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	HNF4A
Previous Symbol	TCF14, MODY, MODY1
Symbol Alias	NR2A1, HNF4
Approved Name	hepatocyte nuclear factor 4, alpha
Location	20q13.12
Position	chr20:44355700-44434596, 1
External Links	HGNC: 5024 Entrez Gene: 3172 Ensembl: ENSG00000101076 UCSC: uc002xma.4
No. of Studies	1 (Positive: 1; Negative: 0; trend: 0)
Overlap with SZ?	YES
Overlap with MDD?	NO

Gene related studies (count: 1)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Kajio, Y., 2014	SNP: rs4812829	SNPs in SLC30A8 (rs3802177, Puncorrected=0.042) and HNF4A(rs4812829, Puncorrected=0.0082), which showed the opposite direction of effect.	Positive	Comment on Study

Gene functional annotation

Gene related GO terms (count: 44)

GO terms by PBA (count: 7)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0004879	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity	molecular function	IEA	7
GO:0005102	receptor binding	molecular function	IDA[12220494]	37
GO:0003707	steroid hormone receptor activity	molecular function	IEA	10
GO:0003700	sequence-specific DNA binding transcription factor activity	molecular function	IDA[10330009]	66
GO:0005634	nucleus	cellular component	IDA[14563941]	283
GO:0030522	intracellular receptor signaling pathway	biological process	IEA	8
GO:0003677	DNA binding	molecular function	IDA[10551874]	83

GO terms by database search (count: 37)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0005504	fatty acid binding	molecular function	IDA[12220494]	1
GO:0006591	ornithine metabolic process	biological process	IMP[17827783]	1
GO:0010470	regulation of gastrulation	biological process	IEA	1
GO:0000979	RNA polymerase II core promoter sequence-specific DNA binding	molecular function	IEA	9
GO:0019216	regulation of lipid metabolic process	biological process	IDA[10551874]	3
GO:0042803	protein homodimerization activity	molecular function	IDA[12220494]	71
GO:0008285	negative regulation of cell proliferation	biological process	IMP[18163890]	41
GO:0008270	zinc ion binding	molecular function	IEA	77
GO:0007548	sex differentiation	biological process	IEA	2
GO:0005654	nucleoplasm	cellular component	TAS	163
GO:0023019	signal transduction involved in regulation of gene expression	biological process	IEA	1
GO:0070328	triglyceride homeostasis	biological process	ISS	3
GO:0001102	RNA polymerase II activating transcription factor binding	molecular function	ISS	5
GO:0042593	glucose homeostasis	biological process	ISS	19
GO:0007596	blood coagulation	biological process	IDA[12911579]	44
GO:0010467	gene expression	biological process	TAS	41
GO:0006367	transcription initiation from RNA polymerase II promoter	biological process	TAS	20
GO:0044212	transcription regulatory region DNA binding	molecular function	IDA[16488887]	17
GO:0055088	lipid homeostasis	biological process	IMP[17827783]	1
GO:0006805	xenobiotic metabolic process	biological process	IMP[17827783]	19
GO:0005515	protein binding	molecular function	IPI[12855700]	563
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	biological process	IDA[7615825]; IMP[17827783]	91
GO:0043401	steroid hormone mediated signaling pathway	biological process	IEA	10
GO:0060398	regulation of growth hormone receptor signaling pathway	biological process	NAS[17991764]	1
GO:0006357	regulation of transcription from RNA polymerase II promoter	biological process	IDA[10330009]; IMP[18163890]	21
GO:0005737	cytoplasm	cellular component	IDA[14563941]	322
GO:0050796	regulation of insulin secretion	biological process	ISS	24
GO:0045893	positive regulation of transcription, DNA-templated	biological process	IDA[16488887]	58
GO:0006629	lipid metabolic process	biological process	IEA	10
GO:0055091	phospholipid homeostasis	biological process	ISS	3
GO:0030308	negative regulation of cell growth	biological process	IMP[18163890]	11
GO:0031018	endocrine pancreas development	biological process	TAS	6
GO:2000189	positive regulation of cholesterol homeostasis	biological process	ISS	2
GO:0003705	RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity	molecular function	IEA	7
GO:0001077	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription	molecular function	ISS	18
GO:0060395	SMAD protein signal transduction	biological process	IEA	4
GO:0009749	response to glucose	biological process	ISS	8

Gene related KEGG pathways (count: 1)

KEGG pathways by PBA (count: 0)

KEGG pathways by database search (count: 1)

ID	Name	No. of Genes in BDgene	Brief Description
hsa04950	Maturity onset diabetes of the young	3

Gene related BioCarta pathways (count: 0)

Gene related interactors from protein-protein interactions data in HPRD (count: 29)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
HNF4A	PRKAA2	NO	in vitro;in vivo	12740371
HNF4A	SUB1	NO	in vitro;in vivo	11741883
HNF4A	NR0B2	NO	yeast 2-hybrid	16488887 , 15604093
HNF4A	ZNHIT3	NO	in vitro;yeast 2-hybrid	11916906
HNF4A	NCOA6	YES	yeast 2-hybrid	15604093
HNF4A	NR2F1	NO	in vitro	10652338
HNF4A	PROX1	NO	in vitro;in vivo;yeast 2-hybrid	16488887 , 15604093
HNF4A	NR2C2	NO	in vitro;in vivo	12522137
HNF4A	FOXO1	NO	in vitro	12519792
HNF4A	MED1	NO	in vitro;in vivo	12089346
HNF4A	PPARGC1A	NO	in vitro;in vivo	15826954 , 15744310
HNF4A	SMAD3	NO	in vitro;in vivo	10995777
HNF4A	UBE2I	NO	yeast 2-hybrid	15604093
HNF4A	SP1	NO	in vitro	19115260
HNF4A	HNF1A	NO	in vitro	9792724
HNF4A	SMAD2	NO	in vivo	11229886
HNF4A	NCOA1	NO	yeast 2-hybrid	9812974
HNF4A	SREBF2	NO	in vitro;in vivo	12855700
HNF4A	NCOA2	NO	in vitro;in vivo;yeast 2-hybrid	9812974
HNF4A	MAPK14	NO	in vitro	16351573
HNF4A	NRBF2	NO	yeast 2-hybrid	10786636
HNF4A	COPS5	NO	yeast 2-hybrid	15604093
HNF4A	SMAD4	NO	in vitro;in vivo	10995777
HNF4A	PNRC2	NO	yeast 2-hybrid	15604093
HNF4A	PNRC1	NO	yeast 2-hybrid	15604093
HNF4A	MED14	NO	in vitro	12101254
HNF4A	NPPA	NO	yeast 2-hybrid	15604093
HNF4A	TP53	NO	in vitro	11818510
HNF4A	MECR	NO	yeast 2-hybrid	9795230

Related other genetic factors

Gene related SNPs (count: 6)

Literature-origin SNPs (count: 1)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs4812829	chr20:44360627 - 44360627(1)	intron_variant	1(1/0/0)

LD-proxies (count: 5)

rs_ID	Location	Functional Annotation
rs6031544	chr20:44353707 - 44353707(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs2144908	chr20:44357077 - 44357077(1)	intron_variant; upstream_gene_variant
rs16988991	chr20:44361137 - 44361137(1)	intron_variant
rs1884613	chr20:44351775 - 44351775(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs1884614	chr20:44351879 - 44351879(1)	downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant

Gene related CNVs (count: 0)

Gene related other variants (count: 0)

Gene related regions (count: 3)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
Chr 20	chr20:0-64444167	4 (0/3/1)
20p11-q13	chr20:17900000-64444167	1 (1/0/0)
20q13	chr20:43100000-64444167	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
24196380	No association was found for SNPs in this gene for SZ.	Negative

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

Gene relationship with MDD

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Region: chr20:44355700..44434596 View in gBrowse