PRDM13

Chr 6

PR/SET domain 13

Also known as: CDIDHH, MU-MB-20.220, PCH17, PFM10

NCBI Gene: 59336ENSG00000112238UniProt: Q9H4Q3

Predicted to enable histone methyltransferase activity. Predicted to be involved in regulation of gene expression. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II and neurogenesis. Predicted to be active in nucleus. Implicated in pontocerebellar hypoplasia. [provided by Alliance of Genome Resources, Jul 2025]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtCerebellar dysfunction, impaired intellectual development, and hypogonadotropic hypogonadism
UniProtPontocerebellar hypoplasia 17

Clinical highlights

Interpreting a novel variant
This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Curated gene-level mechanism — a prior for triage, not a per-variant call.
0
Active trials
9
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.46
LOEUF
LOF
Mechanism· predicted
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GeneReview available — PRDM13
Authoritative clinical overview · Recommended first read
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Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint?
0.46LOEUF
pLI 0.563
Z-score 3.30
OE 0.20 (0.10–0.46)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?
0.42Z-score
OE missense 0.94 (0.86–1.02)
353 obs / 376.1 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.20 (0.10–0.46)
0≤0.351.4
Missense OE?0.94 (0.86–1.02)
0≤0.61.4
Synonymous OE?1.10
0≤1.21.6
LoF obs/exp: 4 / 19.9Missense obs/exp: 353 / 376.1Syn Z: -1.04

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

PRDM13 · protein map & ClinVar variants

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

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