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	TCF4
Symbol Alias	SEF2-1B, ITF2, bHLHb19, E2-2
Approved Name	transcription factor 4
Location	18q21.1
Position	chr18:55222198-55664787, -1
External Links	HGNC: 11634 Entrez Gene: 6925 Ensembl: ENSG00000196628 UCSC: uc002lga.3
No. of Studies	6 (Positive: 1; Negative: 5; trend: 0)
Overlap with SZ?	YES
Overlap with MDD?	NO

Gene related studies (count: 6)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Del-Favero, J.,2002	Other variant: TCF4_CTG18.1	Expanded alleles at the CTG18.1 locus cannot be excluded as a vulnerability factor for BP disorder.	Positive	Comment on Study
McInnis, M. G.,2000	Other variant: TCF4_CTG18.1	There are no data to implicate the CTG18.1 repeat within the SEF2-1b gene, and the current study indicates that CTG18.1 is unlikely to make a substantial contribution to vulnerability to these disorders, though a minor contribution can not be ruled out.	Negative	Comment on Study
Williams, H. J.,2011	SNP: rs9960767	Using data sets entirely independent of their original discoveries, we observed no significant evidence (P < 0.05) that the TCF4 region is associated with BD.	Negative	Comment on Study
Steinberg, S.,2012	SNP: rs4309482, rs9960767	No significant association was observed.	Negative	Comment on Study
Meira-Lima, I. V.,2001	Other variant: TCF4_CAG/CTG repeat	Our data do not support the hypothesis that variation at the polymorphic CAG/CTG repeat loci SEF2-1b influence susceptibility to BPAD in our sample.	Negative	Comment on Study
Jin, D. K.,2001	Other variant: TCF4_CTG18.1	A longer CAG repeat alleles of KCNN3 or CTG 18.1 may not be a risk factor for BPAD in Korean population.	Negative	Comment on Study

Gene functional annotation

Gene related GO terms (count: 19)

GO terms by PBA (count: 3)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0005634	nucleus	cellular component	IDA[1681116]	283
GO:0003700	sequence-specific DNA binding transcription factor activity	molecular function	IDA[11802795]	66
GO:0003677	DNA binding	molecular function	IDA[1681116]	83

GO terms by database search (count: 16)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0045666	positive regulation of neuron differentiation	biological process	ISS	8
GO:0046982	protein heterodimerization activity	molecular function	ISS; NAS[2105528]	42
GO:0045893	positive regulation of transcription, DNA-templated	biological process	IDA[2105528]	58
GO:0001087	TFIIB-class binding transcription factor activity	molecular function	ISS[8978694]	1
GO:0000978	RNA polymerase II core promoter proximal region sequence-specific DNA binding	molecular function	ISS[8978694]	23
GO:0001093	TFIIB-class transcription factor binding	molecular function	ISS[8978694]	1
GO:0005667	transcription factor complex	cellular component	ISS[8978694]	18
GO:0070888	E-box binding	molecular function	ISS	7
GO:0001011	sequence-specific DNA binding RNA polymerase recruiting transcription factor activity	molecular function	ISS[8978694]	1
GO:0005515	protein binding	molecular function	IPI[10903890]	563
GO:0006352	DNA-templated transcription, initiation	biological process	ISS[8978694]	1
GO:0065004	protein-DNA complex assembly	biological process	ISS[8978694]	1
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[8978694]	18
GO:0008022	protein C-terminus binding	molecular function	IPI[10903890]	21
GO:0006367	transcription initiation from RNA polymerase II promoter	biological process	ISS[8978694]	20
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	biological process	ISS[8978694]	91

Gene related KEGG pathways (count: 9)

KEGG pathways by PBA (count: 2)

ID	Name	No. of Genes in BDgene	Brief Description
hsa05217	Basal cell carcinoma	8
hsa05221	Acute myeloid leukemia	7

KEGG pathways by database search (count: 7)

ID	Name	No. of Genes in BDgene
hsa05210	Colorectal cancer	14
hsa04520	Adherens junction	11
hsa05213	Endometrial cancer	10
hsa05215	Prostate cancer	18
hsa05216	Thyroid cancer	4
hsa04310	Wnt signaling pathway	20
hsa04916	Melanogenesis	16

Gene related BioCarta pathways (count: 0)

Gene related interactors from protein-protein interactions data in HPRD (count: 21)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
TCF4	JUN	NO	in vitro;in vivo	16007074
TCF4	EP300	NO	in vitro	17410209
TCF4	PARP1	NO	in vivo	17283121
TCF4	XRCC6	NO	in vivo	17283121
TCF4	ID3	NO	in vitro;in vivo;yeast 2-hybrid	11591653 , 8999959
TCF4	CALM2	NO	in vitro	10757985
TCF4	RUNX1T1	NO	in vitro;in vivo	15333839
TCF4	ASCL1	NO	in vitro;in vivo;yeast 2-hybrid	10903890
TCF4	CDC73	NO	in vitro	16630820
TCF4	ID2	NO	in vivo;yeast 2-hybrid	11591653 , 9242638
TCF4	XRCC5	NO	in vivo	17283121
TCF4	ID4	NO	yeast 2-hybrid	11756408
TCF4	HBP1	NO	in vivo	11500377
TCF4	AR	NO	in vitro;in vivo	12799378
TCF4	JUP	NO	in vitro;in vivo	16306047
TCF4	CALM3	NO	in vitro	10757985
TCF4	CTNNB1	NO	in vitro;in vivo	16724116 , 16007074 , 12944908 , 12657632
TCF4	CALM1	NO	in vitro	10757985
TCF4	NEUROD1	NO	in vivo	11591653
TCF4	MSC	NO	yeast 2-hybrid	9584154
TCF4	MYOD1	NO	in vitro;yeast 2-hybrid	8576241 , 8999959

Related other genetic factors

Gene related SNPs (count: 1)

Literature-origin SNPs (count: 1)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs9960767	chr18:55487771 - 55487771(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	2(0/2/0)

LD-proxies (count: 0)

Gene related CNVs (count: 0)

Gene related other variants (count: 2)

Variant Name	Variant Type	Location in Gene	No. of Studies (Positive/Negative/Trend)
TCF4_CAG/CTG repeat	microsatellite		1 (0/1/0)
TCF4_CTG18.1	microsatellite		3 (1/2/0)

Gene related regions (count: 8)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
18q	chr18:18500000-80373285	1 (0/1/0)
18q12.3-q21.1	chr18:39500000-63900000	1 (1/0/0)
18q12-21	chr18:27500000-63900000	1 (0/1/0)
18q12.3-q22.1	chr18:39500000-69100000	1 (0/1/0)
18q21	chr18:45900000-63900000	3 (2/1/0)
18q21-23	chr18:45900000-80373285	1 (1/0/0)
18q21-q22	chr18:45900000-75400000	1 (0/1/0)
Chr 18	chr18:0-80373285	1 (1/0/0)

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

Gene relationship with SZ

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

Reference	Description	Result Category
23164818	Association results in schizophrenia follow-up samples(10,671 cases; 23,900 controls):OR(95% CI) = 1.08 (1.04, 1.12),P-value = 1.7 x 10-5. No significant association was observed.	Negative
10889556	There are no data to implicate the CTG18.1 repeat within the SEF2-1b gene, and the current study indicates that CTG18.1 is unlikely to make a substantial contribution to vulnerability to these disorders, though a minor contribution can not be ruled out.	Negative

Overlap with SZ from candidate gene intersection analysis (count: 5)

Reference	ID in SZGene	Result Category
10889556	161	Negative
19571808	161	Positive
10909126	161	Negative
20673877	161	Positive
10395212	161	Negative

Gene relationship with MDD

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Region: chr18:55222198..55664787 View in gBrowse