BDgene

Core Gene from Gene Prioritization Pathways from PBA (Pathway-based Analysis) Enriched Pathways for Core Genes Enriched Pathways for Cross-disorder Genes

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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	HTR4
Symbol Alias	5-HT4
Approved Name	5-hydroxytryptamine (serotonin) receptor 4, G protein-coupled
Previous Name	5-hydroxytryptamine (serotonin) receptor 4
Location	5q31-q33
Position	chr5:148451032-148677235, -1
External Links	HGNC: 5299 Entrez Gene: 3360 Ensembl: ENSG00000164270 UCSC: uc021yfj.1
No. of Studies	2 (Positive: 1; Negative: 1; trend: 0)
Overlap with SZ?	YES
Overlap with MDD?	YES

Gene related studies (count: 2)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Yosifova, A.,2009	SNP: rs2278392	No SNP of this gene had significant association with BD in our population.	Negative	Comment on Study
Ohtsuki, T.,2002	Haplotype: (HTR4_SVRSNP1) - (HTR4_SVRSNP4)(C-A), (HTR4_SVRSNP1) - (HTR4_SVRSNP4)(C-G), (HTR4_SVRSNP1) - (HTR4_SVRSNP4)(T-G) Other variant: HTR4_IVS1+15T/C, HTR4_IVS3+63C/T, HTR4_IVS3+6G/A, HTR4_IVS4+36T/C, HTR4_SVRSNP1, HTR4_SVRSNP2, HTR4_SVRSNP3, HTR4_SVRSNP4	These findings suggest that genomic variations in the HTR4 gene may confer susceptibility to mood disorder.	Positive	Comment on Study

Gene functional annotation

Gene related GO terms (count: 15)

GO terms by PBA (count: 4)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0007268	synaptic transmission	biological process	IEA	116
GO:0005887	integral component of plasma membrane	cellular component	IEA	158
GO:0005886	plasma membrane	cellular component	TAS	360
GO:0016020	membrane	cellular component	IDA[16102731]	137

GO terms by database search (count: 11)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0007187	G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger	biological process	TAS[9603189]	17
GO:0032098	regulation of appetite	biological process	IEA	2
GO:0004993	serotonin receptor activity	molecular function	IDA[16102731]	12
GO:0007210	serotonin receptor signaling pathway	biological process	IDA[16102731]; IEA; TAS[9603189]	12
GO:0005737	cytoplasm	cellular component	IDA[15925089]	322
GO:0010579	positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway	biological process	IBA	16
GO:0007214	gamma-aminobutyric acid signaling pathway	biological process	IBA	15
GO:0005768	endosome	cellular component	IEA	27
GO:0007186	G-protein coupled receptor signaling pathway	biological process	TAS[9351641]	64
GO:0007606	sensory perception of chemical stimulus	biological process	IBA	14
GO:0001594	trace-amine receptor activity	molecular function	IBA	4

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
HTR4	ADRB2	YES	in vitro	15896782

Related other genetic factors

Gene related SNPs (count: 10)

Literature-origin SNPs (count: 2)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs5028114	chr5:148632176 - 148632176(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1(1/0/0)
rs2278392	chr5:148548662 - 148548662(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; splice_region_variant	1(0/1/0)

LD-proxies (count: 8)

rs_ID	Location	Functional Annotation
rs12332417	chr5:148556557 - 148556557(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs12055273	chr5:148555164 - 148555164(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs13359903	chr5:148548336 - 148548336(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs11168050	chr5:148551960 - 148551960(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs7701432	chr5:148619016 - 148619016(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs10223307	chr5:148616524 - 148616524(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs867522	chr5:148586683 - 148586683(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs17720733	chr5:148570915 - 148570915(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant

Gene related CNVs (count: 0)

Gene related other variants (count: 8)

Variant Name	Variant Type	No. of Studies (Positive/Negative/Trend)
HTR4_IVS1+15T/C	point mutation	1 (0/1/0)
HTR4_IVS3+6G/A	point mutation	1 (0/1/0)
HTR4_IVS3+63C/T	point mutation	1 (0/1/0)
HTR4_SVRSNP1	point mutation	1 (1/0/0)
HTR4_IVS4+36T/C	point mutation	1 (0/1/0)
HTR4_SVRSNP3	point mutation	1 (1/0/0)
HTR4_SVRSNP2	point mutation	1 (1/0/0)
HTR4_SVRSNP4	point mutation	1 (1/0/0)

Gene related regions (count: 4)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
Chr 5	chr5:0-181538259	3 (0/2/1)
5q31-q33	chr5:131200000-160500000	1 (1/0/0)
5q32	chr5:145100000-150400000	2 (0/2/0)
5q32-5q33.3	chr5:145100000-160500000	1 (0/1/0)

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
12399948	These findings suggest that genomic variations in the HTR4 gene may confer susceptibility to mood disorder.	Negative

Overlap with SZ from candidate gene intersection analysis (count: 3)

Reference	ID in SZGene	Result Category
19892407	336	Trend
12399948	336	Negative
12898568	336	Positive

Gene relationship with MDD

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

Reference	Description	Category in MDD
12399948	These findings suggest that genomic variations in the HTR4 gene may confer susceptibility to mood disorder.	Positive

Overlap with MDD from candidate gene intersection analysis (count: 1)

Reference	Description	Category in MDD	Link in MK4MDD
15303102	Genes altered in major depressive disorder	Pos	HTR4

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Region: chr5:148451032..148677235 View in gBrowse