GP5

glycoprotein V platelet, the group of CD molecules

Basic information

Region (hg38): 3:194394821-194399266

Links

ENSG00000178732 ∙ NCBI:2814 ∙ OMIM:173511 ∙ HGNC:4443 ∙ Uniprot:P40197 ∙ 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 GP5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GP5 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						0
missense			45	1	1	47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	1	1

Variants in GP5

This is a list of pathogenic ClinVar variants found in the GP5 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-194396655-A-G		not specified	Uncertain significance (Jul 05, 2023)
3-194396719-A-T		not specified	Uncertain significance (Jul 05, 2023)
3-194396818-C-T		not specified	Uncertain significance (Aug 01, 2024)
3-194396832-G-T		not specified	Uncertain significance (Jan 07, 2025)
3-194396875-C-A		not specified	Uncertain significance (Nov 09, 2021)
3-194396883-C-G		not specified	Uncertain significance (Dec 21, 2024)
3-194396883-C-T		not specified	Uncertain significance (Mar 29, 2024)
3-194396887-G-A		not specified	Uncertain significance (Oct 24, 2024)
3-194396947-C-T		not specified	Uncertain significance (Oct 13, 2023)
3-194396973-C-T		not specified	Uncertain significance (Sep 22, 2023)
3-194397049-G-C		not specified	Uncertain significance (Feb 28, 2024)
3-194397083-C-A		not specified	Uncertain significance (May 24, 2024)
3-194397195-C-T		not specified	Uncertain significance (Feb 17, 2024)
3-194397199-G-T		not specified	Uncertain significance (Jan 18, 2025)
3-194397202-C-T		not specified	Uncertain significance (Sep 16, 2021)
3-194397217-C-A		not specified	Uncertain significance (Jun 12, 2023)
3-194397217-C-G		not specified	Uncertain significance (Apr 19, 2023)
3-194397219-G-C		not specified	Uncertain significance (Aug 28, 2023)
3-194397295-G-A		not specified	Uncertain significance (Jan 13, 2023)
3-194397306-C-G		not specified	Uncertain significance (Jan 26, 2023)
3-194397310-G-A			Benign (Mar 29, 2018)
3-194397333-C-A		not specified	Uncertain significance (Nov 09, 2021)
3-194397340-G-C		not specified	Likely benign (Jun 22, 2023)
3-194397351-C-T		not specified	Uncertain significance (Jan 16, 2025)
3-194397387-C-A		not specified	Uncertain significance (Feb 02, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GP5	protein_coding	protein_coding	ENST00000401815	1	4446

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000188	0.488	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.11	283	341	0.830	0.0000207	3540
Missense in Polyphen		67	81.123	0.8259		1040
Synonymous	0.833	156	170	0.919	0.0000110	1285
Loss of Function	0.344	6	6.98	0.859	3.54e-7	74

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The GPIb-V-IX complex functions as the vWF receptor and mediates vWF-dependent platelet adhesion to blood vessels. The adhesion of platelets to injured vascular surfaces in the arterial circulation is a critical initiating event in hemostasis.
• Pathway: Platelet activation - Homo sapiens (human);ECM-receptor interaction - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human);Platelet Aggregation Inhibitor Pathway, Pharmacodynamics;GP1b-IX-V activation signalling;Platelet Adhesion to exposed collagen;Platelet Aggregation (Plug Formation);Platelet activation, signaling and aggregation;Intrinsic Pathway of Fibrin Clot Formation;Hemostasis;Formation of Fibrin Clot (Clotting Cascade) (Consensus)

Recessive Scores

• pRec: 0.168

Intolerance Scores

• loftool: 0.560
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.92

Haploinsufficiency Scores

• pHI: 0.0968
• hipred: N
• hipred_score: 0.285

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.746

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gp5
• Phenotype: homeostasis/metabolism phenotype; normal phenotype

Gene ontology

• Biological process: cell adhesion;blood coagulation;blood coagulation, intrinsic pathway;platelet activation
• Cellular component: plasma membrane;integral component of plasma membrane;extracellular exosome
• Molecular function: protein binding