TOM1 target of myb1 membrane trafficking protein [Homo sapiens (human)] - Gene

Summary

Official Symbol: TOM1provided by HGNC
Official Full Name: target of myb1 membrane trafficking proteinprovided by HGNC
Primary source: HGNC:HGNC:11982
See related: Ensembl:ENSG00000100284 MIM:604700; AllianceGenome:HGNC:11982
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: IMD85
Summary: 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]
Expression: Ubiquitous expression in bone marrow (RPKM 24.4), esophagus (RPKM 24.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 22q12.3

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	22	NC_000022.11 (35299275..35347973)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	22	NC_060946.1 (35757154..35805980)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	22	NC_000022.10 (35695268..35743966)

Chromosome 22 - NC_000022.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Study shows that TOM1 regulates neuronal accumulation of amyloid-beta oligomers by FcgammaRIIb2 variant in Alzheimer's Disease (AD). Study provides a molecular mechanism responsible for neuronal uptake of pathogenic Abeta found in AD.
Title: TOM1 Regulates Neuronal Accumulation of Amyloid-β Oligomers by FcγRIIb2 Variant in Alzheimer's Disease.
This study demonstrated that Tom1 is localized in dystrophic neurites of brain in patient with Alzheimer's disease.
Title: Immunolocalization of Tom1 in relation to protein degradation systems in Alzheimer's disease.
Tom1 modulates binding of Tollip to phosphatidylinositol 3-phosphate via a coupled folding and binding mechanism.
Title: Tom1 Modulates Binding of Tollip to Phosphatidylinositol 3-Phosphate via a Coupled Folding and Binding Mechanism.
candidate multiple myeloma risk locus
Title: Variants in ELL2 influencing immunoglobulin levels associate with multiple myeloma.
phosphatidylinositol 5-monophosphate (PI5P) enrichment in signaling endosomes prevents endosomal maturation through the recruitment of TOM1, and point to a new function of PI5P in regulating discrete maturation steps in the endosomal system.
Title: TOM1 is a PI5P effector involved in the regulation of endosomal maturation.
It was shown that that myosin VI, in concert with Tom1, plays a crucial role in autophagy. Tom1 was identified as a myosin VI binding partner on endosomes.
Title: Autophagy receptors link myosin VI to autophagosomes to mediate Tom1-dependent autophagosome maturation and fusion with the lysosome.
TOM1 is a microRNA-126 target that may have an important role in regulating innate immune responses in the cystic fibrosis lung.
Title: miR-126 is downregulated in cystic fibrosis airway epithelial cells and regulates TOM1 expression.
A 3-marker haplotype of SNPs within TOM1 was associated with psychotic bipolar affective disorder linkage
Title: Gene-based SNP mapping of a psychotic bipolar affective disorder linkage region on 22q12.3: association with HMG2L1 and TOM1.
Observational study of gene-disease association. (HuGE Navigator)
Title: Gene-based SNP mapping of a psychotic bipolar affective disorder linkage region on 22q12.3: association with HMG2L1 and TOM1.
Tollip and Tom1 form a complex and regulate endosomal trafficking of ubiquitinated proteins
Title: Tollip and Tom1 form a complex and recruit ubiquitin-conjugated proteins onto early endosomes.

Submit: New GeneRIF Correction See all GeneRIFs (13)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Immunodeficiency 85 and autoimmunity MedGen: C5561976 OMIM: 619510 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
Discovery and refinement of loci associated with lipid levels. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of target of myb1 (TOM1) by siRNA has both activating and inhibiting activities on HIV-1 replication in HeLa P4/R5 cells, suggesting a regulatory role in HIV replication	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G49310 (e-PCR)
- UniSTS:109066

G49311 (e-PCR)
- UniSTS:109067

G49312 (e-PCR)
- UniSTS:109068

G49313 (e-PCR)
- UniSTS:109069

G49314 (e-PCR)
- UniSTS:109070

G49346 (e-PCR)
- UniSTS:109102

G49347 (e-PCR)
- UniSTS:109103

TOM1__5115 (e-PCR)
- UniSTS:466522

D22S424 (e-PCR), detects polymorphism
- UniSTS:79452

G49422 (e-PCR)
- UniSTS:109167

G49423 (e-PCR)
- UniSTS:109168

G49424 (e-PCR)
- UniSTS:109169

G49427 (e-PCR)
- UniSTS:109172

SHGC-153073 (e-PCR)
- UniSTS:173173

D1S3693 (e-PCR)
- UniSTS:474271

SGC31973 (e-PCR)
- UniSTS:58543

SHGC-152032 (e-PCR)
- UniSTS:182974

G49260 (e-PCR)
- UniSTS:109016

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables clathrin binding	IBA Inferred from Biological aspect of Ancestor more info
enables clathrin binding	IDA Inferred from Direct Assay more info	PubMed
enables clathrin heavy chain binding	IDA Inferred from Direct Assay more info	PubMed
enables myosin VI binding	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidylinositol-5-phosphate binding	IDA Inferred from Direct Assay more info	PubMed
enables polyubiquitin modification-dependent protein binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in autophagosome-lysosome fusion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endocytosis	NAS Non-traceable Author Statement more info	PubMed
involved_in endosomal transport	IDA Inferred from Direct Assay more info	PubMed
involved_in endosomal transport	NAS Non-traceable Author Statement more info	PubMed
involved_in endosomal transport	TAS Traceable Author Statement more info	PubMed
involved_in positive regulation of autophagosome maturation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein transport	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of endosome organization	IDA Inferred from Direct Assay more info	PubMed
involved_in signal transduction	IBA Inferred from Biological aspect of Ancestor more info
involved_in substrate localization to autophagosome	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in azurophil granule membrane	TAS Traceable Author Statement more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in early endosome	IDA Inferred from Direct Assay more info	PubMed
located_in early endosome membrane	IEA Inferred from Electronic Annotation more info
is_active_in endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in endosome	IDA Inferred from Direct Assay more info	PubMed
located_in endosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
is_active_in membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info
located_in specific granule membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: target of Myb1 membrane trafficking protein

Names: target of Myb protein 1; target of myb 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001135729.2 → NP_001129201.1 target of Myb1 membrane trafficking protein isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) contains a different 5' terminal exon and uses an alternate donor splice site at the penultimate exon compared to transcript variant 1. This results in translation initiation from a downstream AUG and an isoform (3) with a shorter N-terminus compared to isoform 1.

Source sequence(s)

AJ006973, AK097066, AK293694

Consensus CDS

CCDS46698.1

UniProtKB/TrEMBL

B4DKQ5

Related

ENSP00000398876.1, ENST00000447733.5

Conserved Domains (2) summary

cd14236
Location:181 → 275

GAT_TOM1; GAT domain found in target of Myb protein 1 (Tom1)

cl02544
Location:1 → 119

VHS_ENTH_ANTH; VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal ...
NM_001135730.2 → NP_001129202.1 target of Myb1 membrane trafficking protein isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (4) is missing an in-frame coding exon compared to transcript variant 1, resulting in a shorter isoform (4) lacking an internal 45 aa segment compared to isoform 1.

Source sequence(s)

AJ006973, AK097066, DC297234

Consensus CDS

CCDS46697.1

UniProtKB/TrEMBL

B4DKQ5

Related

ENSP00000394924.1, ENST00000425375.5

Conserved Domains (2) summary

cd14236
Location:169 → 263

GAT_TOM1; GAT domain found in target of Myb protein 1 (Tom1)

cl02544
Location:12 → 123

VHS_ENTH_ANTH; VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal ...
NM_001135732.2 → NP_001129204.1 target of Myb1 membrane trafficking protein isoform 2

See identical proteins and their annotated locations for NP_001129204.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate donor splice site at the penultimate exon compared to transcript variant 1, resulting in an isoform (2) with one extra aa compared to isoform 1.

Source sequence(s)

BC046151, DC297234

Consensus CDS

CCDS46696.1

UniProtKB/TrEMBL

B4DKQ5

Related

ENSP00000413697.1, ENST00000411850.5

Conserved Domains (2) summary

cd03565
Location:12 → 152

VHS_Tom1; VHS domain family, Tom1 subfamily; The VHS domain is an essential part of Tom1 (Target of myb1 - retroviral oncogene) protein. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of ...

cd14236
Location:214 → 308

GAT_TOM1; GAT domain found in target of Myb protein 1 (Tom1)
NM_005488.3 → NP_005479.1 target of Myb1 membrane trafficking protein isoform 1

See identical proteins and their annotated locations for NP_005479.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the most predominant transcript and encodes isoform 1.

Source sequence(s)

AJ006973, AK097066, DC297234

Consensus CDS

CCDS13913.1

UniProtKB/Swiss-Prot

B4DEL9, B4DNA1, O60784, Q5TIJ6, Q86X74

UniProtKB/TrEMBL

B4DKQ5

Related

ENSP00000394466.2, ENST00000449058.7

Conserved Domains (2) summary

cd03565
Location:12 → 152

VHS_Tom1; VHS domain family, Tom1 subfamily; The VHS domain is an essential part of Tom1 (Target of myb1 - retroviral oncogene) protein. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of ...

cd14236
Location:214 → 308

GAT_TOM1; GAT domain found in target of Myb protein 1 (Tom1)

RNA

NR_024194.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (5) uses an alternate acceptor splice site at one of the coding exons compared to transcript variant 1. This results in a frame-shift and premature translation termination, rendering the transcript susceptible to nonsense mediated mRNA decay (NMD). This variant is sufficiently abundant to represent as a RefSeq record, however, the predicted protein is not represented because it is significantly truncated.

Source sequence(s)

AK097066, AK296670, DC297234

Related

ENST00000424387.5
NR_024195.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (6) is missing an internal coding exon and uses an alternate acceptor splice site at another coding exon compared to transcript variant 1. This results in a frame-shift and premature translation termination, rendering the transcript susceptible to nonsense mediated mRNA decay (NMD). This variant is sufficiently abundant to represent as a RefSeq record, however, the predicted protein is not represented because it is significantly truncated.

Source sequence(s)

AJ006973, AK097066, AK295918, DC297234
NR_156428.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (7) is missing an internal coding exon compared to transcript variant 1. This results in a frame-shift and premature translation termination, rendering the transcript susceptible to nonsense mediated mRNA decay (NMD). This variant is sufficiently abundant to represent as a RefSeq record, however, the predicted protein is not represented because it is significantly truncated.

Source sequence(s)

AL008635, Z82244

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000022.11 Reference GRCh38.p14 Primary Assembly

Range

35299275..35347973

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047441068.1 → XP_047297024.1 target of Myb1 membrane trafficking protein isoform X1
XM_047441069.1 → XP_047297025.1 target of Myb1 membrane trafficking protein isoform X2
XM_011529820.3 → XP_011528122.1 target of Myb1 membrane trafficking protein isoform X4

Conserved Domains (1) summary

cd14236
Location:62 → 156

GAT_TOM1; GAT domain found in target of Myb protein 1 (Tom1)
XM_011529818.3 → XP_011528120.1 target of Myb1 membrane trafficking protein isoform X3

UniProtKB/TrEMBL

B4DJ44

Conserved Domains (2) summary

cd14236
Location:147 → 241

GAT_TOM1; GAT domain found in target of Myb protein 1 (Tom1)

cl02544
Location:1 → 85

VHS_ENTH_ANTH; VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal ...
XM_047441070.1 → XP_047297026.1 target of Myb1 membrane trafficking protein isoform X5

Alternate T2T-CHM13v2.0

Genomic

NC_060946.1 Alternate T2T-CHM13v2.0

Range

35757154..35805980

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054324975.1 → XP_054180950.1 target of Myb1 membrane trafficking protein isoform X1
XM_054324976.1 → XP_054180951.1 target of Myb1 membrane trafficking protein isoform X2
XM_054324978.1 → XP_054180953.1 target of Myb1 membrane trafficking protein isoform X4
XM_054324977.1 → XP_054180952.1 target of Myb1 membrane trafficking protein isoform X3
XM_054324979.1 → XP_054180954.1 target of Myb1 membrane trafficking protein isoform X5