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	GAD1
Previous Symbol	GAD
Approved Name	glutamate decarboxylase 1 (brain, 67kDa)
Previous Name	glutamate decarboxylase 1 (brain, 67kD)
Location	2q31
Position	chr2:170813213-170861151, 1
External Links	HGNC: 4092 Entrez Gene: 2571 Ensembl: ENSG00000128683 UCSC: uc002ugi.3
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
Yosifova, A.,2009	SNP: rs769404, rs1978340, rs3749034, rs769390	No SNP of this gene had significant association with BD in our population.	Negative	Comment on Study
Lundorf, M. D.,2005	SNP: rs1978340, rs3749034, rs4668331, rs701492, rs769390, rs769395, rs872123 Haplotype: rs1978340 - rs872123(), rs1978340 - rs872123 - rs3749034(), rs4668331 - rs769395(), rs872123 - rs3749034(), rs872123 - rs3749034 - rs769404() Other variant: rs769404	The results from the association studies indicate that promoter variants are of importance for the Danish BPADcases and we cannot reject the hypothesis of GAD1 as a functional candidate gene for BPAD.	Positive	Comment on Study

Gene functional annotation

Gene related GO terms (count: 18)

GO terms by PBA (count: 2)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0007268	synaptic transmission	biological process	TAS	116
GO:0005886	plasma membrane	cellular component	TAS	360

GO terms by database search (count: 16)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0061202	clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane	cellular component	TAS	3
GO:0005515	protein binding	molecular function	IPI[10671565]	563
GO:0016595	glutamate binding	molecular function	IEA	6
GO:0006540	glutamate decarboxylation to succinate	biological process	TAS[1549570]	2
GO:0030170	pyridoxal phosphate binding	molecular function	IEA	5
GO:0005622	intracellular	cellular component	IDA[10671565]	17
GO:0046982	protein heterodimerization activity	molecular function	IEA	42
GO:0007269	neurotransmitter secretion	biological process	TAS	15
GO:0042493	response to drug	biological process	IEA	57
GO:0012506	vesicle membrane	cellular component	NAS[10671565]	3
GO:0018352	protein-pyridoxal-5-phosphate linkage	biological process	TAS[10671565]	1
GO:0004351	glutamate decarboxylase activity	molecular function	IDA[10671565]; TAS	2
GO:0047485	protein N-terminus binding	molecular function	IEA	12
GO:0009449	gamma-aminobutyric acid biosynthetic process	biological process	IEA	1
GO:0042136	neurotransmitter biosynthetic process	biological process	IEA	10
GO:0006538	glutamate catabolic process	biological process	TAS[10671565]	1

Gene related KEGG pathways (count: 6)

KEGG pathways by PBA (count: 0)

KEGG pathways by database search (count: 6)

ID	Name	No. of Genes in BDgene
hsa00650	Butanoate metabolism	7
hsa04940	Type I diabetes mellitus	10
hsa00410	beta-Alanine metabolism	4
hsa00430	Taurine and hypotaurine metabolism	2
hsa00251	Glutamate metabolism	5
hsa00252	Alanine and aspartate metabolism	5

Gene related BioCarta pathways (count: 0)

Gene related interactors from protein-protein interactions data in HPRD (count: 3)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
GAD1	PPP2CA	NO	in vitro	15147202
GAD1	PPP2CB	NO	in vitro	15147202
GAD1	HAAO	NO	yeast 2-hybrid	16189514

Related other genetic factors

Gene related SNPs (count: 24)

Literature-origin SNPs (count: 9)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs769395	chr2:170860293 - 170860293(1)	3_prime_UTR_variant; downstream_gene_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	1(0/1/0)
rs1978340	chr2:170813611 - 170813611(1)	downstream_gene_variant; intron_variant; upstream_gene_variant	2(1/1/0)
rs2241165	chr2:170821869 - 170821869(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	1(1/0/0)
rs4668331	chr2:170849737 - 170849737(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)
rs701492	chr2:170845970 - 170845970(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant	1(0/1/0)
rs769390	chr2:170836945 - 170836945(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	2(0/2/0)
rs872123	chr2:170814656 - 170814656(1)	downstream_gene_variant; intron_variant; upstream_gene_variant	1(1/0/0)
rs3749034	chr2:170816965 - 170816965(1)	5_prime_UTR_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	2(0/2/0)
rs769404	chr2:170822115 - 170822115(1)	NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant; upstream_gene_variant	1(0/1/0)

LD-proxies (count: 15)

rs_ID	Location	Functional Annotation
rs769407	chr2:170837198 - 170837198(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs3791858	chr2:170833210 - 170833210(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs3791851	chr2:170842162 - 170842162(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs7561581	chr2:170839962 - 170839962(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs2302659	chr2:170843849 - 170843849(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant
rs3749033	chr2:170842889 - 170842889(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs3762555	chr2:170815885 - 170815885(1)	downstream_gene_variant; intron_variant; upstream_gene_variant
rs16858988	chr2:170846450 - 170846450(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant
rs1477061	chr2:170826597 - 170826597(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs4668327	chr2:170835347 - 170835347(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs3791878	chr2:170815681 - 170815681(1)	downstream_gene_variant; intron_variant; upstream_gene_variant
rs16858977	chr2:170845254 - 170845254(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs769391	chr2:170852920 - 170852920(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant
rs7578661	chr2:170858623 - 170858623(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs2241164	chr2:170830049 - 170830049(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant

Gene related CNVs (count: 1)

ID	Location	Size	Band	Type	Inheritance
CNV_Sheng[2012]_1	chr2:171362909-171670922 (Affymetrix SNP 6.0 array reference genome)	308013	2q31

Gene related other variants (count: 1)

Variant Name	Variant Type	Location in Gene	No. of Studies (Positive/Negative/Trend)
rs769404	point mutation		1 (0/1/0)

Gene related regions (count: 3)

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)

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
15806582	The results obtained from the Scottish sample suggest that the GAD1 gene variants do not play a major role in the predisposition to schizophrenia.	Negative

Overlap with SZ from candidate gene intersection analysis (count: 8)

Reference	ID in SZGene	Result Category
17412563	275	Positive
17303389	275	Negative
15091314	275	Negative
15806582	275	Negative
15642443	275	Negative
17767149	275	Positive
19158809	275	Negative
18335162	275	Positive

Gene relationship with MDD

Overlap with MDD from cross-disorder studies (count: 0)

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

Reference	Description	Category in MDD	Link in MK4MDD
16718280	Several of the six single-nucleotide polymorphisms tested in the GAD1 region demonstrated significant association in both stages, and a combined analysis in all 1128 subjects indicated that they formed a common high-risk haplotype that was significantly over-represented in cases (P=0.003) with effect size OR=1.23	Pos	GAD1
14681921	Comparison of SNP and haplotype frequencies between individuals with depression and controls revealed no differences	Neg	GAD1
24652383	We found two datasets where the mRNA levels of GAD1 and SLC1A2 in subregions of the dlPFC were significantly and marginally lower in subjects with MDD (n = 15) than in controls (n = 15) (p = 0.045 and 0.057, respectively)	Pos	GAD1

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Region: chr2:170813213..170861151 View in gBrowse