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	MLC1
Symbol Alias	MLC, KIAA0027, LVM, VL
Approved Name	megalencephalic leukoencephalopathy with subcortical cysts 1
Location	22q13.33
Position	chr22:50059391-50085902, -1
External Links	HGNC: 17082 Entrez Gene: 23209 Ensembl: ENSG00000100427 UCSC: uc003bjg.1
No. of Studies	5 (Positive: 1; Negative: 4; trend: 0)
Overlap with SZ?	YES
Overlap with MDD?	YES

Gene related studies (count: 5)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Selch, S., 2007	SNP: rs137936, rs2076137, rs2235349, rs713809	Both intronic and promoter polymorphisms of MLC1 were specifically and significantly associated with periodic catatonia but not bipolar disorder in general.	Negative	Comment on Study
Verma, R.,2005(b)	SNP: rs11568171, rs11568176, rs11568190, rs137930, rs2076127, rs2076137, rs2235349, rs6010260 Haplotype: rs2076127 - ss16339182(A-T), rs2076127 - ss16339182(G-C), rs2076127 - ss16339182(G-T)	In our present study, we found association of MLC1 gene with SCZ and BPAD. This suggests the involvement of MLC1 gene in a common pathway toward the pathogenesis of these two disorders.	Positive	Comment on Study
Severinsen, J. E., 2006 (b)	SNP: rs137931, rs137932, rs6010260 Haplotype: rs137931 - rs6010260(), rs137932 - rs137931(), rs137932 - rs137931 - rs6010260(), rs137931 - rs6010260 - rs138881(), rs137931 - rs6010260 - rs138881 - rs138880(), rs137932 - rs137931 - rs6010260 - rs138881(), rs6010260 - rs138881(), rs6010260 - rs138881 - rs138880(), rs6010260 - rs138881 - rs138880 - rs2239848(), rs2272843 - rs3810971 - rs137932(), rs2272843 - rs3810971 - rs137932 - rs137931(), rs3810971 - rs137932(), rs3810971 - rs137932 - rs137931(), rs3810971 - rs137932 - rs137931 - rs6010260()	The results do not support an association of the gene with BD.	Negative	Comment on Study
Fallin, M. D.,2005		7 SNP typed, Median D'=0.94, Median r<sup>2</sup> =0.09, 2 LD blocks, 0.93 block coverage, all SNP or haplotype P-value > 0.05 in BP and SZ/SZA.. This gene is not suggestive to BP.	Negative	Comment on Study
Yosifova, A.,2009	SNP: rs11568190, rs2076127	No SNP of this gene had significant association with BD in our population.	Negative	Comment on Study

Gene functional annotation

Gene related GO terms (count: 29)

GO terms by PBA (count: 4)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0005886	plasma membrane	cellular component	IDA[15367490]	360
GO:0005764	lysosome	cellular component	ISS	16
GO:0016021	integral component of membrane	cellular component	IDA[17628813]	219
GO:0006811	ion transport	biological process	IEA	18

GO terms by database search (count: 25)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0047484	regulation of response to osmotic stress	biological process	IMP[22328087]	1
GO:0005783	endoplasmic reticulum	cellular component	IDA[15367490]	49
GO:0016192	vesicle-mediated transport	biological process	ISS	10
GO:0016323	basolateral plasma membrane	cellular component	IDA[18165104]	21
GO:0015031	protein transport	biological process	IEA	21
GO:0071397	cellular response to cholesterol	biological process	ISS	3
GO:0005911	cell-cell junction	cellular component	IEA	16
GO:0072584	caveolin-mediated endocytosis	biological process	ISS	1
GO:0055037	recycling endosome	cellular component	ISS	14
GO:0005515	protein binding	molecular function	IPI[17628813]	563
GO:0005768	endosome	cellular component	IDA[18165104]	27
GO:0008565	protein transporter activity	molecular function	ISS	4
GO:0051259	protein oligomerization	biological process	IDA[15367490]	7
GO:0048471	perinuclear region of cytoplasm	cellular component	IDA[19931615]	50
GO:0030136	clathrin-coated vesicle	cellular component	ISS	9
GO:0006810	transport	biological process	NAS[11254442]	47
GO:0032403	protein complex binding	molecular function	IDA[17628813]	16
GO:0016324	apical plasma membrane	cellular component	IEA	24
GO:0005737	cytoplasm	cellular component	IDA[15892299]	322
GO:0045121	membrane raft	cellular component	ISS	22
GO:0032388	positive regulation of intracellular transport	biological process	IDA[19931615]	2
GO:0031410	cytoplasmic vesicle	cellular component	IDA[15892299]	7
GO:0005769	early endosome	cellular component	ISS	13
GO:0005215	transporter activity	molecular function	NAS[11254442]	8
GO:0005901	caveola	cellular component	ISS	11

Gene related KEGG pathways (count: 0)

Gene related BioCarta pathways (count: 0)

Gene related interactors from protein-protein interactions data in HPRD (count: 2)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
MLC1	DAPK2	NO	in vitro	10376525
MLC1	TPT1	NO	in vitro;in vivo;yeast 2-hybrid	12149273

Related other genetic factors

Gene related SNPs (count: 31)

Literature-origin SNPs (count: 12)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs137932	chr22:50085971 - 50085971(1)	upstream_gene_variant	1(0/1/0)
rs11568176	chr22:50079797 - 50079797(1)	intron_variant	1(0/1/0)
rs11568190	chr22:50064040 - 50064040(1)	non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant	2(1/1/0)
rs2235349	chr22:50079810 - 50079810(1)	intron_variant	2(1/1/0)
rs2076127	chr22:50068239 - 50068239(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant	2(0/2/0)
rs2076137	chr22:50077337 - 50077337(1)	intron_variant; upstream_gene_variant	2(0/2/0)
rs137931	chr22:50085822 - 50085821(1)	5_prime_UTR_variant; upstream_gene_variant	1(0/1/0)
rs137930	chr22:50085004 - 50085004(1)	intron_variant; upstream_gene_variant	1(0/1/0)
rs713809	chr22:50094169 - 50094169(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	1(0/1/0)
rs137936	chr22:50087515 - 50087515(1)	upstream_gene_variant	1(0/1/0)
rs11568171	chr22:50084988 - 50084988(1)	intron_variant; upstream_gene_variant	1(1/0/0)
rs6010260	chr22:50077414 - 50077414(1)	missense_variant; upstream_gene_variant	2(0/2/0)

LD-proxies (count: 19)

rs_ID	Location	Functional Annotation
rs9617018	chr22:50090487 - 50090487(1)	3_prime_UTR_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; synonymous_variant; upstream_gene_variant
rs6010165	chr22:50076844 - 50076844(1)	synonymous_variant; upstream_gene_variant
rs4838816	chr22:50078900 - 50078900(1)	intron_variant; upstream_gene_variant
rs2294391	chr22:50071488 - 50071488(1)	intron_variant; non_coding_transcript_variant
rs5771143	chr22:50069710 - 50069710(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs2076130	chr22:50070273 - 50070273(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs2294387	chr22:50066308 - 50066308(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs137919	chr22:50061535 - 50061535(1)	3_prime_UTR_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant
rs13053780	chr22:50081762 - 50081762(1)	intron_variant
rs5771362	chr22:50074976 - 50074976(1)	intron_variant; upstream_gene_variant
rs2235350	chr22:50082450 - 50082450(1)	intron_variant
rs12484523	chr22:50082044 - 50082044(1)	intron_variant
rs4838820	chr22:50089389 - 50089389(1)	upstream_gene_variant
rs9617062	chr22:50083346 - 50083346(1)	intron_variant
rs137926	chr22:50077766 - 50077766(1)	intron_variant; upstream_gene_variant
rs7285511	chr22:50072945 - 50072945(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs3817809	chr22:50063056 - 50063056(1)	intron_variant; non_coding_transcript_variant
rs3817810	chr22:50063115 - 50063115(1)	intron_variant; non_coding_transcript_variant
rs3817808	chr22:50062852 - 50062852(1)	intron_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)
Chr 22	chr22:0-50818468	2 (0/1/1)
22q12.3-q13.33	chr22:31800000-50818468	1 (1/0/0)
22q13	chr22:37200000-50818468	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: 4)

Reference	Description	Result Category
16380905	This gene is not suggestive to SZ/SZA.	Negative
15992519	In our present study, we found association of MLC1 gene with SCZ and BPAD. This suggests the involvement of MLC1 gene in a common pathway toward the pathogenesis of these two disorders.	Positive
17210142	Both intronic and promoter polymorphisms of MLC1 were specifically and significantly associated with periodic catatonia but not schizophrenia in general.	Negative
16924267	The results do not support an association of the gene with SZ.	Negative

Overlap with SZ from candidate gene intersection analysis (count: 6)

Reference	ID in SZGene	Result Category
16380905	442	Negative
15992519	442	Positive
12111645	442	Negative
12497630	442	Negative
17210142	442	Negative
16924267	442	Negative

Gene relationship with MDD

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

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

Reference	Description	Category in MDD	Link in MK4MDD
20471630	Based on LPS-stimulated blood gene expression using whole-genome microarrays, this gene serves as a molecular signature of MDD	Pos	MLC1

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Region: chr22:50059391..50085902 View in gBrowse