PRDM16

Chr 1

PR/SET domain 16

Also known as: CMD1LL, KMT8F, LVNC8, MEL1, PFM13

NCBI Gene: 63976ENSG00000142611UniProt: Q9HAZ2

The reciprocal translocation t(1;3)(p36;q21) occurs in a subset of myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). This gene is located near the 1p36.3 breakpoint and has been shown to be specifically expressed in the t(1:3)(p36,q21)-positive MDS/AML. The protein encoded by this gene is a zinc finger transcription factor and contains an N-terminal PR domain. The translocation results in the overexpression of a truncated version of this protein that lacks the PR domain, which may play an important role in the pathogenesis of MDS and AML. Alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtLeft ventricular non-compaction 8
UniProtCardiomyopathy, dilated, 1LL

Clinical highlights

Gene-disease validity (ClinGen)
dilated cardiomyopathy · ADStrongappropriate for clinical testing
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.
1
Active trials
161
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.19
LOEUF· LoF intol.
LOF
Mechanism· predicted
📖
GeneReview available — PRDM16
Authoritative clinical overview · Recommended first read
Open GeneReview ↗
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint?
0.19LOEUF
pLI 1.000
Z-score 5.95
OE 0.08 (0.04–0.19)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?
1.35Z-score
OE missense 0.87 (0.82–0.93)
745 obs / 855.9 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.08 (0.04–0.19)
0≤0.351.4
Missense OE?0.87 (0.82–0.93)
0≤0.61.4
Synonymous OE?1.10
0≤1.21.6
LoF obs/exp: 4 / 48.9Missense obs/exp: 745 / 855.9Syn Z: -1.64

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

PRDM16 · 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

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