JMJD4

protein-coding

jumonji domain containing 4, the group of JmjC hydroxylases

Gene summary

Enables peptidyl-lysine 4-dioxygenase activity. Involved in positive regulation of translational termination and protein hydroxylation. Located in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_023007.3

Inheritance

—

ClinVar variants

U:98B:6

Top phenotype

Congenital portosystemic shunt

gnomAD constraint

pLI —, LoF o/e 0.86

Max pathogenic AF

—

Genomic locus

chr1:227,730,425-227,735,411

External References & Databases

Ensembl (ENSG00000081692)

Transcript & Mutation Effects

hg38 • Region Span ~5.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to JMJD4 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 92

not providedTotal: 2

Congenital portosystemic shuntTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_023007.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar		1 clinvar	3
missense			92 clinvar	5 clinvar		97
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	98	5	1	104

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 44 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_023007.3	RefSeq	NP_075383.3	6	MANE Select
ENST00000620518.5	Ensembl	ENSP00000477669.1	6	MANE Select
NM_001161465.2	RefSeq	NP_001154937.2	6	Standard
ENST00000438896.3	Ensembl	ENSP00000387830.3	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000366758
Coding exons: 6
Length: 4987
Individuals with no LoFs: 125513
Homozygous LoFs: 0
Heterozygous LoFs: 218
Defined: 125731
p: 0.000867

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.841	307	268	1.14	0.0000152	2981
Missense (PolyPhen)		40	43.683	0.91568		537
Synonymous	-1.68	144	120	1.20	0.00000772	935
Loss of Function	0.556	15	17.5	0.857	7.61e-7	169

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00020	0.00018	rare
Latino/Admixed American	0.00092	0.00090	rare
Ashkenazi Jewish	0.00043	0.00040	rare
East Asian	0.00022	0.00022	rare
Finnish	0.00016	0.00014	rare
European (Non-Finnish)	0.0011	0.00097	notable
South Asian	0.0021	0.0020	notable
Other	0.00018	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.931
RVIS EVS: 0.04
RVIS percentile EVS: 57.15

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.447

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium