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	NCAM1
Symbol Alias	NCAM, CD56
Approved Name	neural cell adhesion molecule 1
Location	11q23.2
Position	chr11:112961247-113278436, 1
External Links	HGNC: 7656 Entrez Gene: 4684 Ensembl: ENSG00000149294 UCSC: uc031yfl.1
No. of Studies	3 (Positive: 2; Negative: 1; trend: 0)
Overlap with SZ?	YES
Overlap with MDD?	YES

Gene related studies (count: 3)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Arai, M., 2004	SNP: rs646558, rs686050 Other variant: NCAM1_IVS6+32T>C, NCAM1_2208T>G, NCAM1_2256_2257 insATGG, NCAM1_I621G>T, NCAM1_IVS0-49de IG, NCAM1_IVS4+80G>C, NCAM1_IVS7+155G>T	Three single nucleotide polymorphisms, IVS6+32T>C, IVS7+11G>C and IVS12+21C>A, displayed significant associations with bipolar disorder (for allelic associations, nominal p =.04, p =.02, and p =.004, respectively, all p >.05 after Bonferroni corrections). The haplotype located in a linkage disequilibrium block was strongly associated with bipolar disorder (the p value of the most significant three-marker haplotype is .005).. Our results suggest that genetic variations in NCAM1 or nearby genes could confer risks associated with bipolar affective disorder in Japanese individuals.	Positive	Comment on Study
Yosifova, A.,2009	SNP: rs646558, rs686050	No SNP of this gene had significant association with BD in our population.	Negative	Comment on Study
Atz, M. E., 2007	SNP: rs2303377, rs646558 Haplotype: rs646558 - rs2303377(C-T, C-(T/C), (C/A)-(T/C))	A genotypic association between bipolar disorder and rs2303377 were found. Three of the two marker haplotypes for rs646558 and rs2303377 showed varying frequencies between bipolar and controls.	Positive	Comment on Study

Gene functional annotation

Gene related GO terms (count: 14)

GO terms by PBA (count: 5)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0007155	cell adhesion	biological process	IEA	42
GO:0016021	integral component of membrane	cellular component	IEA	219
GO:0016020	membrane	cellular component	IDA[19946888]	137
GO:0005886	plasma membrane	cellular component	TAS	360
GO:0007411	axon guidance	biological process	TAS	60

GO terms by database search (count: 9)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0031225	anchored component of membrane	cellular component	IEA	11
GO:0000139	Golgi membrane	cellular component	TAS	36
GO:0009897	external side of plasma membrane	cellular component	IDA[17213291]	21
GO:0009986	cell surface	cellular component	IDA[10766765]	40
GO:0070062	extracellular vesicular exosome	cellular component	IDA[23376485]	176
GO:0030198	extracellular matrix organization	biological process	TAS	26
GO:0042802	identical protein binding	molecular function	IPI[21115007]	44
GO:0019221	cytokine-mediated signaling pathway	biological process	TAS	23
GO:0060333	interferon-gamma-mediated signaling pathway	biological process	TAS	10

Gene related KEGG pathways (count: 1)

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: 0)

Gene related BioCarta pathways (count: 0)

Gene related interactors from protein-protein interactions data in HPRD (count: 12)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
NCAM1	ST8SIA3	NO	in vitro	10766765
NCAM1	FGFR1	NO	in vivo	12121226
NCAM1	GDNF	YES	in vivo	12837245
NCAM1	ST8SIA4	NO	in vitro	9774483
NCAM1	ST8SIA2	YES	in vitro	8702635
NCAM1	SPTB	NO	in vitro	12743109
NCAM1	NCAN	YES	in vitro	8910306
NCAM1	BDNF	YES	in vitro	10760298
NCAM1	GFRA1	YES	in vivo	12837245
NCAM1	L1CAM	NO	in vitro	10611478 , 8509458
NCAM1	PRNP	NO	in vivo	15146195
NCAM1	FYN	YES	in vitro;in vivo	11839780 , 9079653

Related other genetic factors

Gene related SNPs (count: 10)

Literature-origin SNPs (count: 3)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs686050	chr11:113214522 - 113214522(1)	intron_variant; non_coding_transcript_variant	2(1/1/0)
rs2303377	chr11:113240779 - 113240779(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; splice_region_variant	1(1/0/0)
rs646558	chr11:113235185 - 113235185(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	3(1/2/0)

LD-proxies (count: 7)

rs_ID	Location	Functional Annotation
rs1943620	chr11:113194571 - 113194571(1)	intron_variant; non_coding_transcript_variant
rs965560	chr11:113201883 - 113201883(1)	intron_variant; non_coding_transcript_variant
rs2574824	chr11:113197917 - 113197917(1)	intron_variant; non_coding_transcript_variant
rs1943619	chr11:113209582 - 113209582(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs1975259	chr11:113206260 - 113206260(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs2552513	chr11:113210902 - 113210902(1)	intron_variant; non_coding_transcript_variant
rs677642	chr11:113219458 - 113219458(1)	intron_variant; non_coding_transcript_variant

Gene related CNVs (count: 0)

Gene related other variants (count: 7)

Variant Name	Variant Type	No. of Studies (Positive/Negative/Trend)
NCAM1_I621G>T	point mutation	1 (0/1/0)
NCAM1_IVS0-49de IG	point mutation	1 (0/1/0)
NCAM1_2208T>G	point mutation	1 (0/1/0)
NCAM1_2256_2257 insATGG	point mutation	1 (0/1/0)
NCAM1_IVS7+155G>T	point mutation	1 (0/1/0)
NCAM1_IVS4+80G>C	point mutation	1 (0/1/0)
NCAM1_IVS6+32T>C	point mutation	1 (1/0/0)

Gene related regions (count: 3)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
11q22.3-11q23	chr11:102900000-121200000	2 (0/2/0)
Chr 11	chr11:0-135086622	2 (0/2/0)
11q22-q23	chr11:97200000-121200000	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
17413444	A suggestive association between schizophrenia and rs646558 were found. Three of the two marker haplotypes for rs646558 and rs2303377 showed varying frequencies between schizophrenia and controls.	Positive

Overlap with SZ from candidate gene intersection analysis (count: 3)

Reference	ID in SZGene	Result Category
18601968	104	Negative
9154219	104	Negative
17413444	104	Positive

Gene relationship with MDD

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

Reference	Description	Category in MDD
15050861	NCAM1 displayed a significant association with bipolar disorder but not with unipolar disorder.	Negative

Overlap with MDD from candidate gene intersection analysis (count: 1)

Reference	Description	Category in MDD	Link in MK4MDD
18068248	Genes differentially expressed in major depression	Pos	NCAM1

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Region: chr11:112961247..113278436 View in gBrowse