GAPT

GRB2 binding adaptor protein, transmembrane

Basic information

Region (hg38): 5:58491435-58497090

Previous symbols: [ "C5orf29" ]

Links

ENSG00000175857 ∙ NCBI:202309 ∙ ∙ HGNC:26588 ∙ Uniprot:Q8N292 ∙ 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 GAPT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GAPT 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					1	1
missense			11	3	1	15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	3	2

Variants in GAPT

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

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

Position	Type	Phenotype	Significance	ClinVar
5-58494565-C-T		not specified	Likely benign (Dec 16, 2023)
5-58494610-G-A		not specified	Uncertain significance (Aug 28, 2024)
5-58494645-G-T		not specified	Uncertain significance (Apr 06, 2023)
5-58494672-T-G		not specified	Uncertain significance (Jul 27, 2024)
5-58494709-C-A		not specified	Uncertain significance (Feb 27, 2023)
5-58494738-G-A		not specified	Likely benign (Sep 07, 2022)
5-58494742-T-C		not specified	Likely benign (Nov 03, 2023)
5-58494748-A-G		not specified	Uncertain significance (Feb 28, 2023)
5-58494749-T-A		not specified	Uncertain significance (Feb 22, 2025)
5-58494776-C-T			Benign (May 03, 2018)
5-58494777-A-G		not specified	Uncertain significance (Apr 22, 2022)
5-58494783-G-A			Benign (May 03, 2018)
5-58494786-G-C		not specified	Uncertain significance (Jun 07, 2023)
5-58494868-T-C		not specified	Uncertain significance (Jul 31, 2023)
5-58494931-A-G		not specified	Uncertain significance (Apr 19, 2024)
5-58494937-A-G		not specified	Uncertain significance (Feb 28, 2024)
5-58494985-T-C		not specified	Uncertain significance (Jan 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GAPT	protein_coding	protein_coding	ENST00000396776	1	5656

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.306	0.500	122380	0	3	122383	0.0000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.338	98	89.0	1.10	0.00000488	1020
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000270	0.0000270
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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}.
• Pathway: TYROBP Causal Network (Consensus)

Recessive Scores

• pRec: 0.0309

Intolerance Scores

• rvis_EVS: 0.19
• rvis_percentile_EVS: 66.82

Haploinsufficiency Scores

• pHI: 0.00638
• hipred: N
• hipred_score: 0.123
• ghis: 0.434

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.205

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gapt
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• 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