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

    Gene ID: 146691, updated on 5-May-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
    mouse all
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    Genomic context

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    See TOM1L2 in Genome Data Viewer
    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, Free PMC Article
    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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