TOM1 Gene

Name	target of myb1 (chicken)
Description	This gene was identified as a target of the v-myb oncogene. The encoded protein shares its N-terminal domain in common with proteins associated with vesicular trafficking at the endosome. It is recruited to the endosomes by its interaction with endofin. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2008]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nTOM1 was originally identified as a target of the v‐myb oncogene and is now recognized as an adaptor protein defined by its VHS and GAT domains. These domains enable TOM1 to bind polyubiquitin chains and to interact selectively with Tollip, thereby forming a complex that links ubiquitinated cargo to components of the clathrin machinery. In addition, TOM1 associates with endosomal proteins such as endofin, which recruits TOM1 to early endosomes and facilitates its binding to clathrin heavy chain, collectively supporting its critical role in intracellular trafficking and sorting."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "4"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nExtending beyond its basic trafficking functions, genetic and regulatory studies have underscored broader roles for TOM1. A haplotype spanning part of the TOM1 locus has been associated with psychotic bipolar affective disorder, suggesting that alterations in this gene may influence neuronal signaling. In cystic fibrosis airway epithelial cells, reduced levels of miR‐126 correlate with an upregulation of TOM1 mRNA, pointing to a role for TOM1 in modulating Toll‐like receptor–mediated innate immune signaling. Furthermore, in the context of autophagy, TOM1 interacts with myosin VI and associated adaptor proteins to mediate the delivery of endosomal membranes to the autophagosome—a critical step that promotes autophagosome maturation and its subsequent fusion with lysosomes."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "5", "end_ref": "7"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nAdditional studies have revealed that TOM1 can directly bind phosphoinositide PI5P on signaling endosomes—a process that delays the degradation of receptors such as the epidermal growth factor receptor and modulates fluid‐phase bulk endocytosis. Moreover, structural analyses indicate that TOM1’s interaction with Tollip may promote the release of Tollip from endosomal membranes, thereby fine‐tuning cargo trafficking. In neurodegenerative settings, particularly Alzheimer’s disease, TOM1 has been observed within dystrophic neurites and neurofibrillary tangles, and experimental evidence suggests that by regulating receptor recycling, TOM1 can attenuate the neuronal uptake of pathogenic amyloid‑β."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "8", "end_ref": "11"}]}, {"type": "t", "text": "\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Megumi Yamakami, Tamotsu Yoshimori, Hideyoshi Yokosawa "}, {"type": "b", "children": [{"type": "t", "text": "Tom1, a VHS domain-containing protein, interacts with tollip, ubiquitin, and clathrin."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2003)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.M306740200"}], "href": "https://doi.org/10.1074/jbc.M306740200"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "14563850"}], "href": "https://pubmed.ncbi.nlm.nih.gov/14563850"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Li-Fong Seet, Ningsheng Liu, Brendon J Hanson, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Endofin recruits TOM1 to endosomes."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2004)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.M311228200"}], "href": "https://doi.org/10.1074/jbc.M311228200"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "14613930"}], "href": "https://pubmed.ncbi.nlm.nih.gov/14613930"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Yohei Katoh, Yoko Shiba, Hiroko Mitsuhashi, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Tollip and Tom1 form a complex and recruit ubiquitin-conjugated proteins onto early endosomes."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2004)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.M400059200"}], "href": "https://doi.org/10.1074/jbc.M400059200"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15047686"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15047686"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Li-Fong Seet, Wanjin Hong "}, {"type": "b", "children": [{"type": "t", "text": "Endofin recruits clathrin to early endosomes via TOM1."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Cell Sci (2005)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1242/jcs.01628"}], "href": "https://doi.org/10.1242/jcs.01628"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15657082"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15657082"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "James B Potash, Silvia Buervenich, Nancy J Cox, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Gene-based SNP mapping of a psychotic bipolar affective disorder linkage region on 22q12.3: association with HMG2L1 and TOM1."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Am J Med Genet B Neuropsychiatr Genet (2008)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1002/ajmg.b.30574"}], "href": "https://doi.org/10.1002/ajmg.b.30574"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "17671966"}], "href": "https://pubmed.ncbi.nlm.nih.gov/17671966"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Irene K Oglesby, Isabella M Bray, Sanjay H Chotirmall, et al. "}, {"type": "b", "children": [{"type": "t", "text": "miR-126 is downregulated in cystic fibrosis airway epithelial cells and regulates TOM1 expression."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Immunol (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.4049/jimmunol.0902669"}], "href": "https://doi.org/10.4049/jimmunol.0902669"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20083669"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20083669"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "David A Tumbarello, Bennett J Waxse, Susan D Arden, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Autophagy receptors link myosin VI to autophagosomes to mediate Tom1-dependent autophagosome maturation and fusion with the lysosome."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Cell Biol (2012)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/ncb2589"}], "href": "https://doi.org/10.1038/ncb2589"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "23023224"}], "href": "https://pubmed.ncbi.nlm.nih.gov/23023224"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Frédéric Boal, Rana Mansour, Marion Gayral, et al. "}, {"type": "b", "children": [{"type": "t", "text": "TOM1 is a PI5P effector involved in the regulation of endosomal maturation."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Cell Sci (2015)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1242/jcs.166314"}], "href": "https://doi.org/10.1242/jcs.166314"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "25588840"}], "href": "https://pubmed.ncbi.nlm.nih.gov/25588840"}]}, {"type": "r", "ref": 9, "children": [{"type": "t", "text": "Shuyan Xiao, Mary K Brannon, Xiaolin Zhao, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Tom1 Modulates Binding of Tollip to Phosphatidylinositol 3-Phosphate via a Coupled Folding and Binding Mechanism."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Structure (2015)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.str.2015.07.017"}], "href": "https://doi.org/10.1016/j.str.2015.07.017"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26320582"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26320582"}]}, {"type": "r", "ref": 10, "children": [{"type": "t", "text": "Kouki Makioka, Tsuneo Yamazaki, Masamitsu Takatama, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Immunolocalization of Tom1 in relation to protein degradation systems in Alzheimer's disease."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Neurol Sci (2016)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.jns.2016.03.035"}], "href": "https://doi.org/10.1016/j.jns.2016.03.035"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "27206884"}], "href": "https://pubmed.ncbi.nlm.nih.gov/27206884"}]}, {"type": "r", "ref": 11, "children": [{"type": "t", "text": "Youngdae Gwon, Tae-In Kam, Seo-Hyun Kim, et al. "}, {"type": "b", "children": [{"type": "t", "text": "TOM1 Regulates Neuronal Accumulation of Amyloid-β Oligomers by FcγRIIb2 Variant in Alzheimer's Disease."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Neurosci (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1523/JNEUROSCI.1996-17.2018"}], "href": "https://doi.org/10.1523/JNEUROSCI.1996-17.2018"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "30185465"}], "href": "https://pubmed.ncbi.nlm.nih.gov/30185465"}]}]}]}
Proteins	TOM1_HUMAN
NCBI Gene ID	10043
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Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

TOM1 has 6,601 functional associations with biological entities spanning 9 categories (molecular profile, organism, chemical, functional term, phrase or reference, disease, phenotype or trait, structural feature, cell line, cell type or tissue, gene, protein or microRNA, sequence feature) extracted from 117 datasets.

Click the + buttons to view associations for TOM1 from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

TOM1 Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Achilles Cell Line Gene Essentiality Profiles	cell lines with fitness changed by TOM1 gene knockdown relative to other cell lines from the Achilles Cell Line Gene Essentiality Profiles dataset.
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of TOM1 gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	tissues with high or low expression of TOM1 gene relative to other tissues from the Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of TOM1 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	tissue samples with high or low expression of TOM1 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of TOM1 gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	BioGPS Cell Line Gene Expression Profiles	cell lines with high or low expression of TOM1 gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset.
	BioGPS Human Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of TOM1 gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of TOM1 gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of TOM1 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Gene Expression Profiles	cell lines with high or low expression of TOM1 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with TOM1 protein from the CCLE Cell Line Proteomics dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with TOM1 gene from the CellMarker Gene-Cell Type Associations dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of TOM1 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of TOM1 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of TOM1 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of TOM1 gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing TOM1 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing TOM1 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores 2025	cellular components containing TOM1 protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with TOM1 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with TOM1 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of TOM1 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with TOM1 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Chemical Interactions	chemicals interacting with TOM1 gene/protein from the curated CTD Gene-Chemical Interactions dataset.
	CTD Gene-Disease Associations	diseases associated with TOM1 gene/protein from the curated CTD Gene-Disease Associations dataset.
	DeepCoverMOA Drug Mechanisms of Action	small molecule perturbations with high or low expression of TOM1 protein relative to other small molecule perturbations from the DeepCoverMOA Drug Mechanisms of Action dataset.
	DepMap CRISPR Gene Dependency	cell lines with fitness changed by TOM1 gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	diseases associated with TOM1 gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores 2025 dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with TOM1 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with TOM1 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with TOM1 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with TOM1 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Phenoptype Associations dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at TOM1 gene from the ENCODE Histone Modification Site Profiles dataset.
	ENCODE Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of TOM1 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of TOM1 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	PubMedIDs of publications reporting gene signatures containing TOM1 from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
	GAD Gene-Disease Associations	diseases associated with TOM1 gene in GWAS and other genetic association datasets from the GAD Gene-Disease Associations dataset.
	GAD High Level Gene-Disease Associations	diseases associated with TOM1 gene in GWAS and other genetic association datasets from the GAD High Level Gene-Disease Associations dataset.
	GDSC Cell Line Gene Expression Profiles	cell lines with high or low expression of TOM1 gene relative to other cell lines from the GDSC Cell Line Gene Expression Profiles dataset.