuals with no LoFs: 122380
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 122383
p: 0.0000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.338	98	89.0	1.10	0.00000488	1020
Missense (PolyPhen)		34	27.866	1.2201		368
Synonymous	-0.877	41	34.4	1.19	0.00000204	304
Loss of Function	0.451	0	0.237	0.00	9.65e-9	4

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000027	0.000027	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Negatively regulates B-cell proliferation following stimulation through the B-cell receptor. May play an important role in maintenance of marginal zone (MZ) B-cells (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.0309

Intolerance Scores

RVIS EVS: 0.19
RVIS percentile EVS: 66.82

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.205

Gene Damage Prediction

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