JMJD4

gene
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Also known as FLJ12517

Summary

JMJD4 (jumonji domain containing 4, HGNC:25724) is a protein-coding gene on chromosome 1q42.13, encoding 2-oxoglutarate and iron-dependent oxygenase JMJD4 (Q9H9V9). Catalyzes the 2-oxoglutarate and iron-dependent C4-lysyl hydroxylation of ETF1 at ‘Lys-63’ thereby promoting the translational termination efficiency of ETF1.

Enables peptidyl-lysine 4-dioxygenase activity. Involved in positive regulation of translational termination and protein hydroxylation. Located in cytoplasm.

Source: NCBI Gene 65094 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 123 total
  • MANE Select transcript: NM_023007

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25724
Approved symbolJMJD4
Namejumonji domain containing 4
Location1q42.13
Locus typegene with protein product
StatusApproved
AliasesFLJ12517
Ensembl geneENSG00000081692
Ensembl biotypeprotein_coding
OMIM620928
Entrez65094

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 16 protein_coding, 3 retained_intron

ENST00000438896, ENST00000465251, ENST00000480590, ENST00000485807, ENST00000620518, ENST00000857554, ENST00000857555, ENST00000857556, ENST00000857557, ENST00000857558, ENST00000857559, ENST00000857560, ENST00000857561, ENST00000857562, ENST00000857563, ENST00000972390, ENST00000972391, ENST00000972392, ENST00000972393

RefSeq mRNA: 2 — MANE Select: NM_023007 NM_001161465, NM_023007

CCDS: CCDS1561, CCDS59203

Canonical transcript exons

ENST00000620518 — 6 exons

ExonStartEnd
ENSE00000656184227733414227733681
ENSE00000656185227732881227733027
ENSE00003470380227734651227734816
ENSE00003616824227733907227734032
ENSE00003715063227735012227735302
ENSE00003745451227731191227732676

Expression profiles

Bgee: expression breadth ubiquitous, 178 present calls, max score 87.64.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.8276 / max 189.4281, expressed in 1802 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1780018.82761802

Top tissues by expression

274 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
left adrenal gland cortexUBERON:003582587.64gold quality
left adrenal glandUBERON:000123487.10gold quality
right adrenal glandUBERON:000123386.46gold quality
right adrenal gland cortexUBERON:003582786.25gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099185.32gold quality
adrenal cortexUBERON:000123585.15gold quality
adrenal glandUBERON:000236984.57gold quality
apex of heartUBERON:000209884.34gold quality
left ovaryUBERON:000211984.34gold quality
right ovaryUBERON:000211884.08gold quality
adenohypophysisUBERON:000219684.03gold quality
right lobe of liverUBERON:000111483.62gold quality
left testisUBERON:000453383.61gold quality
right testisUBERON:000453483.15gold quality
left uterine tubeUBERON:000130382.80gold quality
gastrocnemiusUBERON:000138882.21gold quality
mucosa of transverse colonUBERON:000499181.59gold quality
stromal cell of endometriumCL:000225581.57gold quality
pituitary glandUBERON:000000781.54gold quality
muscle of legUBERON:000138381.44gold quality
prefrontal cortexUBERON:000045181.42gold quality
right frontal lobeUBERON:000281081.26gold quality
body of uterusUBERON:000985381.22gold quality
right atrium auricular regionUBERON:000663181.11gold quality
anterior cingulate cortexUBERON:000983580.99gold quality
testisUBERON:000047380.91gold quality
cingulate cortexUBERON:000302780.88gold quality
body of stomachUBERON:000116180.51gold quality
body of pancreasUBERON:000115080.45gold quality
granulocyteCL:000009480.44gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes3.99

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

40 targeting JMJD4, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3689D100.0066.141181
HSA-MIR-6851-5P100.0065.631294
HSA-MIR-4650-5P99.9864.69999
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-449299.8768.253611
HSA-MIR-442099.8270.081624
HSA-MIR-181B-2-3P99.8170.061646
HSA-MIR-181B-3P99.8170.061646
HSA-MIR-76299.5866.611994
HSA-MIR-892A99.5468.161141
HSA-MIR-449899.4767.422360
HSA-MIR-431899.3866.941505
HSA-MIR-1912-3P99.3267.40936
HSA-MIR-6808-5P99.3166.232150
HSA-MIR-6893-5P99.3166.252119
HSA-MIR-450599.2767.812678
HSA-MIR-317699.2564.35954
HSA-MIR-3922-3P99.2564.961136
HSA-MIR-642A-3P99.2367.671258
HSA-MIR-642B-3P99.2367.671258
HSA-MIR-429199.2068.882969
HSA-MIR-465199.0667.572002
HSA-MIR-5001-5P99.0566.761972
HSA-MIR-92299.0267.231838
HSA-MIR-3619-5P99.0068.872308
HSA-MIR-214-3P98.7168.122128
HSA-MIR-76198.7168.072051
HSA-MIR-471098.6165.961048
HSA-MIR-7114-5P98.5167.871349
HSA-MIR-3130-5P98.1466.00711

Literature-anchored findings (GeneRIF, showing 2)

  • It observed significant positivity of JMJD4 between 59 paired samples from colon adenocarcinoma (CA) tissue and adjacent normal tissue. JMJD4 protein expression in CA differed significantly according to the histological grade and M-class (distant metastasis). (PMID:30029884)
  • Jmjd4 Facilitates Pkm2 Degradation in Cardiomyocytes and Is Protective Against Dilated Cardiomyopathy. (PMID:37066795)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriojmjd4ENSDARG00000058995
mus_musculusJmjd4ENSMUSG00000036819
rattus_norvegicusJmjd4ENSRNOG00000022438
drosophila_melanogasterJMJD4FBGN0032671
caenorhabditis_elegansWBGENE00011563

Paralogs (2): JMJD6 (ENSG00000070495), JMJD8 (ENSG00000161999)

Protein

Protein identifiers

2-oxoglutarate and iron-dependent oxygenase JMJD4Q9H9V9 (reviewed: Q9H9V9)

Alternative names: JmjC domain-containing protein 4, Jumonji domain-containing protein 4, Lysyl-hydroxylase JMJD4

All UniProt accessions (1): Q9H9V9

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the 2-oxoglutarate and iron-dependent C4-lysyl hydroxylation of ETF1 at ‘Lys-63’ thereby promoting the translational termination efficiency of ETF1.

Subunit / interactions. Interacts with ETF1. Interacts with the ETF1-GSPT1 complex.

Subcellular location. Cytoplasm.

Similarity. Belongs to the JMJD6 family.

Isoforms (3)

UniProt IDNamesCanonical?
Q9H9V9-33yes
Q9H9V9-11
Q9H9V9-22

RefSeq proteins (2): NP_001154937, NP_075383* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003347JmjC_domDomain
IPR050910JMJD6_ArgDemeth/LysHydroxFamily

Pfam: PF02373

Catalyzed reactions (Rhea), 1 shown:

  • L-lysyl-[protein] + 2-oxoglutarate + O2 = 4-hydroxy-L-lysyl-[protein] + succinate + CO2 (RHEA:57156)

UniProt features (13 total): sequence variant 3, binding site 3, sequence conflict 2, splice variant 2, chain 1, domain 1, mutagenesis site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H9V9-F194.040.89

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (3): 189; 191; 269

Mutagenesis-validated functional residues (1):

PositionPhenotype
189loss of interaction with etf1 and its ability to hydroxylate etf1.

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-9629569Protein hydroxylation
R-HSA-163841Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation
R-HSA-392499Metabolism of proteins
R-HSA-597592Post-translational protein modification

MSigDB gene sets: 123 (showing top): GOMF_OXIDOREDUCTASE_ACTIVITY_ACTING_ON_PAIRED_DONORS_WITH_INCORPORATION_OR_REDUCTION_OF_MOLECULAR_OXYGEN, GOBP_POSITIVE_REGULATION_OF_PROTEIN_CONTAINING_COMPLEX_DISASSEMBLY, GOBP_TRANSLATIONAL_TERMINATION, PATIL_LIVER_CANCER, GOBP_TRANSLATION, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, GOBP_PEPTIDYL_LYSINE_MODIFICATION, DODD_NASOPHARYNGEAL_CARCINOMA_UP, MODULE_397, GOBP_REGULATION_OF_PROTEIN_CONTAINING_COMPLEX_DISASSEMBLY, GOBP_PROTEIN_HYDROXYLATION, GOBP_POSITIVE_REGULATION_OF_TRANSLATION, NUYTTEN_EZH2_TARGETS_DN, GOBP_REGULATION_OF_TRANSLATION, GOBP_POSITIVE_REGULATION_OF_PROTEIN_METABOLIC_PROCESS

GO Biological Process (3): protein hydroxylation (GO:0018126), positive regulation of translational termination (GO:0045905), regulation of gene expression (GO:0010468)

GO Molecular Function (8): 2-oxoglutarate-dependent dioxygenase activity (GO:0016706), sequence-specific DNA binding (GO:0043565), metal ion binding (GO:0046872), peptidyl-lysine 4-dioxygenase activity (GO:0106156), protein binding (GO:0005515), oxidoreductase activity (GO:0016491), dioxygenase activity (GO:0051213), catalytic activity, acting on a protein (GO:0140096)

GO Cellular Component (3): nucleus (GO:0005634), cytoplasm (GO:0005737), cytosol (GO:0005829)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation1
Post-translational protein modification1
Metabolism of proteins1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
catalytic activity2
cellular anatomical structure2
protein modification process1
translational termination1
regulation of translational termination1
positive regulation of protein-containing complex disassembly1
positive regulation of translation1
gene expression1
regulation of macromolecule biosynthetic process1
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen1
dioxygenase activity1
DNA binding1
cation binding1
2-oxoglutarate-dependent dioxygenase activity1
catalytic activity, acting on a protein1
binding1
oxidoreductase activity1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cytoplasm1

Protein interactions and networks

STRING

736 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
JMJD4ALKBH1Q13686965
JMJD4ALKBH5Q6P6C2883
JMJD4ALKBH6Q3KRA9872
JMJD4ALKBH4Q9NXW9870
JMJD4ALKBH7Q9BT30864
JMJD4ALKBH2Q6NS38852
JMJD4RIOX1Q9H6W3737
JMJD4HSPBAP1Q96EW2707
JMJD4RIOX2Q8IUF8703
JMJD4TYW5A2RUC4697
JMJD4OGFOD1Q8N543679
JMJD4ALKBH3Q96Q83625
JMJD4C9K0I3C9K0I3558
JMJD4ALKBH8Q96BT7557
JMJD4ETF1P46055541

IntAct

44 interactions, top by confidence:

ABTypeScore
FAM9CNDC80psi-mi:“MI:0914”(association)0.670
SOCS7NCK2psi-mi:“MI:0914”(association)0.670
PDCL3PEX7psi-mi:“MI:0914”(association)0.640
CCT3TXNDC9psi-mi:“MI:0914”(association)0.640
ODAPHTCAF2psi-mi:“MI:0914”(association)0.530
CCNJLPIK3C2Apsi-mi:“MI:0914”(association)0.530
JMJD4H4C16psi-mi:“MI:0871”(demethylation reaction)0.440
ERBB2JMJD4psi-mi:“MI:0915”(physical association)0.370
JMJD4SPAG8psi-mi:“MI:0915”(physical association)0.370
JMJD4SPTLC1psi-mi:“MI:0914”(association)0.350
CDC16IFT56psi-mi:“MI:0914”(association)0.350
SPANXN4UBA6psi-mi:“MI:0914”(association)0.350
IQCNTARS3psi-mi:“MI:0914”(association)0.350
DUSP16MEIOCpsi-mi:“MI:0914”(association)0.350
TAFA3FUOMpsi-mi:“MI:0914”(association)0.350
CCT2WDR91psi-mi:“MI:0914”(association)0.350
KANSL3POTEFpsi-mi:“MI:0914”(association)0.350
RFPL4BKRBA1psi-mi:“MI:0914”(association)0.350
PRG2ZSWIM8psi-mi:“MI:0914”(association)0.350
NCAPH2MYO9Apsi-mi:“MI:0914”(association)0.350
LYPD4PIK3C2Apsi-mi:“MI:0914”(association)0.350
SNAPC4PIK3C2Apsi-mi:“MI:0914”(association)0.350
CCT3TUBAL3psi-mi:“MI:0914”(association)0.350
VCPIP1USP9Ypsi-mi:“MI:0914”(association)0.350
RBFOX2PRMT5psi-mi:“MI:0914”(association)0.350
APOBEC3DECASC3psi-mi:“MI:0914”(association)0.350
ELOA2XRCC2psi-mi:“MI:0914”(association)0.350
CHST8CALUpsi-mi:“MI:0914”(association)0.350

BioGRID (87): JMJD4 (Affinity Capture-RNA), JMJD4 (Affinity Capture-RNA), JMJD4 (Affinity Capture-MS), JMJD4 (Affinity Capture-MS), JMJD4 (Affinity Capture-MS), JMJD4 (Affinity Capture-MS), JMJD4 (Affinity Capture-MS), JMJD4 (Affinity Capture-MS), JMJD4 (Synthetic Growth Defect), JMJD4 (Affinity Capture-MS), JMJD4 (Affinity Capture-MS), JMJD4 (Affinity Capture-MS), JMJD4 (Affinity Capture-MS), JMJD4 (Affinity Capture-MS), JMJD4 (Affinity Capture-MS)

ESM2 similar proteins: A1A4L8, A2BDX3, A4RPM5, A5GFZ6, A6NK58, B4FAT0, B4NXF7, B6TNK6, O19179, O43323, O95396, O95571, P19971, P55203, P85971, Q02846, Q05922, Q08DH8, Q0VFH3, Q14BV6, Q17CA7, Q1WNP0, Q3KQV9, Q3TW96, Q3UQ84, Q561R2, Q58E95, Q5PQQ1, Q5ZKI2, Q61488, Q66JK4, Q6PAT0, Q7PY41, Q86U10, Q8AWD2, Q8NFV4, Q8VBZ0, Q8VDG5, Q923K4, Q96EY9

Diamond homologs: O13977, Q08BY5, Q5ZMK5, Q8BFT6, Q9H9V9, F4K2M8, Q5ZHV5, Q67ZB6, Q9VJ97, E1C7T6, Q3TA59, Q58CU3, Q5BKC6, Q6AXL5, Q6AY40, Q8BK58, Q96S16, Q9M9E8, Q58DS6, Q5R6G2, Q623U2, Q67XX3, Q6AYK2, Q6GND3, Q6NYC1, Q6PFM0, Q6Q4H1, Q7ZX37, Q9ERI5, Q9GYI4, Q9VD28, A8E534, P59723, Q08BV2, Q4IER0, Q54LV7, Q55DF5, Q5BH52, Q8BLR9, Q8RWR1

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 67 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

GO biological processes:

GO termPartnersFoldFDR
mitotic cell cycle511.0×6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

123 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance90
Likely benign6
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1055 predictions. Top by Δscore:

VariantEffectΔscore
1:227732675:ACC:Aacceptor_loss1.0000
1:227732677:C:CCacceptor_gain1.0000
1:227733023:TCATC:Tacceptor_gain1.0000
1:227733024:CATC:Cacceptor_gain1.0000
1:227733024:CATCC:Cacceptor_gain1.0000
1:227733025:ATCCT:Aacceptor_loss1.0000
1:227733026:TC:Tacceptor_gain1.0000
1:227733026:TCCTG:Tacceptor_loss1.0000
1:227733027:CC:Cacceptor_gain1.0000
1:227733028:C:Aacceptor_loss1.0000
1:227733028:C:CCacceptor_gain1.0000
1:227733029:T:Aacceptor_loss1.0000
1:227733408:CATTA:Cdonor_loss1.0000
1:227733409:ATTAC:Adonor_loss1.0000
1:227733410:TTAC:Tdonor_loss1.0000
1:227733411:TACCA:Tdonor_loss1.0000
1:227733412:A:Cdonor_loss1.0000
1:227733469:T:TAdonor_gain1.0000
1:227733642:CCAG:Cacceptor_gain1.0000
1:227733643:CAGC:Cacceptor_gain1.0000
1:227733901:CCTCA:Cdonor_loss1.0000
1:227733902:CTCA:Cdonor_loss1.0000
1:227733905:A:ACdonor_gain1.0000
1:227733905:ACCAG:Adonor_loss1.0000
1:227733906:C:CCdonor_gain1.0000
1:227733906:CCAG:Cdonor_gain1.0000
1:227734721:T:Adonor_gain1.0000
1:227734977:T:Adonor_gain1.0000
1:227735015:AGGT:Adonor_gain1.0000
1:227735024:G:Cdonor_gain1.0000

AlphaMissense

2758 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:227733001:G:CN329K0.999
1:227733001:G:TN329K0.999
1:227733431:G:CH315D0.999
1:227733614:A:GW254R0.999
1:227733614:A:TW254R0.999
1:227733618:C:AK252N0.999
1:227733618:C:GK252N0.999
1:227733664:T:AD237V0.999
1:227733933:A:CF222L0.999
1:227733933:A:TF222L0.999
1:227733935:A:GF222L0.999
1:227734669:T:AK183I0.999
1:227733007:G:CN327K0.998
1:227733007:G:TN327K0.998
1:227733417:G:CN319K0.998
1:227733417:G:TN319K0.998
1:227733437:A:GW313R0.998
1:227733437:A:TW313R0.998
1:227733625:C:TG250E0.998
1:227733633:A:CN247K0.998
1:227733633:A:TN247K0.998
1:227733644:A:GW244R0.998
1:227733644:A:TW244R0.998
1:227733645:G:CS243R0.998
1:227733645:G:TS243R0.998
1:227733647:T:GS243R0.998
1:227733663:G:CD237E0.998
1:227733663:G:TD237E0.998
1:227733671:G:CH235D0.998
1:227733937:C:GR221P0.998

dbSNP variants (sampled 300 via entrez): RS1000272274 (1:227736405 C>A), RS1001333782 (1:227734184 C>A,T), RS1001557592 (1:227733697 C>G,T), RS1001585426 (1:227733461 C>T), RS1001922513 (1:227732308 G>A), RS1002493790 (1:227730877 G>A,C), RS1002751462 (1:227736555 C>T), RS1003190628 (1:227736402 C>A), RS1005104494 (1:227734516 T>C), RS1005240755 (1:227734901 C>G,T), RS1005780158 (1:227732226 G>A,C), RS1006869408 (1:227735521 T>C), RS1007045285 (1:227731151 G>A,T), RS1007309072 (1:227735820 G>C), RS1008268246 (1:227732848 C>A,G,T)

Disease associations

OMIM: gene MIM:620928 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): congenital portosystemic shunt (MONDO:0018811)

Orphanet (1): Congenital portosystemic shunt (Orphanet:480531)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

StudyTraitp-value
GCST000817_175Height2.000000e-13
GCST90020029_636Waist circumference adjusted for body mass index8.000000e-13

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0007789BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

31 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
aristolochic acid Idecreases expression1
GSK-J4decreases expression1
methylmercuric chloridedecreases expression1
bisphenol Aincreases expression1
beta-lapachoneincreases expression1
zinc chromateincreases abundance, decreases expression1
ferrous chloridedecreases expression1
di-n-butylphosphoric acidaffects expression1
chromium hexavalent iondecreases expression, increases abundance1
pentabromodiphenyl etherdecreases expression1
perfluoro-n-nonanoic acidincreases expression1
jinfukangaffects cotreatment, increases expression1
NSC 689534affects binding, decreases expression1
Sunitinibincreases expression1
Atrazinedecreases expression1
Benzo(a)pyreneaffects methylation1
Cisplatinaffects cotreatment, increases expression1
Copperaffects binding, decreases expression1
Estradiolincreases expression1
Fluorouracildecreases expression1
Gallic Acidincreases expression1
Smokedecreases expression1
Dronabinoldecreases expression1
Thiramdecreases expression1
Tobacco Smoke Pollutionincreases expression1
Tretinoindecreases expression1
Urethanedecreases expression1
Cyclosporinedecreases expression1
Okadaic Acidincreases expression1
Copper Sulfatedecreases expression1

Clinical trials (associated diseases)

2 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT06041906Not specifiedENROLLING_BY_INVITATIONInternational Registry of Congenital Portosystemic Shunt (IRCPSS)
NCT07314814Not specifiedNOT_YET_RECRUITINGGenetic Hallmarks of Patients With Congenital Portosystemic Shunts and Portopulmonary Hypertension
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): congenital portosystemic shunt