GRAP2

GRB2 related adaptor protein 2, the group of SH2 domain containing

Basic information

Region (hg38): 22:39901083-39973721

Links

ENSG00000100351 ∙ NCBI:9402 ∙ OMIM:604518 ∙ HGNC:4563 ∙ Uniprot:O75791 ∙ 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 GRAP2 gene.

• Inborn genetic diseases (9 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GRAP2 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	2
missense			8	1	3	12
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	8	2	4

Variants in GRAP2

This is a list of pathogenic ClinVar variants found in the GRAP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-39947144-G-A		not specified	Uncertain significance (Jan 17, 2024)
22-39955879-C-A		not specified	Uncertain significance (Oct 17, 2023)
22-39960157-C-A		not specified	Uncertain significance (Jan 03, 2024)
22-39966025-G-A		not specified	Uncertain significance (Jan 29, 2024)
22-39966127-T-C		not specified	Uncertain significance (Feb 23, 2023)
22-39966145-C-A		not specified	Uncertain significance (Jan 24, 2023)
22-39966148-G-A		not specified	Uncertain significance (Jul 06, 2021)
22-39968035-C-T			Benign (Apr 16, 2018)
22-39968048-C-T			Benign (May 21, 2018)
22-39968066-C-T		not specified	Uncertain significance (Mar 28, 2023)
22-39968118-G-A			Benign (Jan 17, 2018)
22-39968133-G-A		not specified	Uncertain significance (Jun 16, 2023)
22-39968156-A-C		not specified	Likely benign (Dec 07, 2021)
22-39968257-C-G		not specified	Uncertain significance (Oct 30, 2023)
22-39969435-A-G		not specified	Uncertain significance (May 24, 2023)
22-39969459-G-A			Benign (Aug 16, 2018)
22-39969490-T-A		not specified	Uncertain significance (Jan 24, 2024)
22-39969521-C-G			Benign (Jul 27, 2018)
22-39970921-G-A		not specified	Uncertain significance (Dec 03, 2021)
22-39970925-G-A			Likely benign (Jul 16, 2018)
22-39971025-C-T		not specified	Uncertain significance (Jun 11, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GRAP2	protein_coding	protein_coding	ENST00000344138	7	72640

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000153	0.993	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	154	199	0.776	0.0000114	2176
Missense in Polyphen		42	64.262	0.65357		730
Synonymous	0.699	73	81.0	0.901	0.00000491	626
Loss of Function	2.39	10	22.2	0.451	0.00000152	184

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000206	0.000206
Ashkenazi Jewish	0.000107	0.0000992
East Asian	0.000112	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000714	0.0000703
Middle Eastern	0.000112	0.000109
South Asian	0.0000654	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Interacts with SLP-76 to regulate NF-AT activation. Binds to tyrosine-phosphorylated shc.
• Pathway: T cell receptor signaling pathway - Homo sapiens (human);T-Cell antigen Receptor (TCR) pathway during Staphylococcus aureus infection;T-Cell antigen Receptor (TCR) Signaling Pathway;Signal Transduction;DAP12 signaling;DAP12 interactions;Generation of second messenger molecules;TCR signaling;CD28 co-stimulation;Costimulation by the CD28 family;FCERI mediated MAPK activation;FCERI mediated Ca+2 mobilization;Fc epsilon receptor (FCERI) signaling;TCR;Innate Immune System;Immune System;Adaptive Immune System;Signaling by SCF-KIT;Signaling by Receptor Tyrosine Kinases;TCR signaling in naïve CD8+ T cells;Signaling events mediated by Stem cell factor receptor (c-Kit);JNK signaling in the CD4+ TCR pathway;TCR signaling in naïve CD4+ T cells (Consensus)

Recessive Scores

• pRec: 0.375

Intolerance Scores

• loftool: 0.451
• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.27

Haploinsufficiency Scores

• pHI: 0.872
• hipred: Y
• hipred_score: 0.694
• ghis: 0.483

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.989

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Grap2
• Phenotype: hematopoietic system phenotype; immune system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: Ras protein signal transduction;cell-cell signaling;positive regulation of signal transduction;T cell costimulation;Fc-epsilon receptor signaling pathway;T cell receptor signaling pathway
• Cellular component: nucleus;cytoplasm;endosome;cytosol
• Molecular function: SH3/SH2 adaptor activity;protein binding