PDGFB

Chr 22AD

platelet derived growth factor subunit B

Also known as: IBGC5, PDGF-2, PDGF2, SIS, SSV, c-sis

NCBI Gene: 5155ENSG00000100311UniProt: P01127OMIM: 190040

The protein encodes platelet-derived growth factor subunit B, which regulates embryonic development, cell proliferation, and blood vessel development, particularly for recruiting pericytes and vascular smooth muscle cells in the central nervous system and other organs. Mutations cause autosomal dominant basal ganglia calcification (idiopathic basal ganglia calcification, type 5) and meningioma. The gene is highly constrained against loss-of-function variants, indicating that such variants are likely pathogenic when they occur.

GeneReviewsOMIMResearchSummary from RefSeq, OMIM, UniProt
MultiplemechanismADLOEUF 0.462 OMIM phenotypes
Clinical Summary— PDGFB
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Population Constraint (gnomAD)
Moderately constrained gene (pLI 0.77) — some intolerance to loss-of-function variants.
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ClinVar Variants
41 unique Pathogenic / Likely Pathogenic· 89 VUS of 230 total submissions
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Clinical Trials
3 active or recruiting trials — potential therapeutic options may be available
Explore recent and relevant literature in Research Assistant →
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GeneReview available — PDGFB
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint
0.46LOEUF
pLI 0.770
Z-score 2.92
OE 0.15 (0.06–0.46)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
1.08Z-score
OE missense 0.77 (0.66–0.89)
129 obs / 168.5 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.15 (0.06–0.46)
0≤0.351.4
Missense OE0.77 (0.66–0.89)
0≤0.61.4
Synonymous OE1.05
0≤1.21.6
LoF obs/exp: 2 / 13.6Missense obs/exp: 129 / 168.5Syn Z: -0.32
DN
0.5476th %ile
GOF
0.2099th %ile
LOF
0.60top 25%

This gene has evidence for multiple mechanisms of pathogenicity (loss-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to loss-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

LOF34% of P/LP variants are LoF · LOEUF 0.46
DN1 literature citation

Literature Evidence

DNThe c.456+1G>C mutation in PDGFB resulted in aberrant mRNA splicing, thereby forming mature transcripts containing an in-frame 21 base pair (bp) deletion, which might create a stably truncated protein [p.(Val146_Gln152del)] and exert a dominant negative effect on wild-type PDGFB.PMID:34025715

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

230 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic30
Likely Pathogenic11
VUS89
Likely Benign53
Benign37
Conflicting6
30
Pathogenic
11
Likely Pathogenic
89
VUS
53
Likely Benign
37
Benign
6
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
10
4
16
0
30
Likely Pathogenic
4
4
3
0
11
VUS
5
75
8
1
89
Likely Benign
0
9
23
21
53
Benign
0
1
33
3
37
Conflicting
—6
Total19938325226

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

PDGFB · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Integrated molecular pathology and therapeutic outcomes in dermatofibrosarcoma protuberans: Ki-67, COL1A1::PDGFB, and efficacy of Mohs surgery with postoperative imatinib in 153 Chinese patients.
Guo J et al.·BMC Cancer
2026Cohort
Atypical Gene Rearrangement of the COL1A1::PDGFB Fusion in Dermatofibrosarcoma Protuberans of the Abdominal Wall: A Case Report.
Bejbl J et al.·Clin Case Rep
2026Open AccessCase report
SPP1⁺ macrophage-FADS1⁺ tumor cell crosstalk via the PDGFB-PDGFRB axis drives liver metastasis in colorectal cancer.
Zhao P et al.·Transl Oncol
2026Open Access
A single-dose of PDGFB circular RNA enables sustained growth factor expression to accelerate diabetic wound healing.
Shen YQ et al.·J Nanobiotechnology
2026Open Access
Novel FGL2::PDGFD and TGFBI::PDGFB Fusions Expand the Molecular Spectrum of Dermatofibrosarcoma Protuberans.
Cloutier JM et al.·Genes Chromosomes Cancer
2026
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients