GeneBe

PDGFB

protein-coding

platelet derived growth factor subunit B

Gene summary

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]

Previous symbols:
  • SIS

MANE transcript

NM_002608.4

Inheritance

AD

ClinVar variants

P:26U:83B:48

Top phenotype

Basal ganglia calcification, idiopathic, 5

gnomAD constraint

pLI —, LoF o/e 0.15

Max pathogenic AF

—

Genomic locus

chr22:39,223,359-39,244,982

External References & Databases

Ensembl (ENSG00000100311)NCBI Gene (5155)OMIM (190040)HGNC:8800GenCCUniProt (P01127)AlphaFoldClinVar (PDGFB)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~21.6 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

basal ganglia calcification, idiopathic, 5STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014204

Submitter: PanelApp Australia

basal ganglia calcification, idiopathic, 5STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014204

Submitter: Genomics England PanelApp

bilateral striopallidodentate calcinosisSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0008947

Submitter: Orphanet

basal ganglia calcification, idiopathic, 5MODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0014204

Submitter: Ambry Genetics

basal ganglia calcification, idiopathic, 5STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014204

Submitter: Labcorp Genetics (formerly Invitae)

familial meningiomaLIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0011789

Submitter: Labcorp Genetics (formerly Invitae)

familial meningiomaLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0011789

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Basal ganglia calcification, idiopathic, 5AD

Manifestation: Neurologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 23913003Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PDGFB variants in ClinVar

10 Conditions Cataloged
not providedTotal: 144
Inborn genetic diseasesTotal: 38
not specifiedTotal: 34
PDGFB-related disorderTotal: 15
Basal ganglia calcification, idiopathic, 5Total: 13
Familial meningiomaTotal: 3
Dermatofibrosarcoma protuberansTotal: 2
Idiopathic basal ganglia calcification 1Total: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002608.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
30
clinvar
3
clinvar
 34
missense
2
clinvar
4
clinvar
79
clinvar
15
clinvar
 100
nonsense
4
clinvar
3
clinvar
1
clinvar
 8
start loss
2
clinvar
1
clinvar
 3
frameshift
3
clinvar
2
clinvar
1
clinvar
 6
splice donor/acceptor (+/-2bp)
2
clinvar
3
clinvar
1
clinvar
 6
Total131383453157

Highest pathogenic variant AF is 0.000036557634

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_002608.4RefSeqNP_002599.16MANE Select
ENST00000331163.11EnsemblENSP00000330382.66MANE Select
NM_033016.3RefSeqNP_148937.16Standard
ENST00000381551.8EnsemblENSP00000370963.46Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • PI3K-Akt signaling pathway - Homo sapiens (human)
  • Focal adhesion - Homo sapiens (human)
  • Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human)
  • Renal cell carcinoma - Homo sapiens (human)
  • Choline metabolism in cancer - Homo sapiens (human)

Biological Process

  • MAPK cascade
  • embryonic placenta development
  • positive regulation of endothelial cell proliferation
  • monocyte chemotaxis
  • platelet degranulation

Molecular Function

  • Ras guanyl-nucleotide exchange factor activity
  • platelet-derived growth factor receptor binding
  • protein binding
  • collagen binding
  • growth factor activity

Cellular Component

  • Golgi membrane
  • extracellular region
  • extracellular space
  • cytoplasm
  • endoplasmic reticulum lumen

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000331163
Coding exons
6
Length
21393
Individuals with no LoFs
125730
Homozygous LoFs
0
Heterozygous LoFs
6
Defined
125736
p
0.0000239
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.081291680.7660.00001181529
Missense (PolyPhen)4268.5660.61255601
Synonymous-0.3197470.61.050.00000485501
Loss of Function2.92213.60.1478.36e-7134

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish0.0000990.000099rare
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.0000440.000044rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Growth factor that plays an essential role in the regulation of embryonic development, cell proliferation, cell migration, survival and chemotaxis. Potent mitogen for cells of mesenchymal origin (PubMed:26599395). Required for normal proliferation and recruitment of pericytes and vascular smooth muscle cells in the central nervous system, skin, lung, heart and placenta. Required for normal blood vessel development, and for normal development of kidney glomeruli. Plays an important role in wound healing. Signaling is modulated by the formation of heterodimers with PDGFA (By similarity). {ECO:0000250|UniProtKB:P31240, ECO:0000269|PubMed:26599395}.;
Disease
DISEASE: Note=A chromosomal aberration involving PDGFB is found in dermatofibrosarcoma protuberans. Translocation t(17;22)(q22;q13) with PDGFB. {ECO:0000269|PubMed:12660034}.;

Recessive Scores

pRec
0.914

Intolerance Scores

LoFtool
0.292
RVIS EVS
0
RVIS percentile EVS
53.73

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.751

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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