GRAP

GRB2 related adaptor protein, the group of SH2 domain containing

Basic information

Region (hg38): 17:19020656-19047011

Links

ENSG00000154016 ∙ NCBI:10750 ∙ OMIM:604330 ∙ HGNC:4562 ∙ Uniprot:Q13588 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hearing loss, autosomal recessive 114 (Limited), mode of inheritance: AR
• hearing loss, autosomal recessive (Supportive), mode of inheritance: AR
• hearing loss, autosomal recessive 114 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, autosomal recessive, 114	AR	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic	30610177

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GRAP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GRAP 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		1	10			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	10	1	0

Variants in GRAP

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

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

Position	Type	Phenotype	Significance	ClinVar
17-19022010-G-A		GRAP-related disorder	Likely benign (Jun 28, 2019)
17-19022018-G-T		GRAP-related disorder	Likely benign (Jun 12, 2020)
17-19022023-C-T		not specified	Uncertain significance (Mar 28, 2023)
17-19022024-G-A		not specified	Uncertain significance (Aug 21, 2024)
17-19022044-C-T		not specified	Uncertain significance (Jul 06, 2024)
17-19022067-G-A		GRAP-related disorder	Likely benign (Feb 24, 2020)
17-19022080-C-G		not specified	Uncertain significance (Oct 06, 2021)
17-19022134-G-A		not specified	Uncertain significance (Sep 27, 2021)
17-19024238-G-T		not specified	Uncertain significance (May 01, 2024)
17-19024277-G-A		not specified	Uncertain significance (Apr 20, 2024)
17-19024339-G-A		not specified	Uncertain significance (Sep 26, 2023)
17-19024348-C-A		not specified	Uncertain significance (Nov 11, 2024)
17-19024357-T-C		not specified	Uncertain significance (Jun 26, 2024)
17-19024372-T-A		Hearing loss, autosomal recessive 114	Likely pathogenic (Jul 28, 2019)
17-19041812-G-A			Likely benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GRAP	protein_coding	protein_coding	ENST00000284154	5	26965

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.111	0.787	124531	0	2	124533	0.00000803

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.14	49	77.1	0.635	0.00000524	1392
Missense in Polyphen		9	25.686	0.35038		533
Synonymous	0.504	30	33.7	0.890	0.00000237	410
Loss of Function	1.28	2	5.13	0.390	2.17e-7	120

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000545
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000546	0.0000545
South Asian	0.00	0.00
Other	0.000165	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Couples signals from receptor and cytoplasmic tyrosine kinases to the Ras signaling pathway.
• Pathway: EGF-Core;IGF-Ncore;IGF-Core;Signal Transduction;TCR;KitReceptor;Signaling by SCF-KIT;Signaling by Receptor Tyrosine Kinases (Consensus)

Recessive Scores

• pRec: 0.147

Haploinsufficiency Scores

• pHI: 0.528
• hipred: N
• hipred_score: 0.471
• ghis: 0.674

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.914

Gene Damage Prediction

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

Mouse Genome Informatics

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

Gene ontology

• Biological process: Ras protein signal transduction;cell-cell signaling;positive regulation of signal transduction
• Cellular component: cytoplasm;cytosol
• Molecular function: SH3/SH2 adaptor activity;protein binding