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

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