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	CTLA4
Previous Symbol	CELIAC3, IDDM12
Symbol Alias	CD152, CD, GSE, CD28, ICOS
Approved Name	cytotoxic T-lymphocyte-associated protein 4
Previous Name	celiac disease 3, "insulin-dependent diabetes mellitus 12"
Location	2q33
Position	chr2:203867786-203873960, 1
External Links	HGNC: 2505 Entrez Gene: 1493 Ensembl: ENSG00000163599 UCSC: uc002vak.2
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
Liu, J,2011(a)	SNP: rs16840252, rs231775, rs231777, rs231779, rs3087243, rs5742909	Our results suggest that shared common risk factors for schizophrenia, major depressive disorder and bipolar disorder exist in the CTLA-4 gene in the Chinese Han population.	Positive	Comment on Study
Jun, T. Y., 2004		Genotypic P-value = 0.208, X<sup>2</sup>(df=2)=3.14; allelic P-value = 0.256, X<sup>2</sup>(df=1)=1.29 in patients with bipolar disorder compared with controls.. There were no significant differences in genotype frequencies of CTLA4G/G, CTLA4G/A, and CTLA4A/A between the patients with bipolar disorder and the control group.There were no significant differences in allelic frequencies of CTLA4G and CTLA4*A between the patients with bipolar disorder and the control group. In the present study an association was not found of exon 1 (+49) polymorphism of CTLA4 gene with bipolar disorder in the Korean population.	Negative	Comment on Study

Gene functional annotation

Gene related GO terms (count: 16)

GO terms by PBA (count: 2)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0005886	plasma membrane	cellular component	TAS	360
GO:0005887	integral component of plasma membrane	cellular component	TAS[3220103]	158

GO terms by database search (count: 14)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0045590	negative regulation of regulatory T cell differentiation	biological process	IDA[18641304]	1
GO:0050853	B cell receptor signaling pathway	biological process	IMP[17875758]	4
GO:0005794	Golgi apparatus	cellular component	IDA[15814706]	60
GO:0005515	protein binding	molecular function	IPI[11279501]	563
GO:0009897	external side of plasma membrane	cellular component	IDA[18641304]	21
GO:0042130	negative regulation of T cell proliferation	biological process	IEA	6
GO:0043065	positive regulation of apoptotic process	biological process	IMP[17875758]	25
GO:0006974	cellular response to DNA damage stimulus	biological process	IMP[17875758]	14
GO:0030889	negative regulation of B cell proliferation	biological process	IMP[17875758]	5
GO:0006955	immune response	biological process	IEA	19
GO:0050777	negative regulation of immune response	biological process	IEA	2
GO:0045334	clathrin-coated endocytic vesicle	cellular component	IDA[15814706]	1
GO:0048471	perinuclear region of cytoplasm	cellular component	IDA[15814706]	50
GO:0031295	T cell costimulation	biological process	TAS	6

Gene related KEGG pathways (count: 3)

KEGG pathways by PBA (count: 1)

ID	Name	No. of Genes in BDgene	Brief Description
hsa04514	Cell adhesion molecules (CAMs)	14

KEGG pathways by database search (count: 2)

ID	Name	No. of Genes in BDgene	Brief Description
hsa05320	Autoimmune thyroid disease	6
hsa04660	T cell receptor signaling pathway	13

Gene related BioCarta pathways (count: 1)

BioCarta pathways by PBA (count: 0)

BioCarta pathways by database search (count: 1)

ID	Name	No. of Genes in BDgene	Brief Description
ctla4Pathway	The Co-Stimulatory Signal During T-cell Activation	3

Gene related interactors from protein-protein interactions data in HPRD (count: 13)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
CTLA4	AP1M1	NO	in vitro	9812899 , 11583591
CTLA4	STAT5B	NO	in vivo;yeast 2-hybrid	16476059
CTLA4	STAT5A	NO	in vivo;yeast 2-hybrid	16476059
CTLA4	LYN	NO	in vitro;in vivo	9712716
CTLA4	PTPN11	NO	in vitro;in vivo	8638161
CTLA4	CD86	NO	in vitro;in vivo	11279501 , 11021528 , 12606712 , 12071705 , 12582153 , 7513726 , 7694153 , 11162656
CTLA4	PPP2R5A	NO	in vivo;yeast 2-hybrid	11994459
CTLA4	CD80	NO	in vitro	7545666
CTLA4	TXK	NO	in vitro;in vivo	9813138
CTLA4	PIK3R1	YES	in vitro;in vivo	7807015
CTLA4	AP2M1	NO	in vitro;in vivo;yeast 2-hybrid	9200449 , 9256472 , 11583591
CTLA4	LCK	NO	in vitro;in vivo	9712716 , 9973379
CTLA4	JAK2	NO	in vivo	10842319

Related other genetic factors

Gene related SNPs (count: 17)

Literature-origin SNPs (count: 6)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs5742909	chr2:203867624 - 203867624(1)	upstream_gene_variant	1(0/1/0)
rs231775	chr2:203867991 - 203867991(1)	missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)
rs16840252	chr2:203866796 - 203866796(1)	upstream_gene_variant	1(0/1/0)
rs3087243	chr2:203874196 - 203874196(1)	downstream_gene_variant	1(0/1/0)
rs231779	chr2:203869764 - 203869764(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1(1/0/0)
rs231777	chr2:203868865 - 203868865(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1(1/0/0)

LD-proxies (count: 11)

rs_ID	Location	Functional Annotation
rs231727	chr2:203876827 - 203876827(1)	downstream_gene_variant
rs231725	chr2:203875952 - 203875952(1)	downstream_gene_variant
rs11571315	chr2:203866178 - 203866178(1)	upstream_gene_variant
rs1427676	chr2:203876443 - 203876443(1)	downstream_gene_variant
rs231726	chr2:203876143 - 203876143(1)	downstream_gene_variant
rs4553808	chr2:203866282 - 203866282(1)	upstream_gene_variant
rs10197010	chr2:203875448 - 203875448(1)	downstream_gene_variant
rs11571316	chr2:203866366 - 203866366(1)	upstream_gene_variant
rs231770	chr2:203864430 - 203864430(1)	upstream_gene_variant
rs1427680	chr2:203865072 - 203865072(1)	upstream_gene_variant
rs736611	chr2:203865742 - 203865742(1)	upstream_gene_variant

Gene related CNVs (count: 0)

Gene related other variants (count: 0)

Gene related regions (count: 4)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
2q21-q33	chr2:129100000-208200000	1 (0/0/1)
Chr 2	chr2:0-242193529	3 (0/3/0)
2q24-33	chr2:154000000-208200000	1 (1/0/0)
2q32.3-q33	chr2:191100000-208200000	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
21040781	Our results suggest that shared common risk factors for schizophrenia, major depressive disorder and bipolar disorder exist in the CTLA-4 gene in the Chinese Han population.	Positive

Overlap with SZ from candidate gene intersection analysis (count: 2)

Reference	ID in SZGene	Result Category
12007590	271	Positive
18848621	271	Positive

Gene relationship with MDD

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

Reference	Description	Category in MDD
21040781	Our results suggest that shared common risk factors for schizophrenia, major depressive disorder and bipolar disorder exist in the CTLA-4 gene in the Chinese Han population.	Positive

Overlap with MDD from candidate gene intersection analysis (count: 2)

Reference	Description	Category in MDD	Link in MK4MDD
11555351	There were no significant differences in genotype frequencies of CTLA-4G/G, CTLA-4G/A, and CTLA-4A/A between the patients with major depression and the control group in the Korean population (48.1% vs. 46.3%, 41.6% vs 39.6%, 10.3% vs. 14.1%, respectively). There were no significant differences in allelic frequencies of CTLA-4G and CTLA-4*A between the patients with major depression and the control group in the Korean population (68.8% vs. 66.1%, 31.2% vs. 33.9%, respectively).	Neg	CTLA4

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Region: chr2:203867786..203873960 View in gBrowse