KDM3B

Chr 5

lysine demethylase 3B

Also known as: 5qNCA, C5orf7, DIJOS, JMJD1B, NET22

NCBI Gene: 51780ENSG00000120733UniProt: Q7LBC6

Predicted to enable chromatin DNA binding activity; histone H3K9 demethylase activity; and transcription coregulator activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in nucleoplasm. Biomarker of acute lymphoblastic leukemia; breast cancer; colorectal cancer; and lung non-small cell carcinoma. [provided by Alliance of Genome Resources, Jul 2025]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtDiets-Jongmans syndrome

Clinical highlights

Gene-disease validity (ClinGen)
syndromic intellectual disability · ADDefinitivesufficient evidence for diagnostic panels
Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype) and the gene is intolerant of it in the population — truncating, frameshift and canonical splice variants carry more prior weight here than missense.Curated gene-level mechanism — a prior for triage, not a per-variant call.
1
Active trials
22
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.06
LOEUF· LoF intol.
LOF
Mechanism· G2P
📖
GeneReview available — KDM3B
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
Dual constrained — LoF & missense intolerant
LoF Constraint?
0.06LOEUF
pLI 1.000
Z-score 8.17
OE 0.01 (0.00–0.06)
Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint?
4.98Z-score
OE missense 0.55 (0.51–0.59)
524 obs / 957.6 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios?
LoF OE?0.01 (0.00–0.06)
0≤0.351.4
Missense OE?0.55 (0.51–0.59)
0≤0.61.4
Synonymous OE?0.98
0≤1.21.6
LoF obs/exp: 1 / 79.7Missense obs/exp: 524 / 957.6Syn Z: 0.24

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

KDM3B · 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