PF4

platelet factor 4

Basic information

Region (hg38): 4:73980811-73982027

Links

ENSG00000163737

∙ NCBI:5196 ∙ OMIM:173460 ∙ HGNC:8861 ∙ Uniprot:P02776 ∙ 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 PF4 gene.

not_specified (13 variants)
not_provided (1 variants)

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. These statistics are base on transcript: NM_000002619.4. 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					1 clinvar	1
missense			13 clinvar			13
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	13	0	1

Loading clinvar variants...

GnomAD

Source: gnomAD

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: dbNSFP

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