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	HTR6
Symbol Alias	5-HT6, 5-HT6R
Approved Name	5-hydroxytryptamine (serotonin) receptor 6, G protein-coupled
Previous Name	5-hydroxytryptamine (serotonin) receptor 6
Location	1p36-p35
Position	chr1:19665287-19679562, 1
External Links	HGNC: 5301 Entrez Gene: 3362 Ensembl: ENSG00000158748 UCSC: uc001bcl.4
No. of Studies	3 (Positive: 1; Negative: 2; trend: 0)
Overlap with SZ?	YES
Overlap with MDD?	YES

Gene related studies (count: 3)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Hong, C. J.,1999	Other variant: HTR6_267C/T	The results demonstrated that there were no significant differences in genotype or allele frequencies between controls and all patients, or between controls and patients with bipolar disorders or major depression, separately.	Negative	Comment on Study
Vogt, I. R.,2000	Other variant: HTR6_126G/T, HTR6_873+30C/T, HTR6_267C/T, HTR6_873+128A/C	Our preliminary data suggest that bipolar affective disorder may be associated with variation in the 5-HT(6) gene.	Positive	Comment on Study
Fukuo, Y.,2010	SNP: rs1805054, rs3790757, rs4912138, rs6693503, rs9659997 Haplotype: rs1805054 - rs4912138(), rs1805054 - rs4912138 - rs3790757(), rs1805054 - rs4912138 - rs3790757 - rs9659997(), rs3790757 - rs9659997(), rs4912138 - rs3790757(), rs4912138 - rs3790757 - rs9659997(), rs6693503 - rs1805054(), rs6693503 - rs1805054 - rs4912138(), rs6693503 - rs1805054 - rs4912138 - rs3790757(), rs6693503 - rs1805054 - rs4912138 - rs3790757 - rs9659997()	In conclusion, we found no association involving polymorphism and mood disorder in the Japanese population.	Negative	Comment on Study

Gene functional annotation

Gene related GO terms (count: 21)

GO terms by PBA (count: 3)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0005887	integral component of plasma membrane	cellular component	TAS[8522988]	158
GO:0007268	synaptic transmission	biological process	TAS[8522988]	116
GO:0005886	plasma membrane	cellular component	TAS	360

GO terms by database search (count: 18)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0033603	positive regulation of dopamine secretion	biological process	IEA	4
GO:0042493	response to drug	biological process	IEA	57
GO:0060291	long-term synaptic potentiation	biological process	IEA	14
GO:0032008	positive regulation of TOR signaling	biological process	IDA[23027611]	4
GO:0004969	histamine receptor activity	molecular function	TAS[8522988]	1
GO:0014053	negative regulation of gamma-aminobutyric acid secretion	biological process	IEA	1
GO:0014058	negative regulation of acetylcholine secretion, neurotransmission	biological process	IEA	1
GO:0004993	serotonin receptor activity	molecular function	IEA	12
GO:0021795	cerebral cortex cell migration	biological process	ISS	2
GO:0005929	cilium	cellular component	IEA	10
GO:0007210	serotonin receptor signaling pathway	biological process	IEA	12
GO:0014050	negative regulation of glutamate secretion	biological process	IEA	4
GO:0005515	protein binding	molecular function	IPI[17189269]	563
GO:0014054	positive regulation of gamma-aminobutyric acid secretion	biological process	IEA	3
GO:0007612	learning	biological process	IEA	18
GO:0032355	response to estradiol	biological process	IEA	11
GO:0007187	G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger	biological process	IEA	17
GO:0030425	dendrite	cellular component	IEA	65

Gene related KEGG pathways (count: 2)

KEGG pathways by PBA (count: 1)

ID	Name	No. of Genes in BDgene	Brief Description
hsa04020	Calcium signaling pathway	53

KEGG pathways by database search (count: 1)

ID	Name	No. of Genes in BDgene	Brief Description
hsa04080	Neuroactive ligand-receptor interaction	92

Gene related BioCarta pathways (count: 0)

Gene related interactors from protein-protein interactions data in HPRD (count: 1)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
HTR6	GNAQ	NO	in vivo	12650852

Related other genetic factors

Gene related SNPs (count: 16)

Literature-origin SNPs (count: 5)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs9659997	chr1:19676025 - 19676025(1)	intron_variant	1(0/1/0)
rs4912138	chr1:19666992 - 19666992(1)	intron_variant	1(0/1/0)
rs1805054	chr1:19666020 - 19666020(1)	synonymous_variant	1(0/1/0)
rs6693503	chr1:19660801 - 19660801(1)	downstream_gene_variant; upstream_gene_variant	1(0/1/0)
rs3790757	chr1:19671415 - 19671415(1)	intron_variant	1(0/1/0)

LD-proxies (count: 11)

rs_ID	Location	Functional Annotation
rs6658108	chr1:19668998 - 19668998(1)	intron_variant
rs1977101	chr1:19662401 - 19662401(1)	downstream_gene_variant; upstream_gene_variant
rs10917512	chr1:19679978 - 19679978(1)	downstream_gene_variant
rs4912141	chr1:19675403 - 19675403(1)	intron_variant
rs3790756	chr1:19669739 - 19669739(1)	intron_variant
rs1883565	chr1:19682014 - 19682014(1)	downstream_gene_variant
rs10917513	chr1:19680394 - 19680394(1)	downstream_gene_variant
rs10799831	chr1:19682107 - 19682107(1)	downstream_gene_variant
rs6699866	chr1:19673152 - 19673152(1)	intron_variant
rs2872594	chr1:19669700 - 19669700(1)	intron_variant
rs10917509	chr1:19665573 - 19665573(1)	5_prime_UTR_variant

Gene related CNVs (count: 0)

Gene related other variants (count: 4)

Variant Name	Variant Type	No. of Studies (Positive/Negative/Trend)
HTR6_126G/T	point mutation	1 (0/1/0)
HTR6_873+128A/C	point mutation	1 (1/0/0)
HTR6_267C/T	point mutation	2 (1/1/0)
HTR6_873+30C/T	point mutation	1 (0/1/0)

Gene related regions (count: 4)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
1p35-p36	chr1:0-34300000	1 (1/0/0)
1p33-p36	chr1:0-50200000	1 (0/0/1)
1p36	chr1:0-27600000	1 (0/1/0)
Chr 1	chr1:0-248956422	2 (0/2/0)

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

Gene relationship with SZ

Overlap with SZ from cross-disorder studies (count: 1)

Reference	Description	Result Category
10893499	In schizophrenia patients no significant difference was observed.	Negative

Overlap with SZ from candidate gene intersection analysis (count: 6)

Reference	ID in SZGene	Result Category
10206228	248	Negative
15048641	248	Negative
11524147	248	Negative
11287786	248	Negative
10893499	248	Negative
10477121	248	Positive

Gene relationship with MDD

Overlap with MDD from cross-disorder studies (count: 2)

Reference	Description	Category in MDD
20394784	In conclusion, we found no association involving polymorphism and mood disorder in the Japanese population.	Negative
10581475	The results demonstrated that there were no significant differences in genotype or allele frequencies between controls and all patients, or between controls and patients with bipolar disorders or major depression, separately.	Negative

Overlap with MDD from candidate gene intersection analysis (count: 0)

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Region: chr1:19665287..19679562 View in gBrowse