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	TOM1
Approved Name	target of myb1 (chicken)
Previous Name	target of myb1 (chicken) homolog
Location	22q13.1
Position	chr22:35299275-35347994, 1
External Links	HGNC: 11982 Entrez Gene: 10043 Ensembl: ENSG00000100284 UCSC: uc003anp.3
No. of Studies	1 (Positive: 1; Negative: 0; trend: 0)
Overlap with SZ?	NO
Overlap with MDD?	NO

Gene related studies (count: 1)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Potash, J. B., 2008	SNP: rs11703672, rs138764, rs138773, rs138781, rs138784, rs4462, rs4465, rs4467, rs4511, rs5750102, rs739015, rs743810, rs762967, rs9622182	A 3-marker haplotype of SNPs within TOM1 was associated with BPAD (allele-wise P=0.0011) and with psychotic BPAD (allele-wise P=0.00049).	Positive	Comment on Study

Gene functional annotation

Gene related GO terms (count: 12)

GO terms by PBA (count: 1)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0016020	membrane	cellular component	IDA[14613930]	137

GO terms by database search (count: 11)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0070062	extracellular vesicular exosome	cellular component	IDA[19056867]	176
GO:0005515	protein binding	molecular function	IPI[14563850]	563
GO:0015031	protein transport	biological process	NAS[14613930]	21
GO:0006897	endocytosis	biological process	NAS[10329004]	15
GO:0005768	endosome	cellular component	IDA[16412388]	27
GO:0030276	clathrin binding	molecular function	IDA[16412388]	2
GO:0005829	cytosol	cellular component	IDA[14613930]	223
GO:0006886	intracellular protein transport	biological process	IEA	10
GO:0005769	early endosome	cellular component	IDA[14613930]	13
GO:0005737	cytoplasm	cellular component	IDA[16412388]	322
GO:0016197	endosomal transport	biological process	NAS[14613930]; TAS[10329004]	3

Gene related KEGG pathways (count: 0)

Gene related BioCarta pathways (count: 0)

Gene related interactors from protein-protein interactions data in HPRD (count: 4)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
TOM1	CLTC	YES	in vitro;in vivo;yeast 2-hybrid	14563850
TOM1	ZFYVE16	NO	in vitro;in vivo;yeast 2-hybrid	14613930
TOM1	TOLLIP	NO	in vitro;in vivo;yeast 2-hybrid	14563850
TOM1	EEA1	NO	in vitro	14613930

Related other genetic factors

Gene related SNPs (count: 37)

Literature-origin SNPs (count: 14)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs138773	chr22:35309949 - 35309949(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1(1/0/0)
rs11703672	chr22:35360792 - 35360792(1)		1(1/0/0)
rs5750102	chr22:35358119 - 35358119(1)		1(0/1/0)
rs4462	chr22:35301399 - 35301399(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1(1/0/0)
rs4465	chr22:35312797 - 35312797(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1(1/0/0)
rs4511	chr22:35320601 - 35320601(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1(1/0/0)
rs9622182	chr22:35367321 - 35367321(1)	upstream_gene_variant	1(0/1/0)
rs138784	chr22:35321253 - 35321253(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1(1/0/0)
rs138764	chr22:35307135 - 35307135(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1(1/0/0)
rs739015	chr22:35327725 - 35327725(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1(1/0/0)
rs762967	chr22:35344873 - 35344873(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	1(0/1/0)
rs743810	chr22:35346932 - 35346932(1)	3_prime_UTR_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; splice_region_variant; synonymous_variant	1(1/0/0)
rs138781	chr22:35316621 - 35316621(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1(1/0/0)
rs4467	chr22:35335252 - 35335252(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)

LD-proxies (count: 23)

rs_ID	Location	Functional Annotation
rs138760	chr22:35306075 - 35306075(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs138765	chr22:35307288 - 35307288(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs2267330	chr22:35308619 - 35308619(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs138774	chr22:35312806 - 35312806(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs377904	chr22:35303052 - 35303052(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs4510	chr22:35303460 - 35303460(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs138744	chr22:35303890 - 35303890(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs138745	chr22:35304262 - 35304262(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs4461	chr22:35299809 - 35299809(1)	5_prime_UTR_variant; downstream_gene_variant; intron_variant; upstream_gene_variant
rs138728	chr22:35300084 - 35300084(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs138733	chr22:35301619 - 35301619(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs138738	chr22:35302498 - 35302498(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs4821392	chr22:35294539 - 35294539(1)	3_prime_UTR_variant; downstream_gene_variant; NMD_transcript_variant; upstream_gene_variant
rs4509	chr22:35298216 - 35298216(1)	downstream_gene_variant; upstream_gene_variant
rs138726	chr22:35298302 - 35298302(1)	downstream_gene_variant; upstream_gene_variant
rs138727	chr22:35298900 - 35298900(1)	downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant
rs4820191	chr22:35352215 - 35352215(1)	downstream_gene_variant
rs2267336	chr22:35344135 - 35344135(1)	intron_variant; NMD_transcript_variant; upstream_gene_variant
rs138780	chr22:35316560 - 35316560(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs6518950	chr22:35349203 - 35349203(1)	downstream_gene_variant
rs5750101	chr22:35349531 - 35349531(1)	downstream_gene_variant
rs138779	chr22:35316184 - 35316184(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
rs138777	chr22:35315105 - 35315105(1)	intron_variant; NMD_transcript_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)
22q12.3-13.32	chr22:31800000-49100000	1 (0/1/0)
Chr 22	chr22:0-50818468	2 (0/1/1)
22q12.3-q13.33	chr22:31800000-50818468	1 (1/0/0)

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

Gene relationship with SZ

Gene relationship with MDD

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Region: chr22:35299275..35347994 View in gBrowse