TOM1L2 Gene (Protein Coding)

Target Of Myb1 Like 2 Membrane Trafficking Protein

GC17M017843
GIFtS:
39
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... See more...

Aliases for TOM1L2 Gene

Aliases for TOM1L2 Gene

  • Target Of Myb1 Like 2 Membrane Trafficking Protein 2 3 5
  • Target Of Myb-Like Protein 2 3 4
  • TOM1-Like Protein 2 3 4
  • Target Of Myb1 (Chicken) Homolog-Like 1 2
  • Target Of Myb1-Like 2 (Chicken) 2
  • Target Of Myb1-Like 2 3
  • TOM1L2 5

External Ids for TOM1L2 Gene

Previous GeneCards Identifiers for TOM1L2 Gene

  • GC17U990153
  • GC17M017693
  • GC17M017950
  • GC17M017691
  • GC17M017688
  • GC17M017746
  • GC17M017500

Summaries for TOM1L2 Gene

Entrez Gene Summary for TOM1L2 Gene

  • 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]

GeneCards Summary for TOM1L2 Gene

TOM1L2 (Target Of Myb1 Like 2 Membrane Trafficking Protein) is a Protein Coding gene. Diseases associated with TOM1L2 include Smith-Magenis Syndrome and Pancreatic Acinar Cell Adenocarcinoma. Gene Ontology (GO) annotations related to this gene include protein kinase binding and clathrin binding. An important paralog of this gene is TOM1.

UniProtKB/Swiss-Prot Summary for TOM1L2 Gene

  • Probable role in protein transport. May regulate growth factor-induced mitogenic signaling.

Gene Wiki entry for TOM1L2 Gene

Additional gene information for TOM1L2 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TOM1L2 Gene

Genomics for TOM1L2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for TOM1L2 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TOM1L2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TOM1L2

Top Transcription factor binding sites by QIAGEN in the TOM1L2 gene promoter:
  • AML1a
  • Arnt
  • CP2
  • Evi-1
  • HOXA9
  • LUN-1
  • Nkx2-5
  • p53
  • SRF
  • SRF (504 AA)

Genomic Locations for TOM1L2 Gene

Latest Assembly
chr17:17,843,508-17,972,422
(GRCh38/hg38)
Size:
128,915 bases
Orientation:
Minus strand

Previous Assembly
chr17:17,746,825-17,875,714
(GRCh37/hg19 by Entrez Gene)
Size:
128,890 bases
Orientation:
Minus strand

chr17:17,746,828-17,875,736
(GRCh37/hg19 by Ensembl)
Size:
128,909 bases
Orientation:
Minus strand

Genomic View for TOM1L2 Gene

Genes around TOM1L2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TOM1L2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TOM1L2 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for TOM1L2 Gene

Proteins for TOM1L2 Gene

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  • Protein details for TOM1L2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6ZVM7-TM1L2_HUMAN
    Recommended name:
    TOM1-like protein 2
    Protein Accession:
    Q6ZVM7
    Secondary Accessions:
    • B7Z2L7
    • B7Z7F4
    • Q86V61
    • Q8TDE7
    • Q96M88

    Protein attributes for TOM1L2 Gene

    Size:
    507 amino acids
    Molecular mass:
    55556 Da
    Quaternary structure:
    • Interacts with clathrin, SRC and TOLLIP.
    SequenceCaution:
    • Sequence=AAL78338.1; Type=Frameshift; Evidence={ECO:0000305};

    Alternative splice isoforms for TOM1L2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TOM1L2 Gene

Protein Expression for TOM1L2 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for TOM1L2 Gene

  • Ubiquitination at Lys145, Lys147, Lys101, Lys106, Lys400, and Lys462
  • Modification sites at PhosphoSitePlus

Other Protein References for TOM1L2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for TOM1L2 Gene

Domains & Families for TOM1L2 Gene

Gene Families for TOM1L2 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for TOM1L2 Gene

InterPro:
Blocks:
  • VHS
  • GAT domain
ProtoNet:

Suggested Antigen Peptide Sequences for TOM1L2 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ60511, highly similar to Mus musculus target of myb1-like 2 (chicken) (Tom1l2), transcript variant 1, mRNA (B7Z2L7_HUMAN)
  • cDNA FLJ54050, highly similar to Homo sapiens target of myb1-like 2 (TOM1L2), transcript variant 2, mRNA (B7Z2U2_HUMAN)
  • Target of Myb-like protein 2 (TM1L2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q6ZVM7

UniProtKB/Swiss-Prot:

TM1L2_HUMAN :
  • The GAT domain mediates interaction with TOLLIP.
  • Belongs to the TOM1 family.
Domain:
  • The GAT domain mediates interaction with TOLLIP.
Family:
  • Belongs to the TOM1 family.
genes like me logo Genes that share domains with TOM1L2: view

Function for TOM1L2 Gene

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  6. Cell Lines for research

Molecular function for TOM1L2 Gene

UniProtKB/Swiss-Prot Function:
Probable role in protein transport. May regulate growth factor-induced mitogenic signaling.
GENATLAS Biochemistry:
v-Myb target gene-like 2,retroviral oncogene,involved in transformation of myelomonoctic cells,in the Smith-Magenis critical region

Phenotypes From GWAS Catalog for TOM1L2 Gene

Gene Ontology (GO) - Molecular Function for TOM1L2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16412388
GO:0019901 protein kinase binding IPI 16479011
GO:0030276 clathrin binding IBA,IDA 16412388
genes like me logo Genes that share ontologies with TOM1L2: view
genes like me logo Genes that share phenotypes with TOM1L2: view

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TOM1L2

Clone products for research

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for TOM1L2 Gene

Localization for TOM1L2 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TOM1L2 gene
Compartment Confidence
extracellular 4
endosome 4
nucleus 3
cytosol 3
cytoskeleton 2
golgi apparatus 2
plasma membrane 1
mitochondrion 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (2)
  • Intermediate filaments (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TOM1L2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005768 endosome IBA 21873635
GO:0016020 membrane IBA 21873635
GO:0070062 extracellular exosome HDA 19056867
genes like me logo Genes that share ontologies with TOM1L2: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for TOM1L2 Gene

Pathways & Interactions for TOM1L2 Gene

PathCards logo

SuperPathways for TOM1L2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for TOM1L2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006886 intracellular protein transport IEA --
GO:0007165 signal transduction IBA,IDA 16479011
GO:0015031 protein transport IEA --
GO:0045839 negative regulation of mitotic nuclear division IDA 16479011
genes like me logo Genes that share ontologies with TOM1L2: view

No data available for Pathways by source and SIGNOR curated interactions for TOM1L2 Gene

Drugs & Compounds for TOM1L2 Gene

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  1. Drug products for research
No Compound Related Data Available

Transcripts for TOM1L2 Gene

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mRNA/cDNA for TOM1L2 Gene

10 REFSEQ mRNAs :
17 NCBI additional mRNA sequence :
14 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TOM1L2

Clone products for research

Alternative Splicing Database (ASD) splice patterns (SP) for TOM1L2 Gene

No ASD Table

Relevant External Links for TOM1L2 Gene

GeneLoc Exon Structure for
TOM1L2

Expression for TOM1L2 Gene

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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TOM1L2 Gene

mRNA expression in normal human tissues for TOM1L2 Gene
mRNA expression by GTEx for TOM1L2 GenemRNA expression by BioGPS for TOM1L2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TOM1L2 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (15.2), Adrenal (10.2), and Cervix (8.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TOM1L2 Gene



Protein tissue co-expression partners for TOM1L2 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TOM1L2

SOURCE GeneReport for Unigene cluster for TOM1L2 Gene:

Hs.462379

mRNA Expression by UniProt/SwissProt for TOM1L2 Gene:

Q6ZVM7-TM1L2_HUMAN
Tissue specificity: Ubiquitously expressed with higher expression in heart and skeletal muscle.

Evidence on tissue expression from TISSUES for TOM1L2 Gene

  • Nervous system(4.9)
  • Liver(4.1)
  • Muscle(2.3)
  • Heart(2.2)
  • Skin(2.1)
genes like me logo Genes that share expression patterns with TOM1L2: view

Primer products for research

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for TOM1L2 Gene

Orthologs for TOM1L2 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for TOM1L2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia TOM1L2 30 31
  • 99.67 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia TOM1L2 31
  • 92 (a)
 OneToOne
Dog
(Canis familiaris)
 Mammalia TOM1L2 30 31
  • 91.72 (n)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia TOM1L2 31
  • 89 (a)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Tom1l2 30
  • 88.52 (n)
Mouse
(Mus musculus)
 Mammalia Tom1l2 30 17 31
  • 87.64 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia TOM1L2 30 31
  • 86.42 (n)
 OneToOne
Chicken
(Gallus gallus)
 Aves TOM1L2 30 31
  • 79.68 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia TOM1L2 31
  • 71 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia tom1l2 30
  • 72.87 (n)
African clawed frog
(Xenopus laevis)
 Amphibia Xl.1482 30
Zebrafish
(Danio rerio)
 Actinopterygii TOM1L2 31
  • 72 (a)
 OneToOne
LOC100535615 30
  • 70.36 (n)
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP006097 30
  • 53.67 (n)
Fruit Fly
(Drosophila melanogaster)
 Insecta CG3529 30 31
  • 53.31 (n)
 OneToMany
Worm
(Caenorhabditis elegans)
 Secernentea C07A12.7 30 31
  • 55.18 (n)
 OneToMany
Baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes HSE1 31
  • 13 (a)
 OneToMany
GGA2 33
Species where no ortholog for TOM1L2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for TOM1L2 Gene

ENSEMBL:
Gene Tree for TOM1L2 (if available)
TreeFam:
Gene Tree for TOM1L2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TOM1L2: view image

Paralogs for TOM1L2 Gene

Paralogs for TOM1L2 Gene

(4) SIMAP similar genes for TOM1L2 Gene using alignment to 6 proteins:

  • TM1L2_HUMAN
  • B7Z2L7_HUMAN
  • B7Z2U2_HUMAN
  • F5H3S6_HUMAN
  • K7EKL6_HUMAN
  • K7ENB0_HUMAN
genes like me logo Genes that share paralogs with TOM1L2: view

Variants for TOM1L2 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TOM1L2 Gene

SNP ID Clinical significance and condition Chr 17 pos Variation AA Info Type
rs386352375 Uncertain Significance: not provided 17,898,668(-) C/A
NM_001082968.2(TOM1L2):c.144G>T (p.Lys48Asn) 		MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for TOM1L2 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for TOM1L2 Gene

Variant ID Type Subtype PubMed ID
esv3640138 CNV loss 21293372
nsv155 OTHER inversion 15895083
nsv499114 OTHER inversion 21111241
nsv510701 CNV deletion 20534489
nsv522668 CNV loss 19592680
nsv833385 CNV loss 17160897

Variation tolerance for TOM1L2 Gene

Residual Variation Intolerance Score: 17.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.64; 13.78% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TOM1L2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TOM1L2

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TOM1L2 Gene

Disorders for TOM1L2 Gene

MalaCards: The human disease database

(2) MalaCards diseases for TOM1L2 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
smith-magenis syndrome
  • sms
pancreatic acinar cell adenocarcinoma
  • pancreatic acinar cell carcinoma
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for TOM1L2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with TOM1L2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TOM1L2 Gene

Publications for TOM1L2 Gene

  1. Analysis of lipid pathway genes indicates association of sequence variation near SREBF1/TOM1L2/ATPAF2 with dementia risk. (PMID: 20167577) Reynolds CA … Prince JA (Human molecular genetics 2010) 3 41
  2. The adaptor protein Tom1L1 is a negative regulator of Src mitogenic signaling induced by growth factors. (PMID: 16479011) Franco M … Roche S (Molecular and cellular biology 2006) 3 4
  3. Recruitment of clathrin onto endosomes by the Tom1-Tollip complex. (PMID: 16412388) Katoh Y … Nakayama K (Biochemical and biophysical research communications 2006) 3 4
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4

ExternalLinks

View latest publications for TOM1L2 gene in Mastermind

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