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TOM1L2 target of myb1 like 2 membrane trafficking protein [ Homo sapiens (human) ]

Gene ID: 146691, updated on 7-Apr-2024

Summary

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Official Symbol
TOM1L2provided by HGNC
Official Full Name
target of myb1 like 2 membrane trafficking proteinprovided by HGNC
Primary source
HGNC:HGNC:11984
See related
Ensembl:ENSG00000175662 MIM:615519; AllianceGenome:HGNC:11984
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
Summary
This gene belongs to a small gene family whose members have an N-terminal VHS domain followed by a GAT domain; domains which typically participate in vesicular trafficking. The canonical protein encoded by this gene also has a C-terminal clathrin binding motif. This protein has been shown to interact with Tollip, clathrin and ubiquitin and is thought to play a role in endosomal sorting. This gene resides in the 3.7 Mb deletion of chromosome region 17p11.2 that is associated with Smith-Magenis syndrome. Alternative splicing results in multiple transcript variants encoding distinct proteins. [provided by RefSeq, Apr 2017]
Expression
Broad expression in heart (RPKM 43.2), brain (RPKM 27.4) and 23 other tissues See more
Orthologs
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Genomic context

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Location:
17p11.2
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (17843511..17972400, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (17790194..17919077, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (17746825..17875714, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17722069-17722789 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11811 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:17726733-17726883 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8257 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11812 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11813 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17730461-17731182 Neighboring gene microRNA 6777 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17731183-17731904 Neighboring gene sterol regulatory element binding transcription factor 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17733682-17734430 Neighboring gene microRNA 33b Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17734431-17735178 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17739175-17740076 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17740077-17740979 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:17740980-17741881 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17743523-17744042 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8261 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17745179-17745680 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17747581-17748101 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17751860-17752706 Neighboring gene Sharpr-MPRA regulatory region 7387 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:17762139-17762639 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11815 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:17779053-17780252 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17780613-17781334 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17787373-17788134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17788135-17788894 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17792123-17792624 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11816 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11817 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17817644-17818266 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17823655-17824188 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17824189-17824722 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17825257-17825790 Neighboring gene Sharpr-MPRA regulatory region 12990 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17825791-17826324 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17826325-17826857 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11818 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8262 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17875207-17875776 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11819 Neighboring gene uncharacterized LOC107984989 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17884370-17884870 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:17898150-17898316 Neighboring gene dynein regulatory complex subunit 3 Neighboring gene brain protein I3 pseudogene 3 Neighboring gene ribosomal protein S2 pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: 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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Related articles in PubMed

  1. The ancestral ESCRT protein TOM1L2 selects ubiquitinated cargoes for retrieval from cilia. Shinde SR, et al. Dev Cell, 2023 Apr 24. PMID 37019113,
  2. Bivariate genome-wide association meta-analysis of pediatric musculoskeletal traits reveals pleiotropic effects at the SREBF1/TOM1L2 locus. Medina-Gomez C, et al. Nat Commun, 2017 Jul 25. PMID 28743860, Free PMC Article
  3. Transcription mapping in a medulloblastoma breakpoint interval and Smith-Magenis syndrome candidate region: identification of 53 transcriptional units and new candidate genes. Seranski P, et al. Genomics, 1999 Feb 15. PMID 10036180
  4. Tollip coordinates Parkin-dependent trafficking of mitochondrial-derived vesicles. Ryan TA, et al. EMBO J, 2020 Jun 2. PMID 32311122, Free PMC Article
  5. Autophagy receptors link myosin VI to autophagosomes to mediate Tom1-dependent autophagosome maturation and fusion with the lysosome. Tumbarello DA, et al. Nat Cell Biol, 2012 Oct. PMID 23023224, Free PMC Article

See all (62) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The ancestral ESCRT protein TOM1L2 selects ubiquitinated cargoes for retrieval from cilia.
    Title: The ancestral ESCRT protein TOM1L2 selects ubiquitinated cargoes for retrieval from cilia.
  2. Variants in the TOM1L2/SREBF1 locus exert opposing effects of total-body lean mass (TB-LM) and total-body less head bone mineral density (TBLH-BMD) .
    Title: Bivariate genome-wide association meta-analysis of pediatric musculoskeletal traits reveals pleiotropic effects at the SREBF1/TOM1L2 locus.
  3. Two possible dementia susceptibility genes including ATPAF2 and TOM1L2 near SREBF1 locus were identified.
    Title: Analysis of lipid pathway genes indicates association of sequence variation near SREBF1/TOM1L2/ATPAF2 with dementia risk.
  4. Observational study of gene-disease association. (HuGE Navigator)
    Title: Analysis of lipid pathway genes indicates association of sequence variation near SREBF1/TOM1L2/ATPAF2 with dementia risk.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ21501, FLJ32746

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 phosphatidylinositol binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein kinase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ubiquitin binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in negative regulation of mitotic nuclear division IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in signal transduction IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
is_active_in endosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in extracellular exosome HDA PubMed 
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
TOM1-like protein 2
Names
target of Myb-like protein 2
target of myb1-like 2

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.

Genomic

  1. NG_053113.1 RefSeqGene

    Range
    5071..133960
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001033551.3 → NP_001028723.1  TOM1-like protein 2 isoform 1

    See identical proteins and their annotated locations for NP_001028723.1

    Status: REVIEWED

    Source sequence(s)
    AC122129, BC051650, BM976586
    Consensus CDS
    CCDS32584.1
    UniProtKB/Swiss-Prot
    Q6ZVM7
    Related
    ENSP00000464297.1, ENST00000581396.5
    Conserved Domains (2) summary
    cd14238
    Location:168 → 259
    GAT_TM1L2; GAT domain found in target of Myb-like protein 2 (Tom1L2)
    cl02544
    Location:12 → 98
    VHS_ENTH_ANTH; VHS, ENTH and ANTH domain superfamily

  2. NM_001082968.2 → NP_001076437.1  TOM1-like protein 2 isoform 3

    See identical proteins and their annotated locations for NP_001076437.1

    Status: REVIEWED

    Source sequence(s)
    AC122129, AK124331, BM976586, DA235267, DA335727
    Consensus CDS
    CCDS42270.1
    UniProtKB/Swiss-Prot
    B7Z2L7, B7Z7F4, Q6ZVM7, Q86V61, Q8TDE7, Q96M88
    Related
    ENSP00000368818.3, ENST00000379504.8
    Conserved Domains (2) summary
    cd14238
    Location:218 → 309
    GAT_TM1L2; GAT domain found in target of Myb-like protein 2 (Tom1L2)
    cd16996
    Location:12 → 148
    VHS_Tom1L2; VHS (Vps27/Hrs/STAM) domain of TOM1-like protein 2

  3. NM_001288786.2 → NP_001275715.1  TOM1-like protein 2 isoform 4

    See identical proteins and their annotated locations for NP_001275715.1

    Status: REVIEWED

    Source sequence(s)
    AC122129, AK294846, AK301944, BM976586
    Consensus CDS
    CCDS74003.1
    UniProtKB/TrEMBL
    B7Z671
    Related
    ENSP00000438621.1, ENST00000535933.5
    Conserved Domains (2) summary
    cd16996
    Location:12 → 148
    VHS_Tom1L2; VHS (Vps27/Hrs/STAM) domain of TOM1-like protein 2
    cd14238
    Location:165 → 256
    GAT_TM1L2; canonical GAT domain found in target of Myb-like protein 2 (Tom1L2)

  4. NM_001288787.2 → NP_001275716.1  TOM1-like protein 2 isoform 5

    See identical proteins and their annotated locations for NP_001275716.1

    Status: REVIEWED

    Source sequence(s)
    AC122129, AK301944, BM976586, DA235267
    Consensus CDS
    CCDS74002.1
    UniProtKB/Swiss-Prot
    Q6ZVM7
    Related
    ENSP00000312860.10, ENST00000318094.14
    Conserved Domains (2) summary
    cd14238
    Location:173 → 264
    GAT_TM1L2; canonical GAT domain found in target of Myb-like protein 2 (Tom1L2)
    cl02544
    Location:12 → 123
    VHS_ENTH_ANTH; VHS, ENTH and ANTH domain superfamily

  5. NM_001288788.2 → NP_001275717.1  TOM1-like protein 2 isoform 6

    See identical proteins and their annotated locations for NP_001275717.1

    Status: REVIEWED

    Source sequence(s)
    AC122129, AK295111, AK301944, BM976586, DA235267
    Consensus CDS
    CCDS74001.1
    UniProtKB/TrEMBL
    B7Z2U2, B7Z671
    Related
    ENSP00000437655.1, ENST00000540946.5
    Conserved Domains (2) summary
    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 ...
    cl03906
    Location:122 → 211
    GAT_SF; GAT domain found in eukaryotic ADP-ribosylation factor (Arf)-binding proteins (GGAs), metazoan myb protein 1 (Tom1)-like proteins, and similar proteins

  6. NM_001288789.2 → NP_001275718.1  TOM1-like protein 2 isoform 7

    See identical proteins and their annotated locations for NP_001275718.1

    Status: REVIEWED

    Source sequence(s)
    AC122129, AK299872, AK301944, BM976586
    Consensus CDS
    CCDS74000.1
    UniProtKB/TrEMBL
    B7Z671, F5H3S6
    Related
    ENSP00000445188.1, ENST00000542206.5
    Conserved Domains (2) summary
    cl02544
    Location:12 → 73
    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 ...
    cl03906
    Location:73 → 161
    GAT_SF; GAT domain found in eukaryotic ADP-ribosylation factor (Arf)-binding proteins (GGAs), metazoan myb protein 1 (Tom1)-like proteins, and similar proteins

  7. NM_001350331.2 → NP_001337260.1  TOM1-like protein 2 isoform 8

    Status: REVIEWED

    Source sequence(s)
    AC122129, AK295111, AK301944, BM976586, DA235267
    Conserved Domains (2) summary
    cd14238
    Location:173 → 264
    GAT_TM1L2; canonical GAT domain found in target of Myb-like protein 2 (Tom1L2)
    cl02544
    Location:12 → 123
    VHS_ENTH_ANTH; VHS, ENTH and ANTH domain superfamily

  8. NM_001350332.2 → NP_001337261.1  TOM1-like protein 2 isoform 9

    Status: REVIEWED

    Source sequence(s)
    AC122129, AK294846, BC051650, BM976586
    Conserved Domains (2) summary
    cd14238
    Location:218 → 309
    GAT_TM1L2; GAT domain found in target of Myb-like protein 2 (Tom1L2)
    cd16996
    Location:12 → 148
    VHS_Tom1L2; VHS (Vps27/Hrs/STAM) domain of TOM1-like protein 2

  9. NM_001350333.2 → NP_001337262.1  TOM1-like protein 2 isoform 10

    Status: REVIEWED

    Source sequence(s)
    AC122129, AK294846, BC051650, BM976586
    Conserved Domains (2) summary
    cd14238
    Location:218 → 309
    GAT_TM1L2; GAT domain found in target of Myb-like protein 2 (Tom1L2)
    cd16996
    Location:12 → 148
    VHS_Tom1L2; VHS (Vps27/Hrs/STAM) domain of TOM1-like protein 2

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    17843511..17972400 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047435389.1 → XP_047291345.1  TOM1-like protein 2 isoform X8

  2. XM_047435386.1 → XP_047291342.1  TOM1-like protein 2 isoform X5

  3. XM_011523662.2 → XP_011521964.1  TOM1-like protein 2 isoform X2

    Conserved Domains (2) summary
    cd14238
    Location:168 → 259
    GAT_TM1L2; GAT domain found in target of Myb-like protein 2 (Tom1L2)
    cl02544
    Location:12 → 98
    VHS_ENTH_ANTH; VHS, ENTH and ANTH domain superfamily

  4. XM_047435388.1 → XP_047291344.1  TOM1-like protein 2 isoform X7

  5. XM_005256466.2 → XP_005256523.1  TOM1-like protein 2 isoform X4

    See identical proteins and their annotated locations for XP_005256523.1

    UniProtKB/TrEMBL
    B7Z671
    Conserved Domains (2) summary
    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 ...
    cl03906
    Location:122 → 211
    GAT_SF; GAT domain found in eukaryotic ADP-ribosylation factor (Arf)-binding proteins (GGAs), metazoan myb protein 1 (Tom1)-like proteins, and similar proteins

  6. XM_005256462.2 → XP_005256519.1  TOM1-like protein 2 isoform X1

    Conserved Domains (2) summary
    cd14238
    Location:173 → 264
    GAT_TM1L2; canonical GAT domain found in target of Myb-like protein 2 (Tom1L2)
    cl02544
    Location:12 → 123
    VHS_ENTH_ANTH; VHS, ENTH and ANTH domain superfamily

  7. XM_024450589.2 → XP_024306357.1  TOM1-like protein 2 isoform X6

    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 ...
    cl03906
    Location:165 → 256
    GAT_SF; GAT domain found in eukaryotic ADP-ribosylation factor (Arf)-binding proteins (GGAs), metazoan myb protein 1 (Tom1)-like proteins, and similar proteins

  8. XM_047435385.1 → XP_047291341.1  TOM1-like protein 2 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    17790194..17919077 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054315113.1 → XP_054171088.1  TOM1-like protein 2 isoform X8

  2. XM_054315110.1 → XP_054171085.1  TOM1-like protein 2 isoform X5

  3. XM_054315107.1 → XP_054171082.1  TOM1-like protein 2 isoform X2

  4. XM_054315112.1 → XP_054171087.1  TOM1-like protein 2 isoform X7

  5. XM_054315109.1 → XP_054171084.1  TOM1-like protein 2 isoform X4

  6. XM_054315106.1 → XP_054171081.1  TOM1-like protein 2 isoform X1

  7. XM_054315111.1 → XP_054171086.1  TOM1-like protein 2 isoform X6

  8. XM_054315108.1 → XP_054171083.1  TOM1-like protein 2 isoform X3

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_144678.3: Suppressed sequence

    Description
    NM_144678.3: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6ZVM7.1 GenPept UniProtKB/Swiss-Prot:Q6ZVM7

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