Seroatlas · Human Serome Atlas

PDGFB

Platelet-derived growth factor subunit B

Also known as: PDGFB_HUMAN, SIS, SSV

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: P01127
Gene: PDGFB
Ensembl: ENSG00000100311
Chromosome: 22
Canonical length: 241 aa
Protein class: Cancer-related genes, Candidate cardiovascular disease genes, Disease related genes, Human disease related genes, Plasma proteins, Predicted intracellular proteins, Predicted secreted proteins, RAS pathway related proteins
Subcellular location: Vesicles
Secretome location: Secreted to blood
Quaternary structure: Homodimer

OverviewNCBI Gene

This gene encodes a member of the protein family comprised of both platelet-derived growth factors (PDGF) and vascular endothelial growth factors (VEGF). The encoded preproprotein is proteolytically processed to generate platelet-derived growth factor subunit B, which can homodimerize, or alternatively, heterodimerize with the related platelet-derived growth factor subunit A. These proteins bind and activate PDGF receptor tyrosine kinases, which play a role in a wide range of developmental processes. Mutations in this gene are associated with meningioma. Reciprocal translocations between chromosomes 22 and 17, at sites where this gene and that for collagen type 1, alpha 1 are located, are associated with dermatofibrosarcoma protuberans, a rare skin tumor. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2015]

Canonical amino-acid sequenceUniProt

241 residues, UniProt reviewed canonical sequence.

>P01127|PDGFB
     1  MNRCWALFLS LCCYLRLVSA EGDPIPEELY EMLSDHSIRS FDDLQRLLHG DPGEEDGAEL
    61  DLNMTRSHSG GELESLARGR RSLGSLTIAE PAMIAECKTR TEVFEISRRL IDRTNANFLV
   121  WPPCVEVQRC SGCCNNRNVQ CRPTQVQLRP VQVRKIEIVR KKPIFKKATV TLEDHLACKC
   181  ETVAAARPVT RSPGGSQEQR AKTPQTRVTI RTVRVRRPPK GKHRKFKHTH DKTALKETLG
   241  A

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PDGFB can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Secreted
Secreted: Yes
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.55
Highest tissue expression: 38 nTPM

Expression across tissuesHPA

Tissue

placenta: 38 nTPM
adipose tissue: 30 nTPM
heart muscle: 30 nTPM
lung: 26 nTPM
breast: 22 nTPM
colon: 20 nTPM

Single-cell type

megakaryocytes: 136 nCPM
microglia: 120 nCPM
vascular endothelial cells: 89 nCPM
macrophages: 71 nCPM
platelets: 59 nCPM
salivary myoepithelial cells: 49 nCPM

Immune cell

MAIT T-cell: 10 nTPM
gdT-cell: 7.3 nTPM
memory CD8 T-cell: 5.6 nTPM
memory CD4 T-cell: 4.3 nTPM
naive CD4 T-cell: 3.6 nTPM
T-reg: 2.3 nTPM

Brain region

cerebral cortex: 53 nTPM
thalamus: 40 nTPM
amygdala: 37 nTPM
medulla oblongata: 35 nTPM
midbrain: 33 nTPM
pons: 31 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about PDGFB.

Disease | AllUniProt

Conditions PDGFB is implicated in, by any mechanism.

Basal ganglia calcification, idiopathic, 5 (IBGC5) MIM:615483

Disease | GeneticClinVar

25 pathogenic / likely-pathogenic of 210 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Basal ganglia calcification, idiopathic, 5
Meningioma
PDGFB-related disorder

ReferencesPubMed · IEDB

Publications for PDGFB from three distinct lines of evidence, kept separate because they answer different questions: whether antibodies are directed at the protein, whether a B-cell epitope has been mapped on it, and whether a T-cell epitope has. Each is labelled with its source.

Reference: AutoantibodyPubMed

1 publication

Vaccination with platelet-derived growth factor B kinoids inhibits CCl₄-induced hepatic fibrosis in mice.
2012 · J Pharmacol Exp Ther · RCR 0.5 · 16 citations

Sources: PubMed — antigen-level antibody evidence from a custom retrieval. Records matching a controlled set of autoantibody terms (the MeSH descriptors Autoantibodies and Autoantigens, with title and abstract term variants) were obtained through NCBI E-utilities, and their titles and abstracts parsed for constructions that direct an antibody at a named protein rather than for co-occurrence. Captured names were resolved against UniProt nomenclature and each antigen adjudicated individually against the source text. Bibliographic records from PubMed and MeSH, U.S. National Library of Medicine; citation metrics from NIH iCite (Hutchins et al., PLoS Biology 2016). Titles link to PubMed; abstracts are not reproduced here. The NLM does not endorse this analysis.

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 0.46
gnomAD pLI: 0.77
gnomAD missense Z: 1.08
DepMap mean gene effect: 0.16
DepMap dependency class: none

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 4% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of PDGFB in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads PDGFB as an antibody target. Whether an autoantibody or antibody against PDGFB could matter depends on whether native PDGFB is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PDGFB is annotated as secreted, so native PDGFB circulates and is directly accessible to antibodies. Secreted and cell-surface proteins are the autoantibody targets most likely to act like drugs, blocking or depleting the native protein.

Annotation status

The present source text does not explicitly label PDGFB as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Loading the interactive Seroatlas protein explorer...