KDM4F

Summary

KDM4F (lysine demethylase 4F, HGNC:52413) is a protein-coding gene on chromosome 11q21, encoding Probable lysine-specific demethylase 4F (A0A1W2PPD8). Probable histone demethylase that specifically demethylates ‘Lys-9’ of histone H3, thereby playing a central role in histone code.

Predicted to enable histone H3K9 demethylase activity. Predicted to be involved in chromatin remodeling and regulation of gene expression. Predicted to be active in chromatin and nucleus.

Source: NCBI Gene 100129053 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001413755

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:52413
Approved symbol	KDM4F
Name	lysine demethylase 4F
Location	11q21
Locus type	gene with protein product
Status	Approved
Aliases	JMJD2F
Ensembl gene	ENSG00000255855
Ensembl biotype	protein_coding
Entrez	100129053

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000545950, ENST00000711328

RefSeq mRNA: 1 — MANE Select: NM_001413755 NM_001413755

Canonical transcript exons

ENST00000711328 — 1 exons

Exon	Start	End
ENSE00004015272	95049422	95051338

Expression profiles

Bgee: expression breadth not_expressed, 0 present calls, max score 37.20.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
sural nerve	UBERON:0015488	36.06	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	34.89	gold quality
muscle tissue	UBERON:0002385	32.17	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
right uterine tube	UBERON:0001302	31.60	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
monocyte	CL:0000576	29.50	gold quality
leukocyte	CL:0000738	29.33	gold quality
prefrontal cortex	UBERON:0000451	29.20	gold quality
liver	UBERON:0002107	28.74	gold quality
duodenum	UBERON:0002114	28.14	gold quality
lymph node	UBERON:0000029	27.57	gold quality
tonsil	UBERON:0002372	27.05	gold quality
islet of Langerhans	UBERON:0000006	26.94	gold quality
urinary bladder	UBERON:0001255	26.72	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
gall bladder	UBERON:0002110	25.98	gold quality
muscle of leg	UBERON:0001383	25.95	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	25.89	gold quality
placenta	UBERON:0001987	25.81	gold quality
gastrocnemius	UBERON:0001388	24.90	gold quality
calcaneal tendon	UBERON:0003701	24.83	gold quality
primary visual cortex	UBERON:0002436	24.61	gold quality
uterine cervix	UBERON:0000002	24.42	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.48

Regulation

Is transcription factor: no

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	kdm4c	ENSDARG00000061504
drosophila_melanogaster	Kdm5	FBGN0031759
caenorhabditis_elegans		WBGENE00004319

Paralogs (10): JARID2 (ENSG00000008083), KDM5D (ENSG00000012817), KDM4A (ENSG00000066135), KDM5A (ENSG00000073614), KDM4C (ENSG00000107077), KDM5B (ENSG00000117139), KDM5C (ENSG00000126012), KDM4B (ENSG00000127663), KDM4D (ENSG00000186280), KDM4E (ENSG00000235268)

Protein

Protein identifiers

Probable lysine-specific demethylase 4F — A0A1W2PPD8 (reviewed: A0A1W2PPD8)

All UniProt accessions (1): A0A1W2PPD8

UniProt curated annotations — full annotation on UniProt →

Function. Probable histone demethylase that specifically demethylates ‘Lys-9’ of histone H3, thereby playing a central role in histone code.

Subcellular location. Nucleus.

Cofactor. Binds 1 Fe(2+) ion per subunit.

Similarity. Belongs to the JHDM3 histone demethylase family.

RefSeq proteins (1): NP_001400684* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003347	JmjC_dom	Domain
IPR003349	JmjN	Domain

Pfam: PF02373, PF02375

Catalyzed reactions (Rhea), 1 shown:

• N(6),N(6),N(6)-trimethyl-L-lysyl(9)-[histone H3] + 2 2-oxoglutarate + 2 O2 = N(6)-methyl-L-lysyl(9)-[histone H3] + 2 formaldehyde + 2 succinate + 2 CO2 (RHEA:60200)

UniProt features (16 total): binding site 11, domain 2, chain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A1W2PPD8-F1	67.22	0.46

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 (11): 235; 241; 242; 277; 307; 309; 133; 189; 191; 199; 207

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 14 (showing top): GOMF_OXIDOREDUCTASE_ACTIVITY_ACTING_ON_PAIRED_DONORS_WITH_INCORPORATION_OR_REDUCTION_OF_MOLECULAR_OXYGEN, GOBP_CHROMATIN_REMODELING, GOMF_DEMETHYLASE_ACTIVITY, chr11q21, GOMF_DIOXYGENASE_ACTIVITY, GOMF_HISTONE_H3K9_DEMETHYLASE_ACTIVITY, GOMF_PROTEIN_DEMETHYLASE_ACTIVITY, GOMF_OXIDOREDUCTASE_ACTIVITY, GOMF_HISTONE_H3K9ME2_H3K9ME3_DEMETHYLASE_ACTIVITY, GOMF_HISTONE_MODIFYING_ACTIVITY, GOBP_CHROMATIN_ORGANIZATION, GOMF_HISTONE_H3_DEMETHYLASE_ACTIVITY, GOCC_CHROMATIN, GOMF_2_OXOGLUTARATE_DEPENDENT_DIOXYGENASE_ACTIVITY

GO Biological Process (3): chromatin remodeling (GO:0006338), regulation of gene expression (GO:0010468), chromatin organization (GO:0006325)

GO Molecular Function (4): histone H3K9 demethylase activity (GO:0032454), metal ion binding (GO:0046872), histone H3K9me2/H3K9me3 demethylase activity (GO:0140684), oxidoreductase activity (GO:0016491)

GO Cellular Component (2): chromatin (GO:0000785), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
chromatin organization	1
gene expression	1
regulation of macromolecule biosynthetic process	1
cellular component organization	1
histone H3 demethylase activity	1
cation binding	1
2-oxoglutarate-dependent dioxygenase activity	1
histone H3K9 demethylase activity	1
catalytic activity	1
chromosome	1
cellular anatomical structure	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

240 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KDM4F	JMJD1C	Q15652	624
KDM4F	KDM3A	Q9Y4C1	402
KDM4F	KDM3B	Q7LBC6	362
KDM4F	KDM8	Q8N371	360
KDM4F	KDM7A	Q6ZMT4	345
KDM4F	KDM2A	Q9Y2K7	333
KDM4F	KDM1A	O60341	327
KDM4F	WIZ	O95785	309
KDM4F	JMJD8	Q96S16	306
KDM4F	PHF2	O75151	297
KDM4F	KDM2B	Q8NHM5	294
KDM4F	RIOX2	Q8IUF8	279
KDM4F	RIOX1	Q9H6W3	279
KDM4F	PHF8	Q9UPP1	277
KDM4F	JMJD6	Q6NYC1	256

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1U8QGE6, A0A1W2PPD8, A0A6A6H2E0, A4H5X5, B1NWF3, B1VKF6, I1R9B4, O30075, O83202, P07885, P09003, P09004, P0C7P4, P14975, P15397, P15718, P16130, P22281, P24620, P24621, P27269, P27336, P39308, P44047, P61511, P61512, P83944, P86937, P86938, Q02330, Q03286, Q05106, Q1KXV6, Q1R1Y6, Q2GPK5, Q2YD11, Q41407, Q4DBW3, Q53932, Q5AR53

Diamond homologs: A0A1W2PPD8, A1A5Q5, A1YVX4, B2RXH2, C0SUT9, F4I240, F4I6G4, F4KIX0, O64752, O75164, O94953, P29375, P39956, P41229, P41230, P47156, Q03833, Q10RP4, Q1LVC2, Q23541, Q30DN6, Q336N8, Q38JA7, Q3U2K5, Q3UXZ9, Q53WJ1, Q5F3R2, Q5N712, Q5RD88, Q5XUN4, Q61T02, Q62240, Q62315, Q6B0I6, Q6BDA0, Q6IQX0, Q80Y84, Q8BW72, Q8GUI6, Q8VCD7

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
2-oxoglutarate(2-)	“up-regulates activity”	KDM4F	“chemical activation”

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

0 scored. Top likely-pathogenic:

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

Clinical trials (associated diseases)

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