Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	55693
Gene name	Lysine demethylase 4D
Gene symbol	KDM4D
Synonyms (NCBI Gene)	JMJD2D
Chromosome	11
Chromosome location	11q21

Show/Hide all (30)

miRTarBase ID	miRNA	Experiments	Reference
MIRT024726	hsa-miR-215-5p	Microarray	19074876
MIRT026730	hsa-miR-192-5p	Microarray	19074876
MIRT050602	hsa-miR-20a-5p	CLASH	23622248
MIRT1084614	hsa-miR-200b	CLIP-seq
MIRT1084615	hsa-miR-200c	CLIP-seq
MIRT1084616	hsa-miR-214	CLIP-seq
MIRT1084617	hsa-miR-3619-5p	CLIP-seq
MIRT1084618	hsa-miR-377	CLIP-seq
MIRT1084619	hsa-miR-429	CLIP-seq
MIRT1084620	hsa-miR-4318	CLIP-seq
MIRT1084621	hsa-miR-4504	CLIP-seq
MIRT1084622	hsa-miR-4693-5p	CLIP-seq
MIRT1084623	hsa-miR-542-3p	CLIP-seq
MIRT1084624	hsa-miR-548g	CLIP-seq
MIRT1084625	hsa-miR-549	CLIP-seq
MIRT1084626	hsa-miR-761	CLIP-seq
MIRT1084627	hsa-miR-892a	CLIP-seq
MIRT2252988	hsa-miR-103a	CLIP-seq
MIRT2252989	hsa-miR-107	CLIP-seq
MIRT1084616	hsa-miR-214	CLIP-seq
MIRT2252990	hsa-miR-34a	CLIP-seq
MIRT2252991	hsa-miR-34c-5p	CLIP-seq
MIRT1084617	hsa-miR-3619-5p	CLIP-seq
MIRT1084618	hsa-miR-377	CLIP-seq
MIRT2252992	hsa-miR-4436b-3p	CLIP-seq
MIRT2252993	hsa-miR-449a	CLIP-seq
MIRT2252994	hsa-miR-449b	CLIP-seq
MIRT1084624	hsa-miR-548g	CLIP-seq
MIRT1084626	hsa-miR-761	CLIP-seq
MIRT2252995	hsa-miR-885-3p	CLIP-seq

Show/Hide all (32)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000724	Process	Double-strand break repair via homologous recombination	IMP	24550317
GO:0000785	Component	Chromatin	IBA
GO:0001932	Process	Regulation of protein phosphorylation	IMP	24550317
GO:0003684	Function	Damaged DNA binding	IEA
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IC	27679476
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005721	Component	Pericentric heterochromatin	IEA
GO:0006325	Process	Chromatin organization	IEA
GO:0006338	Process	Chromatin remodeling	IBA
GO:0006954	Process	Inflammatory response	IDA	21914792
GO:0006974	Process	DNA damage response	IEA
GO:0010468	Process	Regulation of gene expression	IBA
GO:0016491	Function	Oxidoreductase activity	IEA
GO:0031490	Function	Chromatin DNA binding	IEA
GO:0032452	Function	Histone demethylase activity	IEA
GO:0032452	Function	Histone demethylase activity	TAS
GO:0032454	Function	Histone H3K9 demethylase activity	IBA
GO:0032454	Function	Histone H3K9 demethylase activity	IDA	25124442
GO:0032454	Function	Histone H3K9 demethylase activity	IEA
GO:0035563	Process	Positive regulation of chromatin binding	IMP	24550317
GO:0035861	Component	Site of double-strand break	IDA	24550317
GO:0035861	Component	Site of double-strand break	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0051213	Function	Dioxygenase activity	IEA
GO:0071479	Process	Cellular response to ionizing radiation	IMP	24550317
GO:0072562	Component	Blood microparticle	HDA	22516433
GO:0140684	Function	Histone H3K9me2/H3K9me3 demethylase activity	IDA	21914792
GO:0140684	Function	Histone H3K9me2/H3K9me3 demethylase activity	IEA
GO:2001034	Process	Positive regulation of double-strand break repair via nonhomologous end joining	IMP	24550317

MIM	HGNC	e!Ensembl
609766	25498	ENSG00000186280

Q6B0I6

Protein name

Lysine-specific demethylase 4D (EC 1.14.11.66) (JmjC domain-containing histone demethylation protein 3D) (Jumonji domain-containing protein 2D) ([histone H3]-trimethyl-L-lysine(9) demethylase 4D)

Protein function

Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-20'. Demethylates both di- and trimethylated

PDB

3DXT , 3DXU , 4D6Q , 4D6R , 4D6S , 4HON , 4HOO , 5F5A , 5F5C , 5FP4 , 5FP7 , 5FP8 , 5FP9 , 5FPA , 5FPB , 5PH0 , 5PH1 , 5PH2 , 5PH3 , 5PH4 , 5PH5 , 5PH6 , 5PH7 , 5PH8 , 5PH9 , 5PHA , 5PHB , 5PHC , 5PHD , 5PHE , 5PHF , 5PHG , 5PHH , 5PHI , 5PHJ , 5PHK , 5PHL , 5PHM , 5PHN , 5PHO , 5PHP , 5PHQ , 5PHR , 5PHS , 5PHT , 5PHU , 5PHV , 5PHW , 5PHX , 5PHY , 5PHZ

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF02375	JmjN	19 → 53	jmjN domain	Family
PF02373	JmjC	179 → 295	JmjC domain, hydroxylase	Domain

Sequence

METMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKAR
ETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFED
LERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYL
YFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGA
FLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRW
IDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQDRAVVDHMEPRVPASQELST
QKEVQLPRRAALGLRQLPSHWARHSPWPMAARSGTRCHTLVCSSLPRRSAVSGTATQPRA
AAVHSSKKPSSTPSSTPGPSAQIIHPSNGRRGRGRPPQKLRAQELTLQTPAKRPLLAGTT
CTASGPEPEPLPEDGALMDKPVPLSPGLQHPVKASGCSWAPVP

Sequence length

523

Interactions

View interactions

	Reactome
			HDMs demethylate histones

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (1)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
DIABETIC NEPHROPATHY	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (16)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Adenocarcinoma	Adenocarcinoma	BEFREE	29599352		★★★★★ ★☆☆☆☆ Found in Text Mining only
Adenocarcinoma of pancreas	Pancreatic adenocarcinoma	BEFREE	29599352		★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	29393482	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	30472235		★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	22514644	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal Neoplasms	BEFREE	30472235		★★★★★ ★☆☆☆☆ Found in Text Mining only
Gastrointestinal Stromal Tumors	Gastrointestinal stromal tumor	BEFREE	30060750, 30213277		★★★★★ ★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung neoplasms	Pubtator	26722485	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Lymphatic Metastasis	Lymphatic metastasis	Pubtator	26722485	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of prostate	Prostate cancer	BEFREE	29393482		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	22514644, 28291760, 29393482		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	29599352, 30472235		★★★★★ ★☆☆☆☆ Found in Text Mining only
Osteosarcoma	Osteosarcoma	BEFREE	22514644		★★★★★ ★☆☆☆☆ Found in Text Mining only
Prostate carcinoma	Prostate cancer	BEFREE	29393482		★★★★★ ★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Prostatic Neoplasms	BEFREE	29393482		★★★★★ ★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	37989263	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

KDM4D (lysine demethylase 4D)