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.	55869
Gene name Gene Name - the full gene name approved by the HGNC.	Histone deacetylase 8
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	HDAC8
Synonyms (NCBI Gene) Gene synonyms aliases	CDA07, CDLS5, HD8, HDACL1, KDAC8, MRXS6, RPD3, WTS
Chromosome Chromosome number	X
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	Xq13.1
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

Show/Hide all(46)

SNP ID	Visualize variation	Clinical significance	Consequence
rs146015223	G>A,T	Benign, pathogenic	5 prime UTR variant, stop gained, synonymous variant, intron variant, non coding transcript variant, genic downstream transcript variant, coding sequence variant
rs397515415	G>A,T	Pathogenic	Coding sequence variant, 5 prime UTR variant, synonymous variant, stop gained, non coding transcript variant, intron variant, genic downstream transcript variant
rs397515416	T>C	Pathogenic	Missense variant, coding sequence variant, 5 prime UTR variant, non coding transcript variant, intron variant, genic downstream transcript variant
rs397515417	G>A	Pathogenic	Non coding transcript variant, genic downstream transcript variant, missense variant, coding sequence variant
rs397515418	T>C	Pathogenic	Non coding transcript variant, genic downstream transcript variant, missense variant, coding sequence variant
rs398122888	C>T	Pathogenic	Intron variant
rs398122909	C>T	Uncertain-significance, pathogenic	Non coding transcript variant, genic downstream transcript variant, missense variant, coding sequence variant
rs587779380	G>A	Pathogenic	Missense variant, 5 prime UTR variant, non coding transcript variant, intron variant, coding sequence variant
rs587783663	A>-	Pathogenic	Non coding transcript variant, stop gained, 5 prime UTR variant, coding sequence variant
rs797045610	TCAA>-	Pathogenic	Frameshift variant, non coding transcript variant, 5 prime UTR variant, coding sequence variant
rs797045611	G>A	Pathogenic	Non coding transcript variant, intron variant, stop gained, 5 prime UTR variant, coding sequence variant
rs797045612	C>T	Likely-pathogenic	Genic downstream transcript variant, non coding transcript variant, intron variant, missense variant, 5 prime UTR variant, coding sequence variant
rs797045613	G>T	Likely-pathogenic	Missense variant, genic downstream transcript variant, coding sequence variant, non coding transcript variant
rs863224877	T>C	Likely-pathogenic	Splice acceptor variant, genic downstream transcript variant
rs869312660	C>T	Likely-pathogenic	Intron variant, genic downstream transcript variant, splice donor variant
rs878853048	C>G	Uncertain-significance, likely-pathogenic	Non coding transcript variant, intron variant, missense variant, 5 prime UTR variant, coding sequence variant
rs886039706	C>A	Pathogenic	Stop gained, genic downstream transcript variant, coding sequence variant, non coding transcript variant
rs886041838	G>A	Pathogenic	Stop gained, genic downstream transcript variant, coding sequence variant, non coding transcript variant
rs886041936	G>A	Pathogenic	Genic downstream transcript variant, non coding transcript variant, intron variant, stop gained, 5 prime UTR variant, coding sequence variant
rs1057516037	TGGAG>AC	Likely-pathogenic	Coding sequence variant, inframe indel, genic downstream transcript variant, non coding transcript variant
rs1057518047	C>A	Likely-pathogenic	5 prime UTR variant, missense variant, coding sequence variant, intron variant, non coding transcript variant
rs1057518126	A>T	Likely-pathogenic	Missense variant, genic downstream transcript variant, coding sequence variant, intron variant, non coding transcript variant
rs1057518727	T>C	Likely-pathogenic	5 prime UTR variant, missense variant, genic downstream transcript variant, coding sequence variant, intron variant, non coding transcript variant
rs1057524379	A>G	Likely-pathogenic	Missense variant, coding sequence variant, genic downstream transcript variant, non coding transcript variant
rs1064793856	T>C	Pathogenic	Splice acceptor variant, intron variant
rs1064796517	CC>AG	Likely-pathogenic	5 prime UTR variant, coding sequence variant, splice donor variant, non coding transcript variant
rs1131691579	C>A	Likely-pathogenic	Missense variant, genic downstream transcript variant, coding sequence variant, intron variant, non coding transcript variant
rs1555948969	G>A	Likely-pathogenic	Genic downstream transcript variant, non coding transcript variant, stop gained, coding sequence variant
rs1555949010	T>C,G	Uncertain-significance, likely-pathogenic	Genic downstream transcript variant, non coding transcript variant, missense variant, coding sequence variant
rs1555991936	G>T	Pathogenic	Genic downstream transcript variant, non coding transcript variant, stop gained, coding sequence variant
rs1555991965	C>-	Pathogenic	Genic downstream transcript variant, non coding transcript variant, splice acceptor variant, coding sequence variant
rs1555993215	GCTTGGT>-	Pathogenic	Genic downstream transcript variant, non coding transcript variant, frameshift variant, coding sequence variant
rs1555993243	C>-	Pathogenic	Genic downstream transcript variant, splice acceptor variant
rs1556007534	G>A	Likely-pathogenic	Intron variant, non coding transcript variant, missense variant, genic downstream transcript variant, coding sequence variant
rs1556009247	A>C,T	Likely-pathogenic	Intron variant, non coding transcript variant, missense variant, genic downstream transcript variant, coding sequence variant, 5 prime UTR variant
rs1556165162	GG>-	Pathogenic	Non coding transcript variant, 5 prime UTR variant, coding sequence variant, frameshift variant
rs1569316085	G>A	Pathogenic	Coding sequence variant, non coding transcript variant, stop gained, genic downstream transcript variant
rs1569317995	C>G	Likely-pathogenic	Coding sequence variant, missense variant, non coding transcript variant, genic downstream transcript variant
rs1569318004	C>T	Likely-pathogenic	Coding sequence variant, missense variant, non coding transcript variant, genic downstream transcript variant
rs1602491207	TTCCCTGCA>-	Pathogenic	Splice acceptor variant, coding sequence variant, intron variant, non coding transcript variant, genic downstream transcript variant
rs1602975122	A>G	Likely-pathogenic	Coding sequence variant, missense variant, non coding transcript variant, genic downstream transcript variant
rs1602975455	G>A	Likely-pathogenic	Coding sequence variant, missense variant, non coding transcript variant, genic downstream transcript variant
rs1602975601	C>T	Pathogenic	Splice acceptor variant, genic downstream transcript variant
rs1603060007	C>T	Likely-pathogenic	Genic downstream transcript variant, coding sequence variant, intron variant, non coding transcript variant, missense variant
rs1603069440	C>T	Pathogenic	Missense variant, coding sequence variant, 5 prime UTR variant, intron variant, non coding transcript variant, genic downstream transcript variant
rs1603083434	T>C	Likely-pathogenic	Missense variant, coding sequence variant, 5 prime UTR variant, intron variant, non coding transcript variant, genic downstream transcript variant

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miRTarBase ID	miRNA	Experiments	Reference
MIRT003761	hsa-miR-449a	Western blot	19252524
MIRT440521	hsa-miR-218-5p	HITS-CLIP	23212916
MIRT440521	hsa-miR-218-5p	HITS-CLIP	23212916
MIRT731866	hsa-miR-216b-5p	Flow, Luciferase reporter assay, qRT-PCR, Western blot	26408293
MIRT731866	hsa-miR-216b-5p	Flow, Luciferase reporter assay, qRT-PCR, Western blot	26408293
MIRT755711	hsa-miR-497�3p	Luciferase reporter assay, Western blotting, qRT-PCR, Immunofluorescence	38577018
MIRT1042544	hsa-miR-1226	CLIP-seq
MIRT1042545	hsa-miR-3591-3p	CLIP-seq
MIRT1042546	hsa-miR-101	CLIP-seq
MIRT1042547	hsa-miR-1278	CLIP-seq
MIRT1042548	hsa-miR-221	CLIP-seq
MIRT1042549	hsa-miR-222	CLIP-seq
MIRT1042550	hsa-miR-452	CLIP-seq
MIRT1042551	hsa-miR-4676-3p	CLIP-seq
MIRT1042552	hsa-miR-548v	CLIP-seq
MIRT1042553	hsa-miR-3974	CLIP-seq
MIRT1042554	hsa-miR-570	CLIP-seq
MIRT1042555	hsa-miR-3121-3p	CLIP-seq
MIRT1042556	hsa-miR-376c	CLIP-seq
MIRT1042557	hsa-miR-3938	CLIP-seq
MIRT1042558	hsa-miR-450b-5p	CLIP-seq
MIRT1042559	hsa-miR-4726-3p	CLIP-seq
MIRT1042560	hsa-miR-4778-3p	CLIP-seq
MIRT1042561	hsa-miR-4789-5p	CLIP-seq
MIRT1042562	hsa-miR-4799-5p	CLIP-seq
MIRT1042563	hsa-miR-548aa	CLIP-seq
MIRT1042564	hsa-miR-642a	CLIP-seq
MIRT1042555	hsa-miR-3121-3p	CLIP-seq
MIRT1042556	hsa-miR-376c	CLIP-seq
MIRT1042561	hsa-miR-4789-5p	CLIP-seq
MIRT2451051	hsa-miR-216b	CLIP-seq
MIRT2451052	hsa-miR-4272	CLIP-seq
MIRT2451053	hsa-miR-4742-3p	CLIP-seq
MIRT2451051	hsa-miR-216b	CLIP-seq
MIRT2451052	hsa-miR-4272	CLIP-seq
MIRT2451053	hsa-miR-4742-3p	CLIP-seq

Transcription factors

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Transcription factor	Regulation	Reference
SOX4	Activation	23482931

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GO ID	Ontology	Definition	Evidence	Reference
GO:0000118	Component	Histone deacetylase complex	IBA
GO:0000118	Component	Histone deacetylase complex	TAS	12711221
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	TAS	10748112
GO:0000228	Component	Nuclear chromosome	TAS	10748112
GO:0004407	Function	Histone deacetylase activity	IBA
GO:0004407	Function	Histone deacetylase activity	IDA	28497810
GO:0004407	Function	Histone deacetylase activity	IEA
GO:0004407	Function	Histone deacetylase activity	TAS	10748112, 12711221
GO:0005515	Function	Protein binding	IPI	16809764, 26221039
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	TAS	12711221
GO:0005654	Component	Nucleoplasm	TAS
GO:0005694	Component	Chromosome	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005737	Component	Cytoplasm	TAS	12711221
GO:0006325	Process	Chromatin organization	IEA
GO:0006325	Process	Chromatin organization	TAS	10748112, 12711221
GO:0007064	Process	Mitotic sister chromatid cohesion	IMP	22885700
GO:0016787	Function	Hydrolase activity	IEA
GO:0030544	Function	Hsp70 protein binding	IPI	16809764
GO:0031397	Process	Negative regulation of protein ubiquitination	IDA	16809764
GO:0031507	Process	Heterochromatin formation	IBA
GO:0031647	Process	Regulation of protein stability	IDA	16809764
GO:0032204	Process	Regulation of telomere maintenance	IMP	16809764
GO:0033558	Function	Protein lysine deacetylase activity	IDA	22885700
GO:0033558	Function	Protein lysine deacetylase activity	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0051879	Function	Hsp90 protein binding	IPI	16809764
GO:0140297	Function	DNA-binding transcription factor binding	TAS	12711221
GO:0141221	Function	Histone deacetylase activity, hydrolytic mechanism	IEA
GO:0160008	Function	Protein decrotonylase activity	IEA
GO:0160009	Function	Histone decrotonylase activity	IDA	28497810

MIM	HGNC	e!Ensembl
300269	13315	ENSG00000147099

Protein

UniProt ID

Q9BY41

Protein name

Histone deacetylase 8 (HD8) (EC 3.5.1.98) (Protein deacetylase HDAC8) (EC 3.5.1.-) (Protein decrotonylase HDAC8) (EC 3.5.1.-)

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) (PubMed:10748112, PubMed:10922473, PubMed:10926844, PubMed:14701748, PubMed:28497810). Histone deacetylatio

PDB

1T64 , 1T67 , 1T69 , 1VKG , 1W22 , 2V5W , 2V5X , 3EW8 , 3EWF , 3EZP , 3EZT , 3F06 , 3F07 , 3F0R , 3MZ3 , 3MZ4 , 3MZ6 , 3MZ7 , 3RQD , 3SFF , 3SFH , 4QA0 , 4QA1 , 4QA2 , 4QA3 , 4QA4 , 4QA5 , 4QA6 , 4QA7 , 4RN0 , 4RN1 , 4RN2 , 5BWZ , 5D1B , 5D1C , 5D1D , 5DC5 , 5DC6 , 5DC7 , 5DC8 , 5FCW , 5THS , 5THT , 5THU , 5THV , 5VI6 , 6HSK , 6ODA , 6ODB , 6ODC , 7JVU

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00850	Hist_deacetyl	31 → 322	Histone deacetylase domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Weakly expressed in most tissues. Expressed at higher level in heart, brain, kidney and pancreas and also in liver, lung, placenta, prostate and kidney. {ECO:0000269|PubMed:10926844, ECO:0000269|PubMed:14701748, ECO:0000269|PubMed:1577

Sequence

MEEPEEPADSGQSLVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPK
VASMEEMATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAAAIGGATI
TAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLH
HGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKY
YQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLI
LGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPH
RIQQILNYIKGNLKHVV

Sequence length

377

Interactions

View interactions

	KEGG		Reactome
	Cell cycle Neutrophil extracellular trap formation Alcoholism Viral carcinogenesis		Separation of Sister Chromatids Resolution of Sister Chromatid Cohesion Constitutive Signaling by NOTCH1 PEST Domain Mutants Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants HDACs deacetylate histones Notch-HLH transcription pathway

Show/Hide Causal Diseases (2)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Cornelia De Lange Syndrome	cornelia de lange syndrome 5, cornelia de lange syndrome 1	rs146015223, rs1602491207, rs797045612, rs1555949010, rs1602975122, rs797045611, rs1569316085, rs1602975601, rs797045610, rs2051897517, rs398122888, rs863224877, rs1569318004, rs2047965357, rs397515415 View all (16 more)	N/A
Mental retardation	intellectual disability	rs1603060007, rs1603069440	N/A

Show/Hide Unknown Diseases (1)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Wilson-Turner Syndrome	Wilson-Turner syndrome	N/A	N/A	GenCC

Show/Hide Text Mining Associations (46)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Acne Vulgaris	Associate	30737272
Aortic Aneurysm Abdominal	Associate	25993293
Autism Spectrum Disorder	Associate	34069769, 35358829
Breast Neoplasms	Associate	29333926, 31817161, 31970414, 32429642
Calcinosis Cutis	Associate	25836739
Carcinogenesis	Associate	16809764, 30292946, 35345359
Carcinoma Pancreatic Ductal	Associate	29374219
Carcinoma Renal Cell	Associate	34308568
Cardiomegaly	Associate	33122805
Colorectal Neoplasms	Associate	25321483, 36575468
Communication Disorders	Associate	35358829
De Lange Syndrome	Associate	22885700, 24403048, 24756084, 24918291, 25075551, 25125236, 25652421, 25655089, 26463496, 26581180, 29991052, 30515000, 30606125, 30614194, 32532882 View all (7 more)
Developmental Disabilities	Associate	33122805, 34069769, 35052418, 36350923
Diabetes Gestational	Associate	34530062
Diabetic Foot	Associate	33096729
Ectodermal Dysplasia	Associate	37887281
Glioblastoma	Associate	34072831
Glioma	Associate	37528157
Hearing Loss	Associate	29293505
Hypertelorism	Associate	24403048
Idiopathic Pulmonary Fibrosis	Associate	30358439
Idiopathic Pulmonary Fibrosis	Stimulate	30358439
Influenza Human	Associate	29888214
Intellectual Disability	Associate	35358829
Leiomyoma	Associate	21685710, 31761932
Leukemia Lymphoma Adult T Cell	Associate	23482931
Lung Neoplasms	Associate	15477595, 28232663
Lymphoma Mantle Cell	Associate	33190829
Melanoma	Stimulate	25836739
Melanoma	Associate	29174371, 38030596
Multiple Myeloma	Associate	25482492
Neoplasm Metastasis	Inhibit	31970414
Neoplasm Metastasis	Associate	35955780, 38030596
Neoplasms	Associate	15477595, 16809764, 22158273, 22272142, 23111066, 24404147, 25089360, 25321483, 25605725, 28390197, 30292946, 32429642, 35345359, 35886887, 35955780
Neoplasms	Stimulate	25482492
Neuroblastoma	Associate	25605725, 29947893, 30292946, 35886887
Osteoarthritis	Associate	30063117
Ovarian Neoplasms	Associate	35955780
Pancreatic Neoplasms	Associate	29374219
Preleukemia	Associate	10922473
Pulmonary Fibrosis	Associate	30358439
Stomach Neoplasms	Stimulate	34232196
Triple Negative Breast Neoplasms	Stimulate	32429642
Urethral Neoplasms	Associate	25011684
Uterine Cervical Neoplasms	Associate	29716651
Volvulus Of Midgut	Associate	30632303

HDAC8 (histone deacetylase 8)