PDGFB

Chr 22AD

platelet derived growth factor subunit B

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

NCBI Gene: 5155ENSG00000100311UniProt: P01127

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]

Primary Disease Associations & Inheritance

Basal ganglia calcification, idiopathic, 5MIM #615483
AD
Meningioma, SIS-relatedMIM #607174
AD
224
ClinVar variants
40
Pathogenic / LP
0.77
pLI score
3
Active trials
Clinical Summary— PDGFB
⚡
Population Constraint (gnomAD)
Moderately constrained gene (pLI 0.77) — some intolerance to loss-of-function variants.
📋
ClinVar Variants
40 Pathogenic / Likely Pathogenic· 88 VUS of 224 total submissions
💊
Clinical Trials
3 active or recruiting trials — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
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?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
1.08Z-score
OE missense 0.77 (0.66–0.89)
129 obs / 168.5 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.15 (0.06–0.46)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.77 (0.66–0.89)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.05
0≤1.21.6
LoF obs/exp: 2 / 13.6Missense obs/exp: 129 / 168.5Syn Z: -0.32

ClinVar Variant Classifications

224 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic29
Likely Pathogenic11
VUS88
Likely Benign53
Benign37
Conflicting6
29
Pathogenic
11
Likely Pathogenic
88
VUS
53
Likely Benign
37
Benign
6
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
6
4
19
0
29
Likely Pathogenic
4
4
3
0
11
VUS
5
73
9
1
88
Likely Benign
0
9
23
21
53
Benign
0
1
33
3
37
Conflicting
—6
Total15918725224

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.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM

Basal ganglia calcification, idiopathic, 5

MIM #615483

Molecular basis of disorder known

Autosomal dominant

Meningioma, SIS-related

MIM #607174

Molecular basis of disorder known

Autosomal dominant
📖
GeneReview available — PDGFB
Authoritative clinical overview · NCBI Bookshelf · Recommended first read
Open GeneReview ↗
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Tubular cells produce FGF2 via autophagy after acute kidney injury leading to fibroblast activation and renal fibrosis.
Livingston MJ et al.·Autophagy
2023
Basal ganglia calcification: 'Fahr's disease'.
Magrinelli F et al.·Pract Neurol
2025Review
Basal ganglia calcifications (Fahr's syndrome): related conditions and clinical features.
Donzuso G et al.·Neurol Sci
2019Review
Endothelial GATA4 controls liver fibrosis and regeneration by preventing a pathogenic switch in angiocrine signaling.
Winkler M et al.·J Hepatol
2021
Cross-species single-cell analysis uncovers the immunopathological mechanisms associated with IgA nephropathy progression.
Chen X et al.·JCI Insight
2024Functional
Uterine sarcomas and rare uterine mesenchymal tumors with malignant potential. Diagnostic guidelines of the French Sarcoma Group and the Rare Gynecological Tumors Group.
Croce S et al.·Gynecol Oncol
2022Review
Ocular neovascularization.
Campochiaro PA·J Mol Med (Berl)
2013Review
The clinical and genetic spectrum of primary familial brain calcification.
Carecchio M et al.·J Neurol
2023
Umbilical Cord-Mesenchymal Stromal Cell-Derived Extracellular Vesicles Target the Liver to Improve Neurovascular Health in Type 2 Diabetes With Non-Alcoholic Fatty Liver Disease.
Du M et al.·J Extracell Vesicles
2025
The Genetics of Primary Familial Brain Calcification: A Literature Review.
Chen SY et al.·Int J Mol Sci
2023Review
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
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
2026🔓 Open 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
2026🔓 Open Access
A single-dose of PDGFB circular RNA enables sustained growth factor expression to accelerate diabetic wound healing.
Shen YQ et al.·J Nanobiotechnology
2026
Novel FGL2::PDGFD and TGFBI::PDGFB Fusions Expand the Molecular Spectrum of Dermatofibrosarcoma Protuberans.
Cloutier JM et al.·Genes Chromosomes Cancer
2026
Co-activation of the super-enhancer complex SOX2 and HDAC1 confers temozolomide resistance by promoting PDGFB transcription in glioblastoma.
Xie H et al.·Neuro Oncol
2026
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov
Prostate CancerProstate Inflammation

Characterization of Microbiological and Genetic Features in Prostate Cancer and Their Association with Disease Stage

ENROLLING BY INVITATION
NCT06505356Phase NAEdgaras BurzinskisStarted 2024-09-01
Prostate biopsy
Porphyria, Acute Intermittent

Clinical Research on Acute Intermittent Porphyria and the Use of Carbohydrate-Rich Diet as a Treatment

RECRUITING
NCT06273644Phase NANordlandssykehuset HFStarted 2024-01-27
Carbohydrates
DysferlinopathyMiyoshi MyopathyLGMDR2

Clinical, Immunological, Morphological and Genetic Characteristics of Patients With Dysferlinopathy (LGMD R2) in the RF

ENROLLING BY INVITATION
NCT04824040Artgen BiotechStarted 2020-01-15

External Resources

Links to major genomics databases and tools