Gene Report

Basic information

Related studies

Functional annotation

Related other genetic factors

Overlap with SZ and MDD

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Basic Info

Approved Symbol	HDAC9
Symbol Alias	KIAA0744, HDAC, MITR, HD7, HDAC7B
Approved Name	histone deacetylase 9
Location	7p21.1
Position	chr7:18086949-19002416, 1
External Links	HGNC: 14065 Entrez Gene: 9734 Ensembl: ENSG00000048052 UCSC: uc003sui.3
No. of Studies	1 (Positive: 1; Negative: 0; trend: 0)
Overlap with SZ?	NO
Overlap with MDD?	NO

Gene related studies (count: 1)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Chen, X., 2015		HDAC9 has been implicated in BPD and mental competency	Positive	Comment on Study

Gene functional annotation

Gene related GO terms (count: 36)

GO terms by PBA (count: 3)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0003714	transcription corepressor activity	molecular function	ISS	21
GO:0006954	inflammatory response	biological process	TAS[12711221]	23
GO:0005634	nucleus	cellular component	IDA[12590135]	283

GO terms by database search (count: 33)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0033558	protein deacetylase activity	molecular function	IDA[11535832]	2
GO:0061647	histone H3-K9 modification	biological process	IEA	2
GO:0045892	negative regulation of transcription, DNA-templated	biological process	IDA[10655483]	43
GO:0097372	NAD-dependent histone deacetylase activity (H3-K18 specific)	molecular function	IEA	1
GO:0005515	protein binding	molecular function	IPI[12590135]	563
GO:0090050	positive regulation of cell migration involved in sprouting angiogenesis	biological process	IMP[19351956]	1
GO:0005667	transcription factor complex	cellular component	IDA[15567413]	18
GO:0007507	heart development	biological process	ISS	20
GO:0007219	Notch signaling pathway	biological process	TAS	14
GO:0004407	histone deacetylase activity	molecular function	IDA[11535832]; IDA[10655483]	2
GO:0034983	peptidyl-lysine deacetylation	biological process	IDA[11535832]	2
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	biological process	IDA[10655483]	62
GO:0006351	transcription, DNA-templated	biological process	IEA	103
GO:0046872	metal ion binding	molecular function	IEA	115
GO:0030183	B cell differentiation	biological process	TAS[12711221]	5
GO:0046970	NAD-dependent histone deacetylase activity (H4-K16 specific)	molecular function	IEA	1
GO:0016575	histone deacetylation	biological process	IDA[11535832]	2
GO:0005654	nucleoplasm	cellular component	TAS	163
GO:0051153	regulation of striated muscle cell differentiation	biological process	ISS	1
GO:0008134	transcription factor binding	molecular function	IDA[11535832]; IPI[10748098]	28
GO:0042113	B cell activation	biological process	TAS[12711221]	3
GO:0070933	histone H4 deacetylation	biological process	IDA[12590135]	2
GO:0048742	regulation of skeletal muscle fiber development	biological process	ISS	1
GO:0070491	repressing transcription factor binding	molecular function	IDA[12590135]; IPI[17360565]; ISS	4
GO:0046969	NAD-dependent histone deacetylase activity (H3-K9 specific)	molecular function	IEA	2
GO:0005737	cytoplasm	cellular component	IDA[12590135]; TAS[12711221]	322
GO:0005080	protein kinase C binding	molecular function	IPI[20188095]	7
GO:0042826	histone deacetylase binding	molecular function	IDA[10655483]; IPI[12590135]	13
GO:0035097	histone methyltransferase complex	cellular component	ISS	1
GO:0032041	NAD-dependent histone deacetylase activity (H3-K14 specific)	molecular function	IEA	1
GO:0032869	cellular response to insulin stimulus	biological process	IDA[19303849]	12
GO:0000118	histone deacetylase complex	cellular component	TAS[12711221]	2
GO:0070932	histone H3 deacetylation	biological process	IDA[12590135]	4

Gene related KEGG pathways (count: 0)

Gene related BioCarta pathways (count: 2)

BioCarta pathways by PBA (count: 0)

BioCarta pathways by database search (count: 2)

ID	Name	No. of Genes in BDgene	Brief Description
MITRPathway	Signal Dependent Regulation of Myogenesis by Corepressor MITR	2
ranbp2Pathway	Sumoylation by RanBP2 Regulates Transcriptional Repression	1

Gene related interactors from protein-protein interactions data in HPRD (count: 15)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
HDAC9	HDAC1	NO	in vitro	12590135
HDAC9	ETV6	NO	in vitro;in vivo	12590135
HDAC9	SIN3A	NO	in vitro;in vivo	12590135
HDAC9	USF1	NO	in vivo	19303849
HDAC9	SIN3B	NO	in vitro;in vivo	12590135
HDAC9	MEF2A	NO	in vitro	10825153
HDAC9	ZBTB16	NO	in vitro	12590135
HDAC9	HDAC4	NO	in vitro;in vivo	12590135
HDAC9	BCL6	NO	in vitro;in vivo	12590135
HDAC9	NCOR1	NO	in vitro;in vivo	12590135 , 11466315
HDAC9	SUMO1	NO	in vitro;in vivo	12590135
HDAC9	CTBP1	NO	in vitro;in vivo;yeast 2-hybrid	11022042
HDAC9	HDAC3	NO	in vitro;in vivo	12590135 , 10655483 , 11466315
HDAC9	SUMO2	NO	in vitro;in vivo	12590135
HDAC9	CBX5	NO	in vitro;in vivo;yeast 2-hybrid	12242305

Related other genetic factors

Gene related SNPs (count: 9)

Literature-origin SNPs (count: 1)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs17350383	chr7:18890590 - 18890590(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1(0/1/0)

LD-proxies (count: 8)

rs_ID	Location	Functional Annotation
rs11768780	chr7:18886960 - 18886960(1)	intron_variant; non_coding_transcript_variant
rs10261390	chr7:18887399 - 18887399(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs17350236	chr7:18884666 - 18884666(1)	intron_variant; non_coding_transcript_variant
rs2024022	chr7:18886480 - 18886480(1)	intron_variant; non_coding_transcript_variant
rs17434924	chr7:18889439 - 18889439(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs17350341	chr7:18888617 - 18888617(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs17350431	chr7:18893487 - 18893487(1)	intron_variant; non_coding_transcript_variant
rs2190278	chr7:18891682 - 18891682(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant

Gene related CNVs (count: 1)

ID	Location	Size	Band	Type	Inheritance
CNV_Zhang[2009]_157	chr7:18172304-18354493 (Affymetrix SNP 6.0 array reference genome)	182189		Singleton deletions

Gene related other variants (count: 0)

Gene related regions (count: 3)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
7p22.2-p21.1	chr7:2800000-20900000	1 (0/0/1)
Chr 7	chr7:0-159345973	3 (0/3/0)
7p21.1	chr7:16500000-20900000	1 (0/0/1)

Overlap with schizophrenia (SZ) and major depressive disorder (MDD)

Gene relationship with SZ

Gene relationship with MDD

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Region: chr7:18086949..19002416 View in gBrowse