Gene Report

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Basic Info

Approved Symbol	ABCA13
Symbol Alias	FLJ33876, FLJ33951
Approved Name	ATP-binding cassette, sub-family A (ABC1), member 13
Location	7p12.3
Position	chr7:48171458-48647496, 1
External Links	HGNC: 14638 Entrez Gene: 154664 Ensembl: ENSG00000179869 UCSC: uc003toq.2
No. of Studies	2 (Positive: 2; Negative: 0; 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
Knight, H. M.,2009	Other variant: ABCA13_exon33_H3609P, ABCA13_exon52_R4590W, ABCA13_exon54_R4728X, ABCA13_exon57_R4843C, ABCA13_exon40_T4031A, ABCA13_exon52_T4550A	The frequency of all rare variants combined was greater than controls in schizophrenia (OR=1.93, P-value = 0.0057) and bipolar disorder (OR=2.71, P-value = 0.00007).These data identify a candidate gene, highlight the genetic overlap between schizophrenia, bipolar disorder, and depression, and suggest that rare coding variants may contribute significantly to risk of these disorders.	Positive	Comment on Study
Chen, X., 2015		ABCA13 has been implicated in SCZ, BPD, depression and autism.	Positive	Comment on Study

Gene functional annotation

Gene related GO terms (count: 10)

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

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0042626	ATPase activity, coupled to transmembrane movement of substances	molecular function	IBA	4
GO:0055085	transmembrane transport	biological process	IBA	77
GO:0033700	phospholipid efflux	biological process	IBA	3
GO:0017127	cholesterol transporter activity	molecular function	IBA	4
GO:0043231	intracellular membrane-bounded organelle	cellular component	IBA	34
GO:0005524	ATP binding	molecular function	IEA	118
GO:0008152	metabolic process	biological process	IEA	50
GO:0005548	phospholipid transporter activity	molecular function	IBA	2
GO:0033344	cholesterol efflux	biological process	IBA	5

Gene related KEGG pathways (count: 1)

ID	Name	No. of Genes in BDgene	Brief Description
hsa02010	ABC transporters	5

Gene related BioCarta pathways (count: 0)

Gene related interactors from protein-protein interactions data in HPRD (count: 0)

Related other genetic factors

Gene related SNPs (count: 0)

Gene related CNVs (count: 0)

Gene related other variants (count: 6)

Variant Name	Variant Type	Location in Gene	No. of Studies (Positive/Negative/Trend)
ABCA13_exon33_H3609P	point mutation	exon33	1 (0/1/0)
ABCA13_exon52_R4590W	point mutation	exon52	1 (0/1/0)
ABCA13_exon40_T4031A	point mutation	exon40	1 (1/0/0)
ABCA13_exon54_R4728X	point mutation	exon54	1 (0/1/0)
ABCA13_exon52_T4550A	point mutation	exon52	1 (1/0/0)
ABCA13_exon57_R4843C	point mutation	exon57	1 (0/1/0)

Gene related regions (count: 3)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
7p11-p13	chr7:43300000-59900000	1 (0/1/0)
Chr 7	chr7:0-159345973	3 (0/3/0)
7p15-q21	chr7:20900000-98400000	1 (0/1/0)

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

Gene relationship with SZ

Reference	Description	Result Category
19944402	The frequency of all rare variants combined was greater than controls in schizophrenia (OR=1.93, P-value = 0.0057) and bipolar disorder (OR=2.71, P-value = 0.00007).These data identify a candidate gene, highlight the genetic overlap between schizophrenia, bipolar disorder, and depression, and suggest that rare coding variants may contribute significantly to risk of these disorders.	Positive

Reference	ID in SZGene	Result Category
19944402	869	Positive

Gene relationship with MDD

Reference	Description	Category in MDD
19944402	The frequency of all rare variants combined was greater than controls in schizophrenia (OR=1.93, P-value = 0.0057) and bipolar disorder (OR=2.71, P-value = 0.00007).These data identify a candidate gene, highlight the genetic overlap between schizophrenia, bipolar disorder, and depression, and suggest that rare coding variants may contribute significantly to risk of these disorders.	Positive

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Region: chr7:48171458..48647496 View in gBrowse