Gene Report

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Basic Info

Approved Symbol	NCAN
Previous Symbol	CSPG3
Approved Name	neurocan
Previous Name	chondroitin sulfate proteoglycan 3
Name Alias	neurocan proteoglycan
Location	19p12
Position	chr19:19211973-19252233, 1
External Links	HGNC: 2465 Entrez Gene: 1463 Ensembl: ENSG00000130287 UCSC: uc002nlz.3
No. of Studies	1 (Positive: 1; Negative: 0; trend: 0)
Overlap with SZ?	NO
Overlap with MDD?	NO

Gene related studies (count: 1)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Cichon, S.,2011	SNP: rs1064395	In summary, the present study has identified a susceptibility factor , NCAN for BD.	Positive	Comment on Study

Gene functional annotation

Gene related GO terms (count: 22)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0030246	carbohydrate binding	molecular function	IEA	6
GO:0007155	cell adhesion	biological process	IBA	42
GO:0005509	calcium ion binding	molecular function	IEA	50
GO:0007411	axon guidance	biological process	TAS	60
GO:0007417	central nervous system development	biological process	IBA	21

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0005540	hyaluronic acid binding	molecular function	IBA	2
GO:0005576	extracellular region	cellular component	TAS	97
GO:0030198	extracellular matrix organization	biological process	TAS	26
GO:0030207	chondroitin sulfate catabolic process	biological process	TAS	1
GO:0005578	proteinaceous extracellular matrix	cellular component	IBA	19
GO:0005975	carbohydrate metabolic process	biological process	TAS	12
GO:0030204	chondroitin sulfate metabolic process	biological process	TAS	2
GO:0030206	chondroitin sulfate biosynthetic process	biological process	TAS	1
GO:0001501	skeletal system development	biological process	IBA	16
GO:0030208	dermatan sulfate biosynthetic process	biological process	TAS	1
GO:0044281	small molecule metabolic process	biological process	TAS	117
GO:0030203	glycosaminoglycan metabolic process	biological process	TAS	5
GO:0009405	pathogenesis	biological process	TAS	13
GO:0043202	lysosomal lumen	cellular component	TAS	4
GO:0005796	Golgi lumen	cellular component	TAS	9
GO:0051823	regulation of synapse structural plasticity	biological process	IEA	2
GO:0005201	extracellular matrix structural constituent	molecular function	IBA	6

Gene related KEGG pathways (count: 0)

Gene related BioCarta pathways (count: 0)

Gene related interactors from protein-protein interactions data in HPRD (count: 5)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
NCAN	PTN	NO	in vitro	9507007
NCAN	TNC	NO	in vivo	9341124
NCAN	L1CAM	NO	in vivo	7513709 , 10934197
NCAN	HMGB1	NO	in vitro	9507007
NCAN	CNTN2	NO	in vitro	8663515

Related other genetic factors

Gene related SNPs (count: 6)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs1064395	chr19:19250926 - 19250926(1)	3_prime_UTR_variant; downstream_gene_variant; upstream_gene_variant	1(0/0/1)

rs_ID	Location	Functional Annotation
rs10423874	chr19:19248691 - 19248691(1)	intron_variant; non_coding_transcript_variant
rs10401714	chr19:19252821 - 19252821(1)	downstream_gene_variant; upstream_gene_variant
rs10407933	chr19:19253510 - 19253510(1)	downstream_gene_variant; upstream_gene_variant
rs4808933	chr19:19253003 - 19253003(1)	downstream_gene_variant; upstream_gene_variant
rs17216041	chr19:19255834 - 19255834(1)	3_prime_UTR_variant; downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_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)
19p13-q13	chr19:0-58617616	1 (0/1/0)
Chr 19	chr19:0-58617616	2 (0/2/0)
19p13	chr19:0-19900000	2 (0/1/1)

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

Gene relationship with SZ

Gene relationship with MDD

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Region: chr19:19211973..19252233 View in gBrowse