JMJD7

gene
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Summary

JMJD7 (jumonji domain containing 7, HGNC:34397) is a protein-coding gene on chromosome 15q15.1, encoding Bifunctional peptidase and (3S)-lysyl hydroxylase JMJD7 (P0C870). Bifunctional enzyme that acts both as an endopeptidase and 2-oxoglutarate-dependent monooxygenase.

This gene encodes a highly conserved protein with a JmjC domain, which are part of the cupin metalloenzyme superfamily. JmjC proteins may function as 2-oxoglutarate-Fe(II)-dependent dioxygenases. Most tissues also express read-through transcripts from this gene into the downstream phospholipase A2, group IVB (cytosolic) gene, some of which may encode fusion proteins combining the N-terminus of this protein with the phospholipase A2, group IVB protein.

Source: NCBI Gene 100137047 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 31 total
  • Druggable target: yes — 2 molecules with ChEMBL bioactivity
  • MANE Select transcript: NM_001114632

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:34397
Approved symbolJMJD7
Namejumonji domain containing 7
Location15q15.1
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000243789
Ensembl biotypeprotein_coding
OMIM621306
Entrez100137047

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 5 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000397299, ENST00000405106, ENST00000408047, ENST00000431823, ENST00000478178, ENST00000562035, ENST00000864345, ENST00000922178

RefSeq mRNA: 1 — MANE Select: NM_001114632 NM_001114632

CCDS: CCDS45240

Canonical transcript exons

ENST00000397299 — 8 exons

ExonStartEnd
ENSE000015507784183706841837581
ENSE000034819824183614841836243
ENSE000035842924182809241828188
ENSE000035963244183497041835223
ENSE000036170774183474041834893
ENSE000036422194183558841835644
ENSE000036647784183678141836940
ENSE000037848094183647541836551

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 93.82.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.0823 / max 136.2197, expressed in 1763 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
14621410.08231763

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
lower esophagus mucosaUBERON:003583493.82gold quality
esophagus mucosaUBERON:000246991.13gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099190.53gold quality
skin of abdomenUBERON:000141690.45gold quality
zone of skinUBERON:000001489.98gold quality
right hemisphere of cerebellumUBERON:001489089.97gold quality
cerebellumUBERON:000203789.77gold quality
cerebellar hemisphereUBERON:000224589.75gold quality
cerebellar cortexUBERON:000212989.72gold quality
skin of legUBERON:000151189.67gold quality
granulocyteCL:000009488.73gold quality
saliva-secreting glandUBERON:000104487.49gold quality
apex of heartUBERON:000209887.49gold quality
minor salivary glandUBERON:000183087.21gold quality
C1 segment of cervical spinal cordUBERON:000646986.71gold quality
vaginaUBERON:000099686.12gold quality
tonsilUBERON:000237285.64gold quality
esophagusUBERON:000104385.40gold quality
olfactory segment of nasal mucosaUBERON:000538685.31gold quality
right lobe of thyroid glandUBERON:000111984.70gold quality
body of pancreasUBERON:000115084.68gold quality
thyroid glandUBERON:000204684.01gold quality
left lobe of thyroid glandUBERON:000112084.00gold quality
heart left ventricleUBERON:000208483.55gold quality
body of stomachUBERON:000116183.45gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047383.16gold quality
substantia nigraUBERON:000203882.99gold quality
prostate glandUBERON:000236782.83gold quality
bloodUBERON:000017882.57gold quality
prefrontal cortexUBERON:000045182.56gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-GEOD-100618yes719.45
E-ANND-3no1.01

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

9 targeting JMJD7, 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-1212399.5271.792990
HSA-MIR-3688-5P99.1269.671091
HSA-MIR-427298.7668.741810
HSA-MIR-767-3P98.6167.691192
HSA-MIR-366197.8367.30705
HSA-MIR-6782-3P97.6067.75931
HSA-MIR-4695-3P96.7167.21836
HSA-MIR-500B-3P96.4965.401087
HSA-MIR-644A96.0266.52786

Literature-anchored findings (GeneRIF, showing 3)

  • JMJD7-PLA2G4B may serve as an important therapeutic target and prognostic marker for head and neck squamous cell carcinoma development and progression. (PMID:28030848)
  • The protease activities of JMJD5 and JMJD7 represent a mechanism for removal of histone tails bearing methylated arginine residues and define a potential mechanism of transcription regulation. (PMID:28847961)
  • Substrate selectivity and inhibition of the human lysyl hydroxylase JMJD7. (PMID:39276004)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriojmjd7ENSDARG00000035546
mus_musculusJmjd7ENSMUSG00000098789
rattus_norvegicusJmjd7ENSRNOG00000050072
drosophila_melanogasterJMJD7FBGN0036366

Paralogs (4): KDM8 (ENSG00000155666), TYW5 (ENSG00000162971), HIF1AN (ENSG00000166135), HSPBAP1 (ENSG00000169087)

Protein

Protein identifiers

Bifunctional peptidase and (3S)-lysyl hydroxylase JMJD7P0C870 (reviewed: P0C870)

Alternative names: JmjC domain-containing protein 7, Jumonji domain-containing protein 7, L-lysine (3S)-hydroxylase JMJD7

All UniProt accessions (3): P0C870, B5MC20, C9K0I3

UniProt curated annotations — full annotation on UniProt →

Function. Bifunctional enzyme that acts both as an endopeptidase and 2-oxoglutarate-dependent monooxygenase. Endopeptidase that cleaves histones N-terminal tails at the carboxyl side of methylated arginine or lysine residues, to generate ’tailless nucleosomes’, which may trigger transcription elongation. Preferentially recognizes and cleaves monomethylated and dimethylated arginine residues of histones H2, H3 and H4. After initial cleavage, continues to digest histones tails via its aminopeptidase activity. Additionally, may play a role in protein biosynthesis by modifying the translation machinery. Acts as a Fe(2+) and 2-oxoglutarate-dependent monooxygenase, catalyzing (S)-stereospecific hydroxylation at C-3 of ‘Lys-22’ of DRG1 and ‘Lys-21’ of DRG2 translation factors (TRAFAC), promoting their interaction with ribonucleic acids (RNA).

Subunit / interactions. Homodimer; disulfide-linked. Interacts with DRG1 and DRG2.

Subcellular location. Nucleus. Cytoplasm.

RefSeq proteins (1): NP_001108104* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003347JmjC_domDomain
IPR014710RmlC-like_jellyrollHomologous_superfamily
IPR041667Cupin_8Domain

Pfam: PF13621

Enzyme classification (BRENDA):

  • EC 1.14.11.27 — [histone H3]-dimethyl-L-lysine36 demethylase (BRENDA: 7 organisms, 38 substrates, 0 inhibitors, 0 Km, 0 kcat entries)
  • EC 1.14.11.63 — peptidyl-lysine (3S)-dioxygenase (BRENDA: 3 organisms, 5 substrates, 7 inhibitors, 0 Km, 0 kcat entries)

Catalyzed reactions (Rhea), 1 shown:

  • L-lysyl-[protein] + 2-oxoglutarate + O2 = (3S)-3-hydroxy-L-lysyl-[protein] + succinate + CO2 (RHEA:57152)

UniProt features (41 total): strand 16, helix 11, mutagenesis site 4, binding site 3, turn 2, sequence variant 2, chain 1, domain 1, disulfide bond 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
5NFOX-RAY DIFFRACTION2.17
5NFNX-RAY DIFFRACTION2.98

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P0C870-F197.890.98

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): 178; 180; 277

Disulfide bonds (1): 47

Mutagenesis-validated functional residues (4):

PositionPhenotype
180loss of peptidase activity toward methylated histones and reduced anchorage-independent growth of transformed cells; whe
277loss of peptidase activity toward methylated histones and reduced anchorage-independent growth of transformed cells; whe
47impairs homodimer formation.
178loss of peptidase activity toward methylated histones and reduced anchorage-independent growth of transformed cells; whe

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: 30 (showing top): GOMF_OXIDOREDUCTASE_ACTIVITY_ACTING_ON_PAIRED_DONORS_WITH_INCORPORATION_OR_REDUCTION_OF_MOLECULAR_OXYGEN, GOBP_PEPTIDYL_LYSINE_MODIFICATION, CADWELL_ATG16L1_TARGETS_DN, GOBP_PROTEIN_HYDROXYLATION, GOBP_PROTEOLYSIS, GOMF_PEPTIDASE_ACTIVITY, GOMF_AMINOPEPTIDASE_ACTIVITY, GOMF_DIOXYGENASE_ACTIVITY, GOMF_EXOPEPTIDASE_ACTIVITY, REACTOME_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, GOMF_MONOOXYGENASE_ACTIVITY, GOBP_PEPTIDYL_LYSINE_HYDROXYLATION, REACTOME_GAMMA_CARBOXYLATION_HYPUSINYLATION_HYDROXYLATION_AND_ARYLSULFATASE_ACTIVATION, FEV_TARGET_GENES, FOXD2_TARGET_GENES

GO Biological Process (2): proteolysis (GO:0006508), protein hydroxylation (GO:0018126)

GO Molecular Function (10): endopeptidase activity (GO:0004175), aminopeptidase activity (GO:0004177), monooxygenase activity (GO:0004497), 2-oxoglutarate-dependent dioxygenase activity (GO:0016706), metal ion binding (GO:0046872), peptidyl-lysine 3-dioxygenase activity (GO:0106155), protein binding (GO:0005515), peptidase activity (GO:0008233), oxidoreductase activity (GO:0016491), hydrolase activity (GO:0016787)

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 activity, acting on a protein2
catalytic activity2
cellular anatomical structure2
protein metabolic process1
protein modification process1
peptidase activity1
exopeptidase activity1
oxidoreductase activity1
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen1
dioxygenase activity1
cation binding1
2-oxoglutarate-dependent dioxygenase activity1
binding1
hydrolase activity1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cytoplasm1

Protein interactions and networks

STRING

236 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
JMJD7RIOX2Q8IUF8513
JMJD7DRG2P55039507
JMJD7JMJD4Q9H9V9506
JMJD7U3KPZ7U3KPZ7445
JMJD7HRO43593444
JMJD7RIOX1Q9H6W3420
JMJD7ZC3H15Q8WU90419
JMJD7RWDD1Q9H446412
JMJD7PLA2G4BP0C869411
JMJD7PRMT9Q6P2P2352
JMJD7JMJD8Q96S16348
JMJD7PLA2G3Q9NZ20326
JMJD7PHF2O75151299
JMJD7KDM4EB2RXH2275
JMJD7JMJD6Q6NYC1273

IntAct

64 interactions, top by confidence:

ABTypeScore
JMJD7VAC14psi-mi:“MI:0915”(physical association)0.560
VAC14JMJD7psi-mi:“MI:0915”(physical association)0.560
JMJD7OXER1psi-mi:“MI:0915”(physical association)0.560
SNRPCJMJD7psi-mi:“MI:0915”(physical association)0.560
JMJD7SAMD11psi-mi:“MI:0915”(physical association)0.560
JMJD7POM121psi-mi:“MI:0915”(physical association)0.560
JMJD7FOXI1psi-mi:“MI:0915”(physical association)0.560
GCM2JMJD7psi-mi:“MI:0915”(physical association)0.560
JMJD7UBAP2psi-mi:“MI:0915”(physical association)0.560
JMJD7DRG2psi-mi:“MI:0915”(physical association)0.560
HGSJMJD7psi-mi:“MI:0915”(physical association)0.560
POGZJMJD7psi-mi:“MI:0915”(physical association)0.560
JMJD7CASP6psi-mi:“MI:0915”(physical association)0.560
JMJD7HSPB1psi-mi:“MI:0915”(physical association)0.560
JMJD7LAMP2psi-mi:“MI:0915”(physical association)0.560
JMJD7RANpsi-mi:“MI:0915”(physical association)0.560
JMJD7WFS1psi-mi:“MI:0915”(physical association)0.560
JMJD7KIF1Bpsi-mi:“MI:0915”(physical association)0.560
JMJD7SH3GLB1psi-mi:“MI:0915”(physical association)0.560
JMJD7PRPF40Apsi-mi:“MI:0915”(physical association)0.560

BioGRID (21): JMJD7 (Two-hybrid), JMJD7 (Two-hybrid), JMJD7 (Two-hybrid), JMJD7 (Two-hybrid), JMJD7 (Two-hybrid), JMJD7 (Two-hybrid), JMJD7 (Two-hybrid), JMJD7 (Two-hybrid), JMJD7 (Two-hybrid), JMJD7 (Two-hybrid), JMJD7 (Two-hybrid), JMJD7 (Affinity Capture-MS), CCT2 (Affinity Capture-MS), CCT7 (Affinity Capture-MS), CCT8 (Affinity Capture-MS)

ESM2 similar proteins: A2AV36, A2RSX7, A2RUC4, A4IHY0, A6QQV6, A8E534, B2GUS6, B5XF11, E1C7T6, E9PYK3, F1RET2, P0C870, P0C872, P47823, P59723, P83006, Q08BV2, Q08BY5, Q0VCA8, Q0WVR4, Q3UDE2, Q3V3E1, Q58CU3, Q5BKC6, Q5EA24, Q5R673, Q5U4E8, Q5ZHV5, Q5ZIB9, Q66KI9, Q67XX3, Q67ZB6, Q6AXL5, Q6PCI6, Q7T0X7, Q7TMC8, Q8BFT6, Q8BGG7, Q8BK58, Q8BLR9

Diamond homologs: A2RSX7, P0C870, P0C872, Q0WVR4, Q54CS7, Q9VU77, O94606, Q8BLR9, Q9NWT6, Q67XX3, F4K2M8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance21
Likely benign5
Benign4

Top pathogenic / likely-pathogenic (0)

SpliceAI

1973 predictions. Top by Δscore:

VariantEffectΔscore
15:41828186:GGG:Gdonor_gain1.0000
15:41828186:GGGGT:Gdonor_loss1.0000
15:41828187:GG:Gdonor_gain1.0000
15:41828187:GGG:Gdonor_gain1.0000
15:41828188:GG:Gdonor_gain1.0000
15:41828188:GGTG:Gdonor_loss1.0000
15:41828189:G:GGdonor_gain1.0000
15:41828189:GT:Gdonor_loss1.0000
15:41828189:GTGA:Gdonor_loss1.0000
15:41828190:T:Adonor_loss1.0000
15:41834870:G:GTdonor_gain1.0000
15:41835222:GG:Gdonor_gain1.0000
15:41835223:GG:Gdonor_gain1.0000
15:41835224:G:GGdonor_gain1.0000
15:41835224:GTGA:Gdonor_loss1.0000
15:41835645:G:GGdonor_gain1.0000
15:41836142:T:Aacceptor_gain1.0000
15:41836241:ATGGT:Adonor_loss1.0000
15:41836242:TGG:Tdonor_loss1.0000
15:41836244:GTAG:Gdonor_loss1.0000
15:41836245:T:Adonor_loss1.0000
15:41836465:T:Aacceptor_gain1.0000
15:41836466:G:Aacceptor_gain1.0000
15:41837066:A:AGacceptor_gain1.0000
15:41837067:G:GGacceptor_gain1.0000
15:41837067:GTGA:Gacceptor_gain1.0000
15:41828185:AGGG:Adonor_gain0.9900
15:41828186:GGGG:Gdonor_gain0.9900
15:41834736:TCAG:Tacceptor_gain0.9900
15:41834738:A:AGacceptor_gain0.9900

AlphaMissense

2046 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
15:41836150:C:GH178D0.998
15:41836157:A:CD180A0.998
15:41836157:A:TD180V0.998
15:41836907:C:GH277D0.998
15:41835046:T:CF99L0.997
15:41835048:C:AF99L0.997
15:41835048:C:GF99L0.997
15:41835610:C:AN165K0.997
15:41835610:C:GN165K0.997
15:41835614:T:AW167R0.997
15:41835614:T:CW167R0.997
15:41837072:T:AN289K0.997
15:41837072:T:GN289K0.997
15:41836156:G:CD180H0.996
15:41836157:A:GD180G0.996
15:41836158:C:AD180E0.996
15:41836158:C:GD180E0.996
15:41836170:C:AN184K0.996
15:41836170:C:GN184K0.996
15:41836787:T:AW237R0.996
15:41836787:T:CW237R0.996
15:41834874:T:AW67R0.995
15:41834874:T:CW67R0.995
15:41835047:T:CF99S0.995
15:41835639:C:TT175I0.995
15:41836904:T:CF276L0.995
15:41836906:C:AF276L0.995
15:41836906:C:GF276L0.995
15:41836150:C:AH178N0.994
15:41836166:A:TE183V0.994

dbSNP variants (sampled 300 via entrez): RS1000072675 (15:41829698 A>G), RS1000127284 (15:41833547 C>T), RS1000783038 (15:41834250 T>G), RS1000880083 (15:41830687 C>G,T), RS1000926219 (15:41835949 C>T), RS1000956142 (15:41826619 G>A), RS1001121060 (15:41835328 C>G,T), RS1001351875 (15:41834567 G>A), RS1001561295 (15:41830926 A>G), RS1001904668 (15:41828579 A>G), RS1001973957 (15:41827451 C>T), RS1002021797 (15:41831889 A>G), RS1002156036 (15:41838073 C>T), RS1002539629 (15:41832016 C>T), RS1002774872 (15:41836035 C>T)

Disease associations

OMIM: gene MIM:621306 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

StudyTraitp-value
GCST90020024_483A body shape index3.000000e-09
GCST90020025_142Waist-to-hip ratio adjusted for BMI2.000000e-08
GCST90020025_450Waist-to-hip ratio adjusted for BMI1.000000e-09
GCST90020027_628Waist-hip index1.000000e-09
GCST90020027_629Waist-hip index1.000000e-08

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0007789BMI-adjusted waist circumference
EFO:0007788BMI-adjusted waist-hip ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4879430 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

2 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 1,281 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

MoleculeNamePhasePatents
CHEMBL197194VIDOFLUDIMUS3808
CHEMBL3982723DAROVASERTIB2473

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

ChEMBL bioactivities

4 potent at pChembl≥5 of 9 total, top 4 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
5.93Kd1180nMCHEMBL4846929
5.42IC503800nMCHEMBL4846929
5.18IC506620nMCHEMBL4846929
5.14IC507160nMVIDOFLUDIMUS

PubChem BioAssay actives

4 with measured affinity, of 11 total; 2 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
(5-nitroquinolin-8-yl) 2,4-dichlorobenzoate1763997: Binding affinity to N-terminal His-tagged human JMJD7 (1 to 316 residues) expressed in Escherichia coli BL21 (DE3) measured by MST assaykd1.1800uM
2-[[2-fluoro-4-(3-methoxyphenyl)phenyl]carbamoyl]cyclopentene-1-carboxylic acid1763996: Inhibition of N-terminal His-tagged human JMJD7 (1 to 316 residues) expressed in Escherichia coli BL21 (DE3) luciferase based succinate-gloTM JmjC demethylase/hydroxylase assayic507.1600uM

CTD chemical–gene interactions

12 total (human), top 12 by PubMed support.

ChemicalActions (top 5)PubMed papers
gallium arsenidedecreases expression1
CGP 52608affects binding, increases reaction1
jinfukangaffects cotreatment, increases expression1
Sunitinibdecreases expression1
Arsenicalsincreases expression1
Benzo(a)pyreneincreases methylation1
Cisplatinaffects cotreatment, increases expression1
Estradiolaffects cotreatment, decreases expression1
Smokedecreases expression1
Tobacco Smoke Pollutionincreases expression1
Urethanedecreases expression1
Valproic Acidincreases methylation1

ChEMBL screening assays

5 unique, capped per target: 5 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4822994BindingInhibition of N-terminal His-tagged human JMJD7 (1 to 316 residues) expressed in Escherichia coli BL21 (DE3) luciferase based succinate-gloTM JmjC demethylase/hydroxylase assayDiscovery of JMJD7 inhibitors with the aid of virtual screening and bioactivity evaluation. — Bioorg Med Chem Lett

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.