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

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