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HDAC4 (histone deacetylase 4)

Gene
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.
9759
Gene nameGene Name - the full gene name approved by the HGNC.
Histone deacetylase 4
Gene symbolGene Symbol - the official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name.
HDAC4
SynonymsGene synonyms aliases
AHO3, BDMR, HA6116, HD4, HDAC-4, HDAC-A, HDACA, NEDCHF, NEDCHID
ChromosomeChromosome number
2
Chromosome locationChromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.
2q37.3
SummarySummary 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
SNPsSNP information provided by dbSNP.
SNP ID Visualize variation Clinical significance Consequence
rs115552422 C>G,T Conflicting-interpretations-of-pathogenicity Coding sequence variant, missense variant
rs138137158 C>T Conflicting-interpretations-of-pathogenicity Synonymous variant, coding sequence variant
rs139841625 G>A Conflicting-interpretations-of-pathogenicity Coding sequence variant, synonymous variant
rs142279745 G>A Conflicting-interpretations-of-pathogenicity Coding sequence variant, synonymous variant
rs148880349 G>A Conflicting-interpretations-of-pathogenicity Genic upstream transcript variant, upstream transcript variant, coding sequence variant, synonymous variant
miRNAmiRNA information provided by mirtarbase database.
miRTarBase ID miRNA Experiments Reference
MIRT001053 hsa-miR-1-3p Western blot 18818206
MIRT000693 hsa-miR-140-5p qRT-PCR, Western blot 19734943
MIRT001053 hsa-miR-1-3p Luciferase reporter assay 18818206
MIRT000693 hsa-miR-140-5p Luciferase reporter assay 19734943
MIRT001053 hsa-miR-1-3p Review 19815577
Transcription factors
Transcription factor Regulation Reference
SP1 Activation 16280357
SP3 Activation 16280357
Gene ontology (GO)Gene ontology information of associated ontologies with gene provided by GO database.
GO ID Ontology Definition Evidence Reference
GO:0000118 Component Histone deacetylase complex IDA 11804585
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IDA 10869435, 16236793
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IGI 15743821
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IMP 18850004, 19276356
GO:0000976 Function Transcription regulatory region sequence-specific DNA binding IDA 18850004
Other IDsOther ids provides unique ids of gene in databases such as OMIM, HGNC, ENSEMBLE.
MIM
HGNC
e!Ensembl
Protein
UniProt ID P56524
Protein name Histone deacetylase 4 (HD4) (EC 3.5.1.98)
Protein function Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell c
PDB 2H8N , 2O94 , 2VQJ , 2VQM , 2VQO , 2VQQ , 2VQV , 2VQW , 3UXG , 3UZD , 3V31 , 4CBT , 4CBY , 5A2S , 5ZOO , 5ZOP , 6FYZ , 7XUZ , 8PDE
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF12203 HDAC4_Gln
62 152
Glutamine rich N terminal domain of histone deacetylase 4
Family
PF00850 Hist_deacetyl
675 992
Histone deacetylase domain
Domain
Sequence
MSSQSHPDGLSGRDQPVELLNPARVNHMPSTVDVATALPLQVAPSAVPMDLRLDHQFSLP
VAEPALREQQLQQELLALKQKQQIQRQILIAEFQRQHEQLSRQHEAQLHEHIKQQQEMLA
MKHQQELLEHQRKLERHRQEQELEKQHREQKL
QQLKNKEKGKESAVASTEVKMKLQEFVL
NKKKALAHRNLNHCISSDPRYWYGKTQHSSLDQSSPPQSGVSTSYNHPVLGMYDAKDDFP
LRKTASEPNLKLRSRLKQKVAERRSSPLLRRKDGPVVTALKKRPLDVTDSACSSAPGSGP
SSPNNSSGSVSAENGIAPAVPSIPAETSLAHRLVAREGSAAPLPLYTSPSLPNITLGLPA
TGPSAGTAGQQDAERLTLPALQQRLSLFPGTHLTPYLSTSPLERDGGAAHSPLLQHMVLL
EQPPAQAPLVTGLGALPLHAQSLVGADRVSPSIHKLRQHRPLGRTQSAPLPQNAQALQHL
VIQQQHQQFLEKHKQQFQQQQLQMNKIIPKPSEPARQPESHPEETEEELREHQALLDEPY
LDRLPGQKEAHAQAGVQVKQEPIESDEEEAEPPREVEPGQRQPSEQELLFRQQALLLEQQ
RIHQLRNYQASMEAAGIPVSFGGHRPLSRAQSSPASATFPVSVQEPPTKPRFTTGLVYDT
LMLKHQCTCGSSSSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHT
LLYGTNPLNRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTIWNEVHSAGAARLAVGCVVE
LVFKVATGELKNGFAVVRPPGHHAEESTPMGFCYFNSVAVAAKLLQQRLSVSKILIVDWD
VHHGNGTQQAFYSDPSVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGFNVNMAFTGGLDP
PMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLGGYNLSARCFGYLTKQL
MGLAGGRIVLALEGGHDLTAICDASEACVSAL
LGNELDPLPEKVLQQRPNANAVRSMEKV
MEIHSKYWRCLQRTTSTAGRSLIEAQTCENEEAETVTAMASLSVGVKPAEKRPDEEPMEE
EPPL
Sequence length 1084
Interactions View interactions
PathwaysPathway information has different metabolic/signaling pathways associated with genes. Each record is hyperlinked to a complete information page which also includes links to the KEGG/Reactome pathway database.
 
KEGG
 
Reactome
  Apelin signaling pathway
Neutrophil extracellular trap formation
Alcoholism
Viral carcinogenesis
MicroRNAs in cancer
  Constitutive Signaling by NOTCH1 PEST Domain Mutants
Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants
Notch-HLH transcription pathway
SUMOylation of intracellular receptors
SUMOylation of chromatin organization proteins
RUNX3 regulates p14-ARF
Associated diseases
Causal
Disease name Disease term dbSNP ID References
2q37 deletion syndrome Chromosome 2q37 deletion syndrome, 2q37 microdeletion syndrome rs748900140, rs1064797002 20691407, 25402011, 19365831, 23188045
Attention deficit hyperactivity disorder Attention deficit hyperactivity disorder rs120074176, rs786205019
Autism Autistic Disorder rs121964908, rs121912597, rs2710102, rs7794745, rs142990298, rs62643608, rs181327458, rs797046134, rs869312704, rs1555013332, rs876657679, rs1057518999, rs1057518658, rs771827120, rs1555187899, rs773080572, rs753871454, rs1684130791, rs1684180699, rs1553510219, rs1684182454, rs1559060428, rs1553510677, rs1576352885, rs1574152522, rs1574152672, rs1696658542, rs1751123722, rs1750373491, rs1751075634
Brachydactyly Brachydactyly rs121908949, rs28937580, rs121909082, rs104894122, rs863223289, rs863223290, rs104894121, rs1587657302, rs863223292, rs74315386, rs74315387, rs28936397, rs753691079, rs121909348, rs121917852, rs121917853, rs121917854, rs121917855, rs121917859, rs121917861, rs267606873, rs267606872, rs267606985, rs267606986, rs267606987, rs267606988, rs28933082, rs397514519, rs869025613, rs869025614, rs886039878, rs1553540620, rs1057518333, rs1948841937, rs1948868228, rs1948842030, rs1948842142 20691407
Unknown
Disease name Disease term dbSNP ID References
Accessory nipple Accessory nipple
Urinary bladder cancer Malignant neoplasm of urinary bladder 21507255
Bladder neoplasm Bladder Neoplasm 21507255
Camptodactyly of fingers Clinodactyly of the 5th finger

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