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

Gene Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	8841
Gene name Gene Name - the full gene name approved by the HGNC.	Histone deacetylase 3
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	HDAC3
Synonyms (NCBI Gene) Gene synonyms aliases	HD3, KDAC3, RPD3, RPD3-2
Chromosome Chromosome number	5
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	5q31.3
Summary Summary of gene provided in NCBI Entrez Gene.	Histones play a critical role in transcriptional regulation, cell cycle progression, and developmental events. Histone acetylation/deacetylation alters chromosome structure and affects transcription factor access to DNA. The protein encoded by this gene b

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SNP ID	Visualize variation	Clinical significance	Consequence
rs1554216303	C>T	Likely-pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs1554216308	T>C	Likely-pathogenic	Coding sequence variant, non coding transcript variant, missense variant

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miRTarBase ID	miRNA	Experiments	Reference
MIRT732569	hsa-miR-4286	Immunofluorescence, Luciferase reporter assay, Western blotting	33973278
MIRT734466	hsa-miR-132-3p	Microarray, RNA-seq	31669733
MIRT737020	hsa-miR-193b-3p	Western blotting, qRT-PCR	32098619
MIRT1042435	hsa-miR-1261	CLIP-seq
MIRT1042436	hsa-miR-1915	CLIP-seq
MIRT1042437	hsa-miR-3124-3p	CLIP-seq
MIRT1042438	hsa-miR-324-5p	CLIP-seq
MIRT1042439	hsa-miR-3925-3p	CLIP-seq
MIRT1042440	hsa-miR-3927	CLIP-seq
MIRT1042441	hsa-miR-4257	CLIP-seq
MIRT1042442	hsa-miR-4690-3p	CLIP-seq
MIRT1042443	hsa-miR-4733-5p	CLIP-seq
MIRT1042444	hsa-miR-548ac	CLIP-seq
MIRT1042445	hsa-miR-548ae	CLIP-seq
MIRT1042446	hsa-miR-548aj	CLIP-seq
MIRT1042447	hsa-miR-548am	CLIP-seq
MIRT1042448	hsa-miR-548d-3p	CLIP-seq
MIRT1042449	hsa-miR-548x	CLIP-seq
MIRT1042450	hsa-miR-548z	CLIP-seq
MIRT1042451	hsa-miR-589	CLIP-seq
MIRT1042452	hsa-miR-765	CLIP-seq
MIRT1042453	hsa-miR-766	CLIP-seq
MIRT2008952	hsa-miR-1225-3p	CLIP-seq
MIRT2008953	hsa-miR-1258	CLIP-seq
MIRT2008954	hsa-miR-1321	CLIP-seq
MIRT2008955	hsa-miR-216a	CLIP-seq
MIRT2008956	hsa-miR-216b	CLIP-seq
MIRT2008957	hsa-miR-3127-3p	CLIP-seq
MIRT2008958	hsa-miR-3152-3p	CLIP-seq
MIRT2008959	hsa-miR-3162-5p	CLIP-seq
MIRT2008960	hsa-miR-4694-5p	CLIP-seq
MIRT2008961	hsa-miR-4739	CLIP-seq
MIRT2008962	hsa-miR-4756-5p	CLIP-seq
MIRT2008963	hsa-miR-4762-5p	CLIP-seq
MIRT2008964	hsa-miR-671-5p	CLIP-seq
MIRT1042453	hsa-miR-766	CLIP-seq
MIRT1042436	hsa-miR-1915	CLIP-seq
MIRT2241315	hsa-miR-3936	CLIP-seq
MIRT2241316	hsa-miR-4688	CLIP-seq
MIRT1042452	hsa-miR-765	CLIP-seq
MIRT2437560	hsa-miR-1236	CLIP-seq
MIRT2008956	hsa-miR-216b	CLIP-seq
MIRT2008963	hsa-miR-4762-5p	CLIP-seq
MIRT2437561	hsa-miR-670	CLIP-seq
MIRT2437560	hsa-miR-1236	CLIP-seq
MIRT2008956	hsa-miR-216b	CLIP-seq
MIRT2008963	hsa-miR-4762-5p	CLIP-seq
MIRT2437561	hsa-miR-670	CLIP-seq
MIRT2545021	hsa-miR-1231	CLIP-seq
MIRT2545022	hsa-miR-362-5p	CLIP-seq
MIRT2545023	hsa-miR-4288	CLIP-seq
MIRT2545024	hsa-miR-4742-3p	CLIP-seq
MIRT2545025	hsa-miR-500b	CLIP-seq
MIRT2545026	hsa-miR-501-5p	CLIP-seq
MIRT2545027	hsa-miR-632	CLIP-seq
MIRT2545021	hsa-miR-1231	CLIP-seq
MIRT2545022	hsa-miR-362-5p	CLIP-seq
MIRT2545023	hsa-miR-4288	CLIP-seq
MIRT2545024	hsa-miR-4742-3p	CLIP-seq
MIRT2545025	hsa-miR-500b	CLIP-seq
MIRT2545026	hsa-miR-501-5p	CLIP-seq
MIRT2545027	hsa-miR-632	CLIP-seq

Transcription factors

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Transcription factor	Regulation	Reference
HDAC4	Unknown	11804585
YY1	Unknown	19279113

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GO ID	Ontology	Definition	Evidence	Reference
GO:0000118	Component	Histone deacetylase complex	IBA	21873635
GO:0000118	Component	Histone deacetylase complex	IDA	18326024
GO:0000118	Component	Histone deacetylase complex	TAS	12711221
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IDA	16569215, 18417529, 18854353
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IMP	12628926
GO:0001226	Function	RNA polymerase II transcription corepressor binding	IPI	12535528
GO:0001934	Process	Positive regulation of protein phosphorylation	IDA	25190803
GO:0003682	Function	Chromatin binding	IDA	16569215, 18417529
GO:0003714	Function	Transcription corepressor activity	IDA	16569215, 18417529
GO:0003714	Function	Transcription corepressor activity	IMP	12628926
GO:0004407	Function	Histone deacetylase activity	IBA	21873635
GO:0004407	Function	Histone deacetylase activity	IMP	16924111, 18326024
GO:0004407	Function	Histone deacetylase activity	TAS	12711221
GO:0005515	Function	Protein binding	IPI	10898795, 11006275, 11013263, 11259576, 11641274, 11861901, 15016912, 15194749, 15805470, 16432238, 16461912, 16847267, 16917504, 16924111, 16980585, 17053781, 17075044, 17172643, 17895379, 17956988, 18279852, 18854353, 19409814, 20385135, 21030595, 21258344, 21624135, 21914818, 221
GO:0005634	Component	Nucleus	IDA	18326024, 18347167, 21030595
GO:0005634	Component	Nucleus	TAS	12711221
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005737	Component	Cytoplasm	IDA	25190803
GO:0005737	Component	Cytoplasm	TAS	12711221
GO:0005794	Component	Golgi apparatus	IDA
GO:0005829	Component	Cytosol	IDA	21030595
GO:0005886	Component	Plasma membrane	IDA
GO:0006325	Process	Chromatin organization	TAS	12711221
GO:0006476	Process	Protein deacetylation	IDA	17172643, 21030595
GO:0007623	Process	Circadian rhythm	TAS
GO:0008134	Function	Transcription factor binding	IPI	16569215
GO:0008134	Function	Transcription factor binding	TAS	12711221
GO:0010832	Process	Negative regulation of myotube differentiation	IMP	10983972
GO:0017053	Component	Transcription repressor complex	IDA	11804585, 12628926, 16569215, 18417529
GO:0019216	Process	Regulation of lipid metabolic process	TAS
GO:0019899	Function	Enzyme binding	IPI	11641274
GO:0030332	Function	Cyclin binding	IPI	18417529
GO:0031398	Process	Positive regulation of protein ubiquitination	ISS
GO:0031647	Process	Regulation of protein stability	IDA	25190803
GO:0032008	Process	Positive regulation of TOR signaling	IMP	25190803
GO:0032041	Function	NAD-dependent histone deacetylase activity (H3-K14 specific)	IEA
GO:0032922	Process	Circadian regulation of gene expression	ISS
GO:0033558	Function	Protein deacetylase activity	IDA	17172643
GO:0042307	Process	Positive regulation of protein import into nucleus	IDA	25190803
GO:0042752	Process	Regulation of circadian rhythm	ISS
GO:0042826	Function	Histone deacetylase binding	IPI	10869435, 12590135, 23867755
GO:0043066	Process	Negative regulation of apoptotic process	TAS	10777477
GO:0045892	Process	Negative regulation of transcription, DNA-templated	IMP	16924111
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IBA	21873635
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IDA	25190803
GO:0046329	Process	Negative regulation of JNK cascade	IMP	11931768
GO:0051059	Function	NF-kappaB binding	IPI	17785205
GO:0051225	Process	Spindle assembly	IMP	18326024
GO:0070932	Process	Histone H3 deacetylation	IBA	21873635
GO:0070933	Process	Histone H4 deacetylation	IBA	21873635
GO:0071498	Process	Cellular response to fluid shear stress	IDA	25190803
GO:0072686	Component	Mitotic spindle	IDA	18326024
GO:0120162	Process	Positive regulation of cold-induced thermogenesis	ISS	28614293

MIM	HGNC	e!Ensembl
605166	4854	ENSG00000171720

Protein

UniProt ID

O15379

Protein name

Histone deacetylase 3 (HD3) (EC 3.5.1.98) (Protein deacetylase HDAC3) (EC 3.5.1.-) (Protein deacylase HDAC3) (EC 3.5.1.-) (RPD3-2) (SMAP45)

Protein function

Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4), and some other non-histone substrates (PubMed:21030595, PubMed:21444723, PubMed:23911289, PubMed:25301942,

PDB

4A69

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00850	Hist_deacetyl	22 → 314	Histone deacetylase domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Widely expressed. {ECO:0000269|PubMed:9464271}.

Sequence

MAKTVAYFYDPDVGNFHYGAGHPMKPHRLALTHSLVLHYGLYKKMIVFKPYQASQHDMCR
FHSEDYIDFLQRVSPTNMQGFTKSLNAFNVGDDCPVFPGLFEFCSRYTGASLQGATQLNN
KICDIAINWAGGLHHAKKFEASGFCYVNDIVIGILELLKYHPRVLYIDIDIHHGDGVQEA
FYLTDRVMTVSFHKYGNYFFPGTGDMYEVGAESGRYYCLNVPLRDGIDDQSYKHLFQPVI
NQVVDFYQPTCIVLQCGADSLGCDRLGCFNLSIRGHGECVEYVKSFNIPLLVLGGGGYTV
RNVARCWTYETSLLVEEAISEELPYSEYFEYFAPDFTLHPDVSTRIENQNSRQYLDQIRQ
TIFENLKMLNHAPSVQIHDVPADLLTYDRTDEADAEERGPEENYSRPEAPNEFYDGDHDN
DKESDVEI

Sequence length

428

Interactions

View interactions

	KEGG		Reactome
	Neutrophil extracellular trap formation Thyroid hormone signaling pathway Alcoholism Viral carcinogenesis		PPARA activates gene expression Transcriptional activation of mitochondrial biogenesis Constitutive Signaling by NOTCH1 PEST Domain Mutants Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants HDACs deacetylate histones Notch-HLH transcription pathway Transcriptional regulation of white adipocyte differentiation Regulation of lipid metabolism by PPARalpha Circadian Clock NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux HCMV Early Events

Show/Hide Causal Diseases (1)

Disease term	Disease name	dbSNP ID	References
Causal
Schizophrenia	Schizophrenia	rs13447324, rs387906932, rs387906933, rs863223354, rs863223355, rs776061422, rs863223349, rs748809996, rs759748655, rs863223353, rs863223350, rs863223356, rs781821239, rs863223348, rs863223346 View all (12 more)	25445625, 17961987, 25196196, 20471694

Show/Hide Unknown Diseases (1)

Disease term	Disease name	Evidence	References	Source
Unknown
Neurodevelopmental Disorders	complex neurodevelopmental disorder, neurodevelopmental disorder			GenCC

Show/Hide Text Mining Associations (101)

Disease Name	Relationship Type	References
Associations from Text Mining
Adenocarcinoma	Associate	25644061
Adenocarcinoma of Lung	Associate	20563766, 37553641, 38149244
Anemia Diamond Blackfan	Associate	34036344
Arthritis Rheumatoid	Associate	27457515
Arthritis Rheumatoid	Inhibit	30402512
Astrocytoma	Associate	21143702
Brain Neoplasms	Stimulate	32686908
Breast Neoplasms	Associate	17699109, 20473547, 23627572, 29680858, 31084542, 32455774, 32686908, 33962648, 37414914
Burkitt Lymphoma	Stimulate	34658308
Calcinosis	Inhibit	34980138
Calcinosis Cutis	Associate	25836739
Carcinogenesis	Associate	23894374, 37632052
Carcinoma Hepatocellular	Associate	21206745, 25892518, 32021097, 34319031, 35187863, 37632052
Carcinoma Hepatocellular	Stimulate	27342975, 27758890
Carcinoma Non Small Cell Lung	Associate	22965008, 24760274
Carcinoma Ovarian Epithelial	Associate	18714364, 24774302
Carcinoma Renal Cell	Associate	19099586, 33137873
Cerebrovascular Disorders	Associate	30347434
Chordoma	Associate	23893747
Colonic Neoplasms	Stimulate	16533812
Colonic Neoplasms	Associate	18769117
Colorectal Neoplasms	Associate	16533812, 18769117, 24324066, 29558042
Coronary Disease	Associate	32513988
COVID 19	Associate	36840831
Craniopharyngioma	Associate	34980138
Diabetes Mellitus Type 2	Stimulate	27904654
Diabetes Mellitus Type 2	Associate	30139387
Diabetic Foot	Associate	33096729
Drug Related Side Effects and Adverse Reactions	Associate	23913134, 36870998
Duodenitis	Stimulate	16533812
Emphysema	Inhibit	37373058
Encephalitis Herpes Simplex	Stimulate	19099586
Endometrial Neoplasms	Associate	21543766
Esophageal Neoplasms	Associate	25644061
Friedreich Ataxia	Associate	24933366
Glioma	Associate	17007107, 25940092, 35545840, 37528157
Glioma	Stimulate	30654849
Headache Disorders Secondary	Associate	26542778
Hematologic Diseases	Stimulate	36293392
Hepatitis C	Associate	29680858
Hepatitis C Chronic	Associate	37632052
Hereditary leiomyomatosis and renal cell cancer	Associate	29481474
Hodgkin Disease	Associate	29481474
Huntington Disease	Associate	22741533
Idiopathic Pulmonary Fibrosis	Inhibit	37048093
Inflammation	Associate	27457515, 35618935
Insulin Resistance	Associate	27904654
Kidney Neoplasms	Associate	19099586
Leiomyoma	Associate	31761932
Leiomyosarcoma	Associate	36497061
Leukemia	Associate	35371279, 36894687
Leukemia Lymphocytic Chronic B Cell	Associate	23108383
Leukemia Myeloid Acute	Associate	29781401, 34016956, 34665271, 36424383
Leukemia Myeloid Acute	Stimulate	35371279
Leukemia Promyelocytic Acute	Associate	36894687
Lung Neoplasms	Associate	20563766, 30258097
Lung Neoplasms	Stimulate	24441677
Lupus Erythematosus Systemic	Inhibit	25611806
Lymphatic Metastasis	Stimulate	25521755, 26918727
Lymphoma	Stimulate	34658308
Lymphoma B Cell	Associate	22002311
Lymphoma Large B Cell Diffuse	Associate	22116549
Lymphoma Mantle Cell	Associate	22002311
Lymphoma Non Hodgkin	Associate	23992009
Lymphoma T Cell Cutaneous	Associate	23894374
Melanoma	Associate	25521755, 25836739, 30936219
Mental Disorders	Associate	28094813
Mitochondrial Diseases	Associate	37655754
Multiple Myeloma	Associate	23913134, 25482492, 36846090
Multiple Sclerosis	Stimulate	21346816
Neoplasm Metastasis	Associate	32686908, 35468964
Neoplasms	Associate	12502735, 15720800, 16309230, 17007107, 19099586, 21143702, 21206745, 21346816, 22964155, 23627572, 23894374, 23992009, 25482492, 25521755, 26918727 View all (7 more)
Neoplasms	Stimulate	25940092
Neoplasms Squamous Cell	Stimulate	22029821
Neuroblastoma	Associate	38063204
Neuroectodermal Tumors Primitive	Associate	30223590
Neuroendocrine Tumors	Associate	30223590
Neurologic Manifestations	Associate	30347434
Obesity	Associate	37174649
Obsessive Compulsive Disorder	Associate	34730715
Osteoglophonic dwarfism	Stimulate	30347434
Osteosarcoma	Associate	28984297
Ovarian Neoplasms	Associate	17387270
Pancreatic Neoplasms	Associate	20484017, 25275504, 26918727, 32398667
Precursor T Cell Lymphoblastic Leukemia Lymphoma	Associate	20636436
Prostatic Neoplasms	Associate	18212746, 22531786, 25991668, 27462923, 35468964
Pulmonary Disease Chronic Obstructive	Associate	37373058
Schizophrenia	Associate	17961987
Spinal Cord Injuries	Associate	25973054, 33637528
Spondylitis Ankylosing	Associate	26531724
Squamous Cell Carcinoma of Head and Neck	Associate	36505439
Stomach Neoplasms	Associate	28951520, 34284078
Thrombosis	Associate	17675290
Urethral Neoplasms	Associate	27250763
Urinary Bladder Neoplasms	Associate	35035776
Uterine Cervical Dysplasia	Associate	22029821
Uterine Diseases	Associate	18714364
Uveal melanoma	Associate	35332245
Varicose Veins	Associate	36293392
Virus Diseases	Associate	22685561
Xeroderma Pigmentosum Complementation Group C	Associate	32527949

HDAC3 (histone deacetylase 3)