PPBP

pro-platelet basic protein, the group of Receptor ligands

Basic information

Region (hg38): 4:73985966-73988276

Previous symbols: [ "THBGB1" ]

Links

ENSG00000163736 ∙ NCBI:5473 ∙ OMIM:121010 ∙ HGNC:9240 ∙ Uniprot:P02775 ∙ 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 PPBP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPBP 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in PPBP

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

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

Position	Type	Phenotype	Significance	ClinVar
4-73987316-T-C		not specified	Uncertain significance (Dec 09, 2023)
4-73987334-C-T		not specified	Uncertain significance (Aug 17, 2022)
4-73987367-G-C		not specified	Uncertain significance (Dec 24, 2024)
4-73987599-T-C		not specified	Uncertain significance (Feb 13, 2025)
4-73987608-A-G		not specified	Uncertain significance (Mar 06, 2025)
4-73987617-G-A		not specified	Uncertain significance (Aug 28, 2023)
4-73987628-T-C		not specified	Uncertain significance (Sep 08, 2024)
4-73988024-G-A		not specified	Uncertain significance (Jul 10, 2024)
4-73988033-A-C		not specified	Uncertain significance (May 17, 2023)
4-73988060-C-T		not specified	Uncertain significance (Feb 13, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPBP	protein_coding	protein_coding	ENST00000296028	3	1160

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0577	0.727	125660	0	3	125663	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.01	91	67.7	1.34	0.00000336	827
Missense in Polyphen		27	19.188	1.4071		269
Synonymous	-0.357	30	27.6	1.09	0.00000146	258
Loss of Function	0.781	2	3.60	0.556	1.50e-7	52

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)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: LA-PF4 stimulates DNA synthesis, mitosis, glycolysis, intracellular cAMP accumulation, prostaglandin E2 secretion, and synthesis of hyaluronic acid and sulfated glycosaminoglycan. It also stimulates the formation and secretion of plasminogen activator by human synovial cells. NAP-2 is a ligand for CXCR1 and CXCR2, and NAP-2, NAP-2(73), NAP-2(74), NAP-2(1-66), and most potent NAP-2(1-63) are chemoattractants and activators for neutrophils. TC-1 and TC-2 are antibacterial proteins, in vitro released from activated platelet alpha-granules. CTAP-III(1-81) is more potent than CTAP-III desensitize chemokine-induced neutrophil activation. {ECO:0000269|PubMed:10877842, ECO:0000269|PubMed:7890771, ECO:0000269|PubMed:8950790, ECO:0000269|PubMed:9794434}.
• Pathway: Chemokine signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Chemokine signaling pathway;Signaling by GPCR;Neutrophil degranulation;Signal Transduction;Innate Immune System;Immune System;Chemokine receptors bind chemokines;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis;G alpha (i) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.386

Intolerance Scores

• loftool: 0.527
• rvis_EVS: -0.14
• rvis_percentile_EVS: 42.88

Haploinsufficiency Scores

• pHI: 0.348
• hipred: N
• hipred_score: 0.112
• ghis: 0.594

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.732

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppbp
• Phenotype: hematopoietic system phenotype; immune system phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: platelet degranulation;inflammatory response;immune response;G protein-coupled receptor signaling pathway;regulation of signaling receptor activity;neutrophil chemotaxis;leukocyte chemotaxis;defense response to bacterium;neutrophil degranulation;positive regulation of cell division;antimicrobial humoral immune response mediated by antimicrobial peptide;chemokine-mediated signaling pathway;cellular response to lipopolysaccharide;glucose transmembrane transport
• Cellular component: extracellular region;extracellular space;platelet alpha granule lumen;tertiary granule lumen
• Molecular function: glucose transmembrane transporter activity;protein binding;chemokine activity;growth factor activity