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	MDGA1
Symbol Alias	GPIM, MAMDC3
Approved Name	MAM domain containing glycosylphosphatidylinositol anchor 1
Location	6p21
Position	chr6:37630679-37699306, -1
External Links	HGNC: 19267 Entrez Gene: 266727 Ensembl: ENSG00000112139 UCSC: uc003onu.1
No. of Studies	1 (Positive: 1; Negative: 0; trend: 0)
Overlap with SZ?	YES
Overlap with MDD?	YES

Gene related studies (count: 1)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Li, J.,2011(a)	SNP: rs10807187, rs11759115, rs12191311, rs1883901, rs3846881, rs6900617, rs7769372, rs804831, rs9462341, rs9462343, rs989713 Haplotype: rs11759115 - rs7769372(C-C), rs11759115 - rs7769372(T-C), rs11759115 - rs7769372(T-T), rs1883901 - rs10807187 - rs9462343(A-G-G), rs1883901 - rs10807187 - rs9462343(G-G-A), rs1883901 - rs10807187 - rs9462343(G-G-G), rs1883901 - rs10807187 - rs9462343(G-T-G)	The MDGA1 gene may confer risk to schizophrenia and bipolar disorder in Chinese Han population.	Positive	Comment on Study

Gene functional annotation

Gene related GO terms (count: 9)

GO terms by PBA (count: 2)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0005886	plasma membrane	cellular component	IDA	360
GO:0007420	brain development	biological process	ISS[15019943]	25

GO terms by database search (count: 7)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0046658	anchored component of plasma membrane	cellular component	IDA[15922729]; ISS[15019943]	1
GO:0005794	Golgi apparatus	cellular component	IDA	60
GO:0001764	neuron migration	biological process	ISS	18
GO:0003674	molecular_function	molecular function	ND	24
GO:0021799	cerebral cortex radially oriented cell migration	biological process	IEA	5
GO:0021527	spinal cord association neuron differentiation	biological process	ISS[15019943]	1
GO:0005615	extracellular space	cellular component	IDA[22664934]	85

Gene related KEGG pathways (count: 0)

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: 59)

Literature-origin SNPs (count: 11)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs9462341	chr6:37643605 - 37643605(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant	1(0/1/0)
rs12191311	chr6:37635931 - 37635931(1)	3_prime_UTR_variant; downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	1(0/1/0)
rs989713	chr6:37681935 - 37681935(1)	intron_variant	1(0/1/0)
rs9462343	chr6:37653000 - 37653000(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)
rs804831	chr6:37641965 - 37641965(1)	downstream_gene_variant; intron_variant; upstream_gene_variant	1(0/1/0)
rs1883901	chr6:37663255 - 37663255(1)	intron_variant; non_coding_transcript_variant	1(1/0/0)
rs7769372	chr6:37670786 - 37670786(1)	intron_variant	1(0/1/0)
rs3846881	chr6:37667783 - 37667783(1)	intron_variant; upstream_gene_variant	1(0/1/0)
rs10807187	chr6:37661874 - 37661874(1)	intron_variant; non_coding_transcript_variant	1(0/1/0)
rs6900617	chr6:37684410 - 37684410(1)	intron_variant	1(0/1/0)
rs11759115	chr6:37673254 - 37673254(1)	intron_variant	1(0/1/0)

LD-proxies (count: 48)

rs_ID	Location	Functional Annotation
rs3905219	chr6:37641529 - 37641529(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs9462340	chr6:37642573 - 37642573(1)	downstream_gene_variant; intron_variant; upstream_gene_variant
rs4714089	chr6:37643128 - 37643128(1)	downstream_gene_variant; intron_variant; upstream_gene_variant
rs876796	chr6:37679868 - 37679868(1)	intron_variant
rs9394449	chr6:37680951 - 37680951(1)	intron_variant
rs4236056	chr6:37656977 - 37656977(1)	intron_variant; non_coding_transcript_variant
rs7452676	chr6:37656671 - 37656671(1)	intron_variant; non_coding_transcript_variant
rs3846874	chr6:37655790 - 37655790(1)	downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant
rs804859	chr6:37646686 - 37646686(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs2395678	chr6:37663036 - 37663036(1)	intron_variant; non_coding_transcript_variant
rs16890055	chr6:37662244 - 37662244(1)	intron_variant; non_coding_transcript_variant
rs6458011	chr6:37693091 - 37693091(1)	intron_variant
rs9394450	chr6:37681036 - 37681036(1)	intron_variant
rs6458012	chr6:37693265 - 37693265(1)	intron_variant
rs1883899	chr6:37663094 - 37663094(1)	intron_variant; non_coding_transcript_variant
rs12195277	chr6:37662477 - 37662477(1)	intron_variant; non_coding_transcript_variant
rs9394448	chr6:37673199 - 37673199(1)	intron_variant
rs9394447	chr6:37663235 - 37663235(1)	intron_variant; non_coding_transcript_variant
rs9296229	chr6:37668578 - 37668578(1)	intron_variant; upstream_gene_variant
rs3846883	chr6:37667932 - 37667932(1)	intron_variant; upstream_gene_variant
rs3846882	chr6:37667903 - 37667903(1)	intron_variant; upstream_gene_variant
rs6458009	chr6:37667037 - 37667037(1)	intron_variant; upstream_gene_variant
rs6458008	chr6:37666559 - 37666559(1)	intron_variant; upstream_gene_variant
rs6909816	chr6:37666398 - 37666398(1)	intron_variant; upstream_gene_variant
rs7775837	chr6:37659162 - 37659162(1)	intron_variant; non_coding_transcript_variant
rs3846879	chr6:37660421 - 37660421(1)	intron_variant; non_coding_transcript_variant
rs4711509	chr6:37661623 - 37661623(1)	intron_variant; non_coding_transcript_variant
rs3857571	chr6:37662812 - 37662812(1)	intron_variant; non_coding_transcript_variant
rs7452692	chr6:37656698 - 37656698(1)	intron_variant; non_coding_transcript_variant
rs3846876	chr6:37656894 - 37656894(1)	intron_variant; non_coding_transcript_variant
rs13198513	chr6:37657914 - 37657914(1)	intron_variant; non_coding_transcript_variant
rs13212859	chr6:37658001 - 37658001(1)	intron_variant; non_coding_transcript_variant
rs13204070	chr6:37655850 - 37655850(1)	downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant
rs6930085	chr6:37657310 - 37657310(1)	intron_variant; non_coding_transcript_variant
rs2273110	chr6:37658366 - 37658366(1)	non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant
rs9366945	chr6:37659030 - 37659030(1)	intron_variant; non_coding_transcript_variant
rs1883900	chr6:37663219 - 37663219(1)	intron_variant; non_coding_transcript_variant
rs4357132	chr6:37663604 - 37663604(1)	intron_variant; non_coding_transcript_variant
rs804830	chr6:37641681 - 37641681(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs813079	chr6:37650531 - 37650531(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs9357252	chr6:37702601 - 37702601(1)	upstream_gene_variant
rs6933764	chr6:37700368 - 37700368(1)	upstream_gene_variant
rs6936811	chr6:37688705 - 37688705(1)	intron_variant
rs9394452	chr6:37688024 - 37688024(1)	intron_variant
rs9394451	chr6:37688005 - 37688005(1)	intron_variant
rs9380699	chr6:37685865 - 37685865(1)	intron_variant
rs13195437	chr6:37681909 - 37681909(1)	intron_variant
rs4714091	chr6:37675885 - 37675885(1)	intron_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)
Chr 6	chr6:0-170805979	3 (0/3/0)
6p21	chr6:30500000-46200000	1 (0/1/0)
6p21.2	chr6:36600000-40500000	1 (0/1/0)
6p23-p21.1	chr6:13400000-46200000	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
21146959	The MDGA1 gene may confer risk to schizophrenia and bipolar disorder in Chinese Han population.	Positive

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

Reference	ID in SZGene	Result Category
18384059	711	Positive
20036297	711	Positive

Gene relationship with MDD

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

Reference	Description	Category in MDD
21146959	No individual SNP or haplotype was associated with major depressive disorder after permutations.	Negative

Overlap with MDD from candidate gene intersection analysis (count: 0)

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Region: chr6:37630679..37699306 View in gBrowse