GAB3

GRB2 associated binding protein 3, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): X:154675249-154751583

Links

ENSG00000160219 ∙ NCBI:139716 ∙ OMIM:300482 ∙ HGNC:17515 ∙ Uniprot:Q8WWW8 ∙ 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 GAB3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GAB3 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			18		1	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	2

Variants in GAB3

This is a list of pathogenic ClinVar variants found in the GAB3 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-154678192-G-C		not specified	Uncertain significance (Mar 21, 2024)
X-154678246-C-T		not specified	Uncertain significance (Feb 28, 2024)
X-154680220-C-G			Benign (Apr 17, 2018)
X-154680239-G-C		not specified	Uncertain significance (May 28, 2024)
X-154695973-C-T		not specified	Uncertain significance (Aug 04, 2023)
X-154695978-T-C		not specified	Uncertain significance (Aug 04, 2023)
X-154695992-T-A		not specified	Uncertain significance (Jan 27, 2022)
X-154697138-A-G		not specified	Uncertain significance (Sep 22, 2023)
X-154699497-G-A		not specified	Uncertain significance (Feb 14, 2023)
X-154699507-T-A		not specified	Uncertain significance (Jun 03, 2022)
X-154700038-A-G		not specified	Uncertain significance (Feb 16, 2023)
X-154712333-C-T		not specified	Uncertain significance (Jul 12, 2022)
X-154712462-C-A		not specified	Uncertain significance (Jul 20, 2022)
X-154712469-G-A			Benign (Apr 30, 2018)
X-154712519-C-T		not specified	Uncertain significance (Jun 17, 2024)
X-154712546-G-A		not specified	Uncertain significance (Aug 04, 2023)
X-154712553-G-A		not specified	Uncertain significance (Jul 17, 2023)
X-154712621-C-T		not specified	Uncertain significance (Feb 17, 2024)
X-154713342-C-A		not specified	Uncertain significance (Apr 25, 2023)
X-154716110-C-T		not specified	Uncertain significance (Jan 30, 2024)
X-154716149-C-T		not specified	Uncertain significance (Feb 17, 2022)
X-154716212-C-T		not specified	Uncertain significance (Dec 06, 2022)
X-154716293-G-A		not specified	Uncertain significance (Dec 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GAB3	protein_coding	protein_coding	ENST00000424127	10	76330

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.954	0.0464	125325	0	2	125327	0.00000798

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.47	161	223	0.723	0.0000174	3830
Missense in Polyphen		41	67.061	0.61139		1120
Synonymous	0.850	76	86.0	0.883	0.00000670	1165
Loss of Function	3.55	2	18.5	0.108	0.00000144	318

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	0.0000625	0.0000463
European (Non-Finnish)	0.0000138	0.00000882
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.102

Intolerance Scores

• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.01

Haploinsufficiency Scores

• pHI: 0.237
• hipred: Y
• hipred_score: 0.580
• ghis: 0.520

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.734

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gab3
• Phenotype: normal phenotype

Gene ontology

• Biological process: macrophage differentiation