GP9

glycoprotein IX platelet, the group of CD molecules

Basic information

Region (hg38): 3:129060779-129062406

Links

ENSG00000169704 ∙ NCBI:2815 ∙ OMIM:173515 ∙ HGNC:4444 ∙ Uniprot:P14770 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Bernard-Soulier syndrome (Strong), mode of inheritance: AR
• Bernard-Soulier syndrome (Supportive), mode of inheritance: AD
• Bernard-Soulier syndrome (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Bernard-Soulier syndrome, type C	AR	Hematologic	Preventive measures (eg, in the case of surgery) and treatment of bleeding episodes can be beneficial; Specific medications (eg, certain anesthetics) that interfere with platelet function should be avoided	Hematologic	18116504; 14081293; 6019024; 1901273; 8481514; 9616133; 16268478; 17109744; 21173099; 21699652

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GP9 gene.

• Bernard Soulier syndrome (5 variants)
• not provided (4 variants)
• Bernard-Soulier syndrome type C (2 variants)
• Macrothrombocytopenia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GP9 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	52	2	55
missense	2	2	22	1	1	28
nonsense		1				1
start loss	1					1
frameshift	2					2
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region	1			1		2
non coding			7	2	1	10
Total	5	3	31	55	4

Highest pathogenic variant AF is 0.00000657

Variants in GP9

This is a list of pathogenic ClinVar variants found in the GP9 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-129061491-C-G		Bernard Soulier syndrome	Likely benign (Jan 12, 2018)
3-129061504-C-T		Bernard Soulier syndrome	Likely benign (Jan 12, 2018)
3-129061508-C-T		Bernard Soulier syndrome	Uncertain significance (Feb 02, 2018)
3-129061545-T-C		Bernard Soulier syndrome	Benign (Jan 12, 2018)
3-129061554-C-A		Bernard Soulier syndrome	Uncertain significance (Jan 12, 2018)
3-129061593-G-A		Bernard Soulier syndrome	Uncertain significance (Jan 13, 2018)
3-129061602-T-C		Bernard Soulier syndrome	Uncertain significance (Jan 13, 2018)
3-129061616-G-T		Bernard Soulier syndrome	Uncertain significance (Jan 13, 2018)
3-129061621-T-C		Bernard Soulier syndrome	Uncertain significance (Mar 05, 2018)
3-129061741-T-C			Pathogenic (Dec 18, 2021)
3-129061740-A-ATGCC		Bernard Soulier syndrome	Pathogenic (Jun 05, 2023)
3-129061757-C-T		Bernard Soulier syndrome	Conflicting classifications of pathogenicity (Oct 30, 2023)
3-129061759-T-C		Bernard-Soulier syndrome type C	Uncertain significance (Nov 19, 2023)
3-129061769-C-G			Likely benign (May 20, 2020)
3-129061783-A-AG		Bernard Soulier syndrome	Pathogenic (Sep 19, 2024)
3-129061808-A-G			Likely benign (Dec 12, 2023)
3-129061809-T-C		Bernard-Soulier syndrome type C • Bernard Soulier syndrome	Pathogenic (Apr 09, 2023)
3-129061814-C-T			Likely benign (Oct 01, 2020)
3-129061817-C-T			Likely benign (Nov 25, 2022)
3-129061819-G-A			Likely benign (Jan 22, 2024)
3-129061826-G-A			Likely benign (Aug 19, 2023)
3-129061832-C-T			Likely benign (Nov 24, 2023)
3-129061838-G-A			Likely benign (Jan 30, 2024)
3-129061838-G-T			Likely benign (May 08, 2023)
3-129061841-G-A			Likely benign (Nov 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GP9	protein_coding	protein_coding	ENST00000307395	1	1640

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.476	0.446	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.163	109	114	0.957	0.00000776	1080
Missense in Polyphen		27	31.977	0.84436		369
Synonymous	-0.465	63	58.5	1.08	0.00000419	414
Loss of Function	1.22	0	1.72	0.00	7.44e-8	16

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. GP-IX may provide for membrane insertion and orientation of GP-Ib.
• Disease: DISEASE: Bernard-Soulier syndrome (BSS) [MIM:231200]: A coagulation disorder characterized by a prolonged bleeding time, unusually large platelets, thrombocytopenia, and impaired prothrombin consumption. {ECO:0000269|PubMed:10583255, ECO:0000269|PubMed:11167791, ECO:0000269|PubMed:11758225, ECO:0000269|PubMed:12100158, ECO:0000269|PubMed:8481514, ECO:0000269|PubMed:9163595, ECO:0000269|PubMed:9886312}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Platelet activation - Homo sapiens (human);ECM-receptor interaction - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human);Platelet Aggregation Inhibitor Pathway, Pharmacodynamics;Hematopoietic Stem Cell Differentiation;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: 0.227

Haploinsufficiency Scores

• pHI: 0.236
• hipred: N
• hipred_score: 0.146
• ghis: 0.599

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0845

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gp9
• Phenotype: hematopoietic system phenotype

Gene ontology

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