PF4
platelet factor 4
Basic information
Region (hg38): 4:73980811-73982027
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PF4 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 | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 0 | 0 |
Variants in PF4
This is a list of pathogenic ClinVar variants found in the PF4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 4-73981224-T-C | not specified | Uncertain significance (Jun 19, 2024) | ||
| 4-73981419-C-G | Benign (Apr 06, 2018) | |||
| 4-73981435-C-A | not specified | Uncertain significance (Feb 23, 2023) | ||
| 4-73981445-C-T | not specified | Uncertain significance (Dec 13, 2023) | ||
| 4-73981460-C-G | not specified | Uncertain significance (Dec 18, 2023) | ||
| 4-73981468-G-T | not specified | Uncertain significance (Jun 06, 2023) | ||
| 4-73981500-C-A | not specified | Uncertain significance (Jan 31, 2024) | ||
| 4-73981902-C-T | not specified | Uncertain significance (Mar 01, 2023) | ||
| 4-73981916-C-T | not specified | Uncertain significance (Nov 22, 2022) | ||
| 4-73981935-A-G | not specified | Uncertain significance (Jun 01, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PF4 | protein_coding | protein_coding | ENST00000296029 | 3 | 1048 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0431 | 0.679 | 125530 | 0 | 16 | 125546 | 0.0000637 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.259 | 51 | 56.5 | 0.903 | 0.00000319 | 627 |
| Missense in Polyphen | 13 | 12.305 | 1.0565 | 154 | ||
| Synonymous | 0.177 | 27 | 28.2 | 0.958 | 0.00000174 | 217 |
| Loss of Function | 0.533 | 2 | 3.00 | 0.668 | 1.27e-7 | 36 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000913 | 0.0000907 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000106 | 0.000106 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Released during platelet aggregation. Neutralizes the anticoagulant effect of heparin because it binds more strongly to heparin than to the chondroitin-4-sulfate chains of the carrier molecule. Chemotactic for neutrophils and monocytes. Inhibits endothelial cell proliferation, the short form is a more potent inhibitor than the longer form. {ECO:0000269|PubMed:7644496}.;
- Pathway
- Chemokine signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Chemokine signaling pathway;RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function;Signaling by GPCR;Signal Transduction;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function;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;Cell surface interactions at the vascular wall;Hemostasis;Common Pathway of Fibrin Clot Formation;Formation of Fibrin Clot (Clotting Cascade);G alpha (i) signalling events;GPCR downstream signalling;Transcriptional regulation by RUNX1;CXCR3-mediated signaling events
(Consensus)
Recessive Scores
- pRec
- 0.313
Intolerance Scores
- loftool
- 0.628
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 52.85
Haploinsufficiency Scores
- pHI
- 0.0553
- hipred
- N
- hipred_score
- 0.284
- ghis
- 0.535
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.257
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pf4
- Phenotype
- hematopoietic system phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- platelet degranulation;inflammatory response;immune response;G protein-coupled receptor signaling pathway;adenylate cyclase-activating G protein-coupled receptor signaling pathway;regulation of signaling receptor activity;positive regulation of gene expression;positive regulation of macrophage derived foam cell differentiation;negative regulation of angiogenesis;cytokine-mediated signaling pathway;platelet activation;neutrophil chemotaxis;leukocyte chemotaxis;positive regulation of tumor necrosis factor production;regulation of cell population proliferation;defense response to protozoan;positive regulation of cAMP-mediated signaling;negative regulation of MHC class II biosynthetic process;positive regulation of macrophage differentiation;regulation of megakaryocyte differentiation;negative regulation of megakaryocyte differentiation;negative regulation of cytolysis;positive regulation of transcription by RNA polymerase II;killing by host of symbiont cells;antimicrobial humoral immune response mediated by antimicrobial peptide;chemokine-mediated signaling pathway;cellular response to lipopolysaccharide;negative regulation of extrinsic apoptotic signaling pathway in absence of ligand
- Cellular component
- extracellular region;extracellular space;cytoplasm;symbiont-containing vacuole membrane;platelet alpha granule lumen;collagen-containing extracellular matrix;other organism cytoplasm
- Molecular function
- protein binding;chemokine activity;heparin binding;CXCR3 chemokine receptor binding