GeneBe

GP1BA

glycoprotein Ib platelet subunit alpha, the group of CD molecules

Basic information

Region (hg38): 17:4932277-4935023

Previous symbols: [ "GP1B" ]

Links

ENSG00000185245 ∙ NCBI:2811 ∙ OMIM:606672 ∙ HGNC:4439 ∙ Uniprot:P07359 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • Bernard-Soulier syndrome (Definitive), mode of inheritance: Semidominant
  • Bernard-Soulier syndrome (Supportive), mode of inheritance: AD
  • platelet-type von Willebrand disease (Supportive), mode of inheritance: AD
  • autosomal dominant macrothrombocytopenia (Supportive), mode of inheritance: AD
  • Bernard-Soulier syndrome, type A2, autosomal dominant (Strong), mode of inheritance: AD
  • platelet-type von Willebrand disease (Strong), mode of inheritance: AD
  • Bernard-Soulier syndrome (Strong), mode of inheritance: AR
  • Bernard-Soulier syndrome (Definitive), mode of inheritance: AR
  • platelet-type von Willebrand disease (Definitive), mode of inheritance: AD
  • Bernard-Soulier syndrome (Definitive), mode of inheritance: AR
  • platelet-type von Willebrand disease (Moderate), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Bernard-Soulier syndrome, type A2; Bernard-Soulier syndrome, type A1; von Willebrand disease, platelet-typeAD/ARHematologic; PharmacogenomicPreventive 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 avoidedHematologic18116504; 14081293; 6019024; 6286015; 6798442; 6333901; 2308962; 2052556; 1901273; 1730088; 8384898; 9616133; 11222377; 14711733; 21173099; 22102188; 23014764

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GP1BA gene.

  • Inborn_genetic_diseases (74 variants)
  • not_provided (67 variants)
  • Bernard_Soulier_syndrome (64 variants)
  • not_specified (54 variants)
  • GP1BA-related_disorder (48 variants)
  • Bernard-Soulier_syndrome,_type_A2,_autosomal_dominant (48 variants)
  • Pseudo_von_Willebrand_disease (34 variants)
  • Nonarteritic_anterior_ischemic_optic_neuropathy,_susceptibility_to (24 variants)
  • Thrombocytopenia (10 variants)
  • Macrothrombocytopenia (7 variants)
  • Bernard-Soulier_syndrome,_type_A1 (5 variants)
  • Abnormal_bleeding (4 variants)
  • PLATELET_GLYCOPROTEIN_Ib_POLYMORPHISM (1 variants)
  • Impaired_ristocetin-induced_platelet_aggregation (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GP1BA gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000173.7. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
38
clinvar
 39
missense
8
clinvar
18
clinvar
131
clinvar
13
clinvar
4
clinvar
 174
nonsense
5
clinvar
9
clinvar
2
clinvar
 16
start loss
0
frameshift
7
clinvar
25
clinvar
4
clinvar
1
clinvar
 37
splice donor/acceptor (+/-2bp)
0
Total 20 52 138 52 4

Highest pathogenic variant AF is 0.00011030487

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
GP1BAprotein_codingprotein_codingENST00000329125 12734
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.003230.62012450501481246530.000594
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.3033683521.050.00002084149
Missense in Polyphen6873.8150.92122941
Synonymous-0.8111781651.080.00001051501
Loss of Function0.46345.130.7792.67e-755

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004010.000400
Ashkenazi Jewish0.000.00
East Asian0.0005030.000445
Finnish0.0007900.000789
European (Non-Finnish)0.001050.000974
Middle Eastern0.0005030.000445
South Asian0.00009970.0000980
Other0.0006870.000495

dbNSFP

Source: dbNSFP

Function
FUNCTION: GP-Ib, a surface membrane protein of platelets, participates in the formation of platelet plugs by binding to the A1 domain of vWF, which is already bound to the subendothelium.;
Disease
DISEASE: Non-arteritic anterior ischemic optic neuropathy (NAION) [MIM:258660]: An ocular disease due to ischemic injury to the optic nerve. It usually affects the optic disk and leads to visual loss and optic disk swelling of a pallid nature. Visual loss is usually sudden, or over a few days at most and is usually permanent, with some recovery possibly occurring within the first weeks or months. Patients with small disks having smaller or non- existent cups have an anatomical predisposition for non-arteritic anterior ischemic optic neuropathy. As an ischemic episode evolves, the swelling compromises circulation, with a spiral of ischemia resulting in further neuronal damage. {ECO:0000269|PubMed:14711733}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; 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:10089893, ECO:0000269|PubMed:1730088, ECO:0000269|PubMed:7690774, ECO:0000269|PubMed:7819107, ECO:0000269|PubMed:7873390, ECO:0000269|PubMed:9639514}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Bernard-Soulier syndrome A2, autosomal dominant (BSSA2) [MIM:153670]: A coagulation disorder characterized by mild to moderate bleeding tendency, thrombocytopenia, and an increased mean platelet volume. Some individuals have no symptoms. Mild bleeding tendencies manifest as epistaxis, gingival bleeding, menorrhagia, easy bruising, or prolonged bleeding after dental surgery. {ECO:0000269|PubMed:11222377}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Pseudo-von Willebrand disease (VWDP) [MIM:177820]: A bleeding disorder characterized by abnormally enhanced binding of von Willebrand factor by the platelet glycoprotein Ib (GP Ib) receptor complex. Hemostatic function is impaired due to the removal of VWF multimers from the circulation. {ECO:0000269|PubMed:14521605, ECO:0000269|PubMed:2052556, ECO:0000269|PubMed:8384898, ECO:0000269|PubMed:8486780}. 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);RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function;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);Transcriptional regulation by RUNX1;Beta2 integrin cell surface interactions (Consensus)

Recessive Scores

pRec
0.550

Intolerance Scores

loftool
0.630
rvis_EVS
0.14
rvis_percentile_EVS
63.62

Haploinsufficiency Scores

pHI
0.109
hipred
N
hipred_score
0.327
ghis
0.412

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.883

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Gp1ba
Phenotype
hematopoietic system phenotype; homeostasis/metabolism phenotype; cellular phenotype;

Gene ontology

Biological process
cell morphogenesis;cell adhesion;cell surface receptor signaling pathway;blood coagulation;blood coagulation, intrinsic pathway;platelet activation;regulation of blood coagulation;fibrinolysis;regulation of megakaryocyte differentiation;thrombin-activated receptor signaling pathway;platelet aggregation
Cellular component
extracellular space;plasma membrane;integral component of plasma membrane;cell surface;membrane;extracellular matrix;anchored component of external side of plasma membrane;extracellular exosome
Molecular function
protein binding;thrombin-activated receptor activity