PRDM5
Chr 4ARPR/SET domain 5
Also known as: BCS2, PFM2
PRDM5 encodes a transcription factor that represses gene expression through recruitment of histone methyltransferases and deacetylases, and regulates expression of extracellular matrix proteins including fibrillar collagens. Mutations cause brittle cornea syndrome 2, an autosomal recessive connective tissue disorder characterized by fragile corneas and associated ocular abnormalities. The gene shows very low constraint against loss-of-function variants (pLI near zero), consistent with its recessive inheritance pattern.
Primary Disease Associations & Inheritance
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Typical tolerance to LoF variation
Mild missense constraint
This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.
Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
600 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 7 | 0 | 17 | 0 | 24 |
Likely Pathogenic | 13 | 2 | 4 | 0 | 19 |
VUS | 2 | 170 | 12 | 0 | 184 |
Likely Benign | 1 | 14 | 148 | 130 | 293 |
Benign | 0 | 0 | 46 | 0 | 46 |
Conflicting | — | 25 | |||
| Total | 23 | 186 | 227 | 130 | 591 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
PRDM5 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools