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TMC2 Gene

protein-coding   GIFtS: 48
GCID: GC20P002517

Transmembrane Channel-Like 2

(Previous names: transmembrane, cochlear expressed, 2)
(Previous symbol: C20orf145)
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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Transmembrane Channel-Like 21 2
C20orf1451 2 3
Transmembrane, Cochlear Expressed, 21 2
Transmembrane Cochlear-Expressed Protein 22 3
dJ686C3.32
Transmembrane Channel-Like Protein 22

External Ids:    HGNC: 165271   Entrez Gene: 1175322   Ensembl: ENSG000001494887   OMIM: 6067075   UniProtKB: Q8TDI73   

Export aliases for TMC2 gene to outside databases

Previous GC identifers: GC20P002505 GC20P002512 GC20P002465


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for TMC2 Gene:
This gene is considered a member of a gene family predicted to encode transmembrane proteins. The specific
function of this gene is unknown; however, expression in the inner ear suggests that it may be crucial for normal
auditory function. Mutations in this gene may underlie hereditary disorders of balance and hearing. (provided by
RefSeq, Jul 2008)

GeneCards Summary for TMC2 Gene:
TMC2 (transmembrane channel-like 2) is a protein-coding gene. An important paralog of this gene is TMC7.

UniProtKB/Swiss-Prot: TMC2_HUMAN, Q8TDI7
Function: Probable ion channel required for the normal function of cochlear hair cells

Gene Wiki entry for TMC2 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000020.10  NT_011387.9  NC_018931.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the TMC2 gene promoter:
         Bach1   Pbx1a   Pax-6   Bach2   CUTL1   GATA-1   S8   Nkx6-1   Chx10   Pax-4a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTMC2 promoter sequence
   Search Chromatin IP Primers for TMC2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TMC2


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 20p13   Ensembl cytogenetic band:  20p13   HGNC cytogenetic band: 20p13

TMC2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TMC2 gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20P002517:  view genomic region     (about GC identifiers)

Start:
2,517,253 bp from pter      End:
2,622,430 bp from pter
Size:
105,178 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: TMC2_HUMAN, Q8TDI7 (See protein sequence)
Recommended Name: Transmembrane channel-like protein 2  
Size: 906 amino acids; 102610 Da
Sequence caution: Sequence=AAQ88976.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=BAC04423.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Secondary accessions: Q5JXT0 Q5JXT1 Q6UWW4 Q6ZS41 Q8N9F3 Q9BYN2 Q9BYN3 Q9BYN4 Q9BYN5
Alternative splicing: 3 isoforms:  Q8TDI7-1   Q8TDI7-3   Q8TDI7-4   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for TMC2: NX_Q8TDI7

Explore proteomics data for TMC2 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See TMC2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_542789.2  
    ENSEMBL proteins: 
     ENSP00000351732  

    TMC2 Human Recombinant Protein Products:

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR012496 TMC

    Graphical View of Domain Structure for InterPro Entry Q8TDI7

    ProtoNet protein and cluster: Q8TDI7

    1 Blocks protein domain: IPB012496 TMC

    UniProtKB/Swiss-Prot: TMC2_HUMAN, Q8TDI7
    Similarity: Belongs to the TMC family


    Find genes that share domains with TMC2           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: TMC2_HUMAN, Q8TDI7
    Function: Probable ion channel required for the normal function of cochlear hair cells

    Phenotypes:
         3 MGI mutant phenotypes (inferred from 1 allele(MGI details for Tmc2):

     behavior/neurological  hearing/vestibular/ear  nervous system 

    Find genes that share phenotypes with TMC2           About GenesLikeMe

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for TMC2
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    TMC2_HUMAN, Q8TDI7: Membrane; Multi-pass membrane protein (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane3
    nucleus2
    cytosol1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral component of membrane IEA--
    GO:0032426stereocilium bundle tip IEA--

    Find genes that share ontologies with TMC2           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for TMC2
    Interactions:

        Search GeneGlobe Interaction Network for TMC2

    Gene Ontology (GO): 3 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006811ion transport IEA--
    GO:0050910detection of mechanical stimulus involved in sensory perception of sound IEA--
    GO:0060005vestibular reflex IEA--

    Find genes that share ontologies with TMC2           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for TMC2



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for TMC2 gene: 
    NM_080751.2  

    Unigene Cluster for TMC2:

    Transmembrane channel-like 2
    Hs.352626  [show with all ESTs]
    Unigene Representative Sequence: AK127751
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000358864(uc010zpw.1 uc010zpx.1 uc002wgf.1 uc002wgg.1)
    ENST00000496948
    miRNA
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    GenScript: all cDNA clones in your preferred vector: TMC2 (NM_080751)
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    Additional mRNA sequence: 

    AF417580.2 AK127751.1 AK294013.1 AK309782.1 AK316261.1 

    4 DOTS entries:

    DT.100697670  DT.101979004  DT.120802760  DT.99933917 

    5 AceView cDNA sequences:

    AF417580 NM_080751 AY358613 AK127751 CD635963 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for TMC2    About this scheme

    ExUns: 1 ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16a · 16b ^ 17 ^ 18 ^ 19 ^ 20
    SP1:              -                                                                                         -                 -                           
    SP2:                                                                                                                                                      
    SP3:                                                                                                                                                      


    ECgene alternative splicing isoforms for TMC2

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    TMC2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GGATACAGTT
    TMC2 Expression
    About this image

    TMC2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    TMC2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.352626

    UniProtKB/Swiss-Prot: TMC2_HUMAN, Q8TDI7
    Tissue specificity: Detected in fetal cochlea

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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for TMC2 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Tmc21 , 5 transmembrane channel-like gene family 21, 5 84.46(n)1
    83.52(a)1
      2 (63.19 cM)5
    1921401  NM_138655.11  NP_619596.11 
     1301951945 
    chicken
    (Gallus gallus)
    Aves TMC21 transmembrane channel-like 2 71.43(n)
    73.24(a)
      428456  NM_001039324.1  NP_001034413.1 
    lizard
    (Anolis carolinensis)
    Reptilia TMC26
    transmembrane channel-like 2
    67(a)
    1 ↔ 1
    GL343224.1(2086998-2170474)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia LOC1004903201 uncharacterized LOC100490320 65.39(n)
    68.02(a)
      100490320  XM_002938307.2  XP_002938353.2 
    zebrafish
    (Danio rerio)
    Actinopterygii si:dkey-267i17.61 si:dkey-267i17.6 62.51(n)
    61.66(a)
      571240  XM_694811.5  XP_699903.5 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG32806
    --
    16(a)
    1 → many
    3L(9596701-9607009)
    worm
    (Caenorhabditis elegans)
    Secernentea T13G4.33   -- 37(a)
    (best of 2)
      X(1202384-1212051)   --


    ENSEMBL Gene Tree for TMC2 (if available)
    TreeFam Gene Tree for TMC2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for TMC2 gene
    TMC72  TMC32  TMC82  TMC52  TMC42  TMC12  TMC62  
    2 SIMAP similar genes for TMC2 using alignment to 1 protein entry:     TMC2_HUMAN:
    TMC1    TMC3

    Find genes that share paralogs with TMC2           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for TMC2 (see all 2698)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 20 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1428190051,2
    --2515278(+) TTTGCA/GGCTGC 1 -- us2k10--------
    rs1460980221,2
    C--2515319(+) ACTGAG/TATCCT 1 -- us2k10--------
    rs1401107401,2
    C--2515413(+) AGCTTC/TAAAGC 1 -- us2k10--------
    rs173175171,2
    C,F,H--2515431(+) GAACCG/ATTGCA 1 -- us2k126Minor allele frequency- A:0.07NA NS EA WA 2906
    rs1437821141,2
    --2515473(+) TCCCTC/TGCCAA 1 -- us2k10--------
    rs736161481,2
    C--2515653(+) TTTTTT/-ATTTT 1 -- us2k11Minor allele frequency- -:0.50CSA 2
    rs1508847571,2
    --2515692(+) ATCACA/CCAGGG 1 -- us2k10--------
    rs1394073051,2
    --2515886(+) TGATCC/TGTCTG 1 -- us2k10--------
    rs1500728621,2
    --2515887(+) GATCCA/GTCTGC 1 -- us2k10--------
    rs1863456431,2
    --2516138(+) GATAAC/TATGTA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for TMC2 (2517253 - 2622430 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for TMC2:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv470535CNV Gain18288195
    esv32983CNV Gain17666407
    esv28094CNV Gain19812545

    Site Specific Mutation Identification with PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 606707    OMIM disorders: --

    1 disease from the University of Copenhagen DISEASES database for TMC2:
    Epidermodysplasia verruciformis

    Find genes that share disorders with TMC2           About GenesLikeMe

    Genetic Association Database (GAD): TMC2

    Export disorders for TMC2 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for TMC2 gene, integrated from 10 sources (see all 12):
    (articles sorted by number of sources associating them with TMC2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Dominant and recessive deafness caused by mutations of a novel gene, TMC1, required for cochlear hair-cell function. (PubMed id 11850618)1, 2, 3, 9 Kurima K.... Griffith A.J. (Nat. Genet. 2002)
    2. Characterization of the transmembrane channel-like (TMC) gene family: functional clues from hearing loss and epidermodysplasia verruciformis. (PubMed id 12906855)1, 3, 9 Kurima K.... Griffith A.J. (Genomics 2003)
    3. Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production. (PubMed id 21408207)1, 4 Chung S.A....Criswell L.A. (PLoS Genet. 2011)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    5. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)1, 2 Clark H.F.... Gray A.M. (Genome Res. 2003)
    6. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)1, 2 Deloukas P....Rogers J. (Nature 2001)
    7. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. (PubMed id 23251661)1 Comuzzie A.G....Butte N.F. (PLoS ONE 2012)
    8. TMC1 but not TMC2 is responsible for autosomal recessive nonsyndromic hearing impairment in Tunisian families. (PubMed id 18259073)1 Tlili A....Masmoudi S. (amp 2008)
    9. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
    10. TMC and EVER genes belong to a larger novel family, the TMC gene family encoding transmembrane proteins. (PubMed id 12812529)1 Keresztes G.... Heller S. (BMC Genomics 2003)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 117532 HGNC: 16527 AceView: TMC2 Ensembl:ENSG00000149488 euGenes: HUgn117532
    ECgene: TMC2 H-InvDB: TMC2

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for TMC2 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for TMC2 gene:
    Search GeneIP for patents involving TMC2

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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