PPBP
Basic information
Region (hg38): 4:73985966-73988276
Previous symbols: [ "THBGB1" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (13 variants)
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. These statistics are base on transcript: NM_000002704.3. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 13 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 13 | 0 | 0 |
GnomAD
Source:
| 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:
- 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