KDM4D

Chr 11

lysine demethylase 4D

Also known as: JMJD2D

NCBI Gene: 55693 ENSG00000186280 UniProt: Q6B0I6 OMIM: 609766

Enables histone H3K9me2/H3K9me3 demethylase activity. Involved in inflammatory response. Acts upstream of or within several processes, including cellular response to ionizing radiation; double-strand break repair via homologous recombination; and positive regulation of double-strand break repair via nonhomologous end joining. Located in site of double-strand break. Biomarker of nephroblastoma. [provided by Alliance of Genome Resources, Jul 2025]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

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P/LP submissions

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P/LP missense

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LOEUF

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Mechanism

Some data sources returned errors (1)

gnomad: Error: gnomAD API error: 400

Population Genetics & Constraint

gnomAD

Constraint data not available from gnomAD.

Background carrier burden — how many people carry a rare variant somewhere in KDM4D?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 160

462 rare PASS variants

Rare truncating (LoF)

1 in 6,700

37 rare PASS variants

Rare synonymous (reference)

1 in 110

267 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for KDM4D. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 200	1 in 15,000
South Asian	~43k	1 in 100	≈ 1 in 43,000
Remaining (unassigned)	~30k	1 in 130	≈ 1 in 7,500
European (Finnish)	~27k	1 in 440	none seen
Admixed American	~22k	1 in 140	1 in 3,000
African / African American	~21k	1 in 130	1 in 3,200
East Asian	~20k	1 in 99	1 in 1,400
Ashkenazi Jewish	~13k	1 in 280	≈ 1 in 6,500
Middle Eastern	~2,884	1 in 130	none seen

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 1 coding exons well covered in gnomAD exomes and genomes.? see exons ↓