GAB2

GRB2 associated binding protein 2, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 11:78215292-78418348

Links

ENSG00000033327 ∙ NCBI:9846 ∙ OMIM:606203 ∙ HGNC:14458 ∙ Uniprot:Q9UQC2 ∙ 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 GAB2 gene.

• Inborn genetic diseases (23 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GAB2 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	2	3
missense			24		2	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	24	1	4

Variants in GAB2

This is a list of pathogenic ClinVar variants found in the GAB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-78219281-G-A			Benign/Likely benign (Apr 01, 2022)
11-78219356-C-T			Benign (Mar 30, 2018)
11-78219400-C-T		not specified	Uncertain significance (Mar 04, 2024)
11-78220323-C-G		not specified	Uncertain significance (Nov 15, 2021)
11-78220323-C-T		not specified	Uncertain significance (Jul 20, 2021)
11-78220405-T-C		not specified	Uncertain significance (Oct 13, 2023)
11-78221679-T-C		not specified	Uncertain significance (Dec 15, 2023)
11-78221732-G-T		not specified	Uncertain significance (Nov 08, 2022)
11-78221772-A-T		not specified	Uncertain significance (Dec 15, 2023)
11-78222097-G-A			Benign/Likely benign (Dec 01, 2022)
11-78222180-A-G		not specified	Uncertain significance (Apr 12, 2022)
11-78223480-C-T		not specified	Uncertain significance (May 15, 2023)
11-78223544-T-C		not specified	Uncertain significance (Oct 14, 2023)
11-78223612-T-C		not specified	Uncertain significance (Oct 06, 2021)
11-78223630-T-A		not specified	Uncertain significance (Apr 18, 2023)
11-78225112-A-G		not specified	Uncertain significance (Mar 27, 2023)
11-78226467-C-T		not specified	Uncertain significance (Oct 13, 2023)
11-78226489-T-C		not specified	Uncertain significance (Feb 05, 2024)
11-78226506-C-T		not specified	Uncertain significance (Dec 19, 2022)
11-78226549-T-C		not specified	Uncertain significance (Sep 22, 2023)
11-78226606-G-C			Uncertain significance (Oct 01, 2022)
11-78226612-G-A		not specified	Uncertain significance (Sep 29, 2022)
11-78226696-T-A		not specified	Uncertain significance (Mar 07, 2023)
11-78226722-G-A			Benign (Jun 20, 2018)
11-78226731-A-G		not specified	Uncertain significance (Dec 07, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GAB2	protein_coding	protein_coding	ENST00000361507	10	203052

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.983	0.0168	125735	0	12	125747	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.622	426	391	1.09	0.0000228	4433
Missense in Polyphen		102	99.855	1.0215		1283
Synonymous	0.423	144	151	0.956	0.00000883	1340
Loss of Function	4.41	4	30.1	0.133	0.00000200	312

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000213	0.000213
Ashkenazi Jewish	0.000112	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000454	0.0000439
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Adapter protein which acts downstream of several membrane receptors including cytokine, antigen, hormone, cell matrix and growth factor receptors to regulate multiple signaling pathways. Regulates osteoclast differentiation mediating the TNFRSF11A/RANK signaling. In allergic response, it plays a role in mast cells activation and degranulation through PI-3-kinase regulation. Also involved in the regulation of cell proliferation and hematopoiesis. {ECO:0000269|PubMed:15750601, ECO:0000269|PubMed:19172738}.
• Pathway: Chronic myeloid leukemia - Homo sapiens (human);Fc epsilon RI signaling pathway - Homo sapiens (human);Fc gamma R-mediated phagocytosis - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);Sphingolipid signaling pathway - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Osteoclast differentiation - Homo sapiens (human);Fc Epsilon Receptor I Signaling in Mast Cells;RANKL-RANK (Receptor activator of NFKB (ligand)) Signaling Pathway;Prolactin Signaling Pathway;Thymic Stromal LymphoPoietin (TSLP) Signaling Pathway;B Cell Receptor Signaling Pathway;IL-3 Signaling Pathway;Kit receptor signaling pathway;Imatinib and Chronic Myeloid Leukemia;BDNF-TrkB Signaling;IL-4 Signaling Pathway;Ras Signaling;EGF-EGFR Signaling Pathway;IL-2 Signaling Pathway;Interferon type I signaling pathways;T-Cell antigen Receptor (TCR) Signaling Pathway;Developmental Biology;Signaling by GPCR;Disease;Signal Transduction;Signaling by Interleukins;Cytokine Signaling in Immune system;Fc epsilon receptor (FCERI) signaling;TCR;Innate Immune System;Immune System;Interleukin receptor SHC signaling;Interleukin-2 family signaling;SHP2 signaling;IL2;IL3;IL2-mediated signaling events;RET signaling;Axon guidance;Signaling by SCF-KIT;Signaling by FGFR in disease;IL6;Signaling by cytosolic FGFR1 fusion mutants;FGFR1 mutant receptor activation;Signaling by FGFR1 in disease;Signaling by Receptor Tyrosine Kinases;G beta:gamma signalling through PI3Kgamma;G-protein beta:gamma signalling;GPCR downstream signalling;GMCSF-mediated signaling events;IL2 signaling events mediated by STAT5;Neurotrophic factor-mediated Trk receptor signaling;Diseases of signal transduction;Signaling events mediated by Hepatocyte Growth Factor Receptor (c-Met);Fc-epsilon receptor I signaling in mast cells;IL2 signaling events mediated by PI3K;IL6-mediated signaling events;TCR signaling in naïve CD4+ T cells;IL3-mediated signaling events;Role of LAT2/NTAL/LAB on calcium mobilization;Interleukin-3, 5 and GM-CSF signaling (Consensus)

Recessive Scores

• pRec: 0.454

Intolerance Scores

• loftool: 0.292
• rvis_EVS: -1.04
• rvis_percentile_EVS: 7.77

Haploinsufficiency Scores

• pHI: 0.338
• hipred: N
• hipred_score: 0.252
• ghis: 0.510

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.791

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gab2
• Phenotype: immune system phenotype; skeleton phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; muscle phenotype; cellular phenotype

Gene ontology

• Biological process: transmembrane receptor protein tyrosine kinase signaling pathway;axon guidance;positive regulation of cell population proliferation;cytokine-mediated signaling pathway;osteoclast differentiation;phosphatidylinositol-3-phosphate biosynthetic process;Fc-epsilon receptor signaling pathway;positive regulation of mast cell degranulation;phosphatidylinositol-mediated signaling
• Cellular component: cytoplasm;cytosol;plasma membrane
• Molecular function: transmembrane receptor protein tyrosine kinase adaptor activity;protein binding;phosphatidylinositol-3,4,5-trisphosphate binding;1-phosphatidylinositol-3-kinase activity;phosphatidylinositol-3,4-bisphosphate binding