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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

TMC2 Gene

protein-coding   GIFtS: 48
GCID: GC20P002465

transmembrane channel-like 2

(Previous names: transmembrane, cochlear expressed, 2 )
(Previous symbol: C20orf145)
 Explore 4 diseases affiliated with
TMC2 via our new
 Human Malady Compendium 
Biological research products
for TMC2
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Transmembrane Channel-Like 21 2
C20orf1451 2 3
DJ686C3.31
Transmembrane, Cochlear Expressed, 21 2
Transmembrane Cochlear-Expressed Protein 22 3
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


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for TMC2:
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)

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

Gene Wiki entry for TMC2


(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000020.10  NC_018931.1  NT_011387.8  
Regulatory elements:
   SABiosciences 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 SABiosciences Chromatin IP Primers for TMC2

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 GC20P002465:  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, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: TMC2_HUMAN, Q8TDI7 (See protein sequence)
Recommended Name: Transmembrane channel-like protein 2  
Size: 906 amino acids; 102610 Da
Subcellular location: Membrane; Multi-pass membrane protein (Potential)
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

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q8TDI7

  • TMC2 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_542789.2  
    ENSEMBL proteins: 
     ENSP00000351732  

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    Uscn Proteins for TMC2

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

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


    TMC2 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    TMC2 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR012496 TMC

    Graphical View of Domain Structure for InterPro Entry Q8TDI7

    ProtoNet protein and cluster: Q8TDI7

    1 Blocks protein family: IPB012496 TMC

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


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

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

    miRNA
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    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TMC2

    Animal Models:
         3 MGI mutant phenotypes (inferred from 1 allele(MGI details for Tmc2):
     behavior/neurological  hearing/vestibular/ear  nervous system 

    TMC2 for phenotypes           About GeneDecksing


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for TMC2

    Gene Ontology (GO): 2 biological process terms (GO ID links to tree view):    About this table

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


    TMC2 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for TMC2
    Search CenterWatch for drugs/clinical trials and news about TMC2 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    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

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    Inhib. RNA
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    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for TMC2 (see all 7)
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    Clone
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat TMC2 
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat TMC2
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    Additional cDNA 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 AK127751 AY358613 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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    TMC2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GGATACAGTT

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See TMC2 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for TMC2

    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
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TMC2

    (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)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for TMC2 gene from 5/17 species (see all 17)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves TMC21 transmembrane channel-like 2 70.76(n)
    72.44(a)
      428456  NM_001039324.1  NP_001034413.1 
    lizard
    (Anolis carolinensis)
    Reptilia TMC26
    --
    67(a)
    1 ↔ 1
    GL343224.1(2086998-2170474)
    zebrafish
    (Danio rerio)
    Actinopterygii LOC5712401 transmembrane channel-like gene family 2-like 63.03(n)
    62.32(a)
      571240  XM_694811.4  XP_699903.4 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG32801 CG3280 48.85(n)
    40.23(a)
      39117  NM_140079.3  NP_648336.3 
    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)
    About This Section
    Paralogs for TMC2 gene
    TMC72  TMC32  TMC82  TMC52  TMC62  TMC12  TMC42  
    2 SIMAP similar genes for TMC2 using alignment to 1 protein entry:     TMC2_HUMAN:
    TMC1    TMC3

    TMC2 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/2283 NCBI SNPs in TMC2 are shown (see all 2283    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
    --2515319(+) ACTGAG/TATCCT 1 -- us2k10--------
    rs1401107401,2
    --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,--2515652(+) TTATAT/-TTTTT 1 -- us2k11Minor allele frequency- -:0.50CSA 2
    rs736161491,2
    C--2515654(+) TTTTT-/TATTTT 1 -- us2k10--------
    rs1508847571,2
    --2515692(+) ATCACA/CCAGGG 1 -- us2k10--------
    rs1394073051,2
    --2515886(+) TGATCC/TGTCTG 1 -- us2k10--------
    rs1500728621,2
    --2515887(+) GATCCA/GTCTGC 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for TMC2 (2517253 - 2622430 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 2 variations for TMC2
         1 CNV: 73459
         1 Indel: 40434

    SABiosciences Cancer Mutation 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.)
    About This Section

    TMC2 for disorders           About GeneDecksing

    OMIM gene information: 606707    OMIM disorders: --

    4 diseases for TMC2:    About MalaCards
    epidermodysplasia verruciformis    systemic lupus erythematosus    lupus erythematosus    hearing loss

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

    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)
    About This Section

    PubMed articles for TMC2 gene, integrated from 9 sources (see all 11):
    (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. (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. (2003)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. 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. (2003)
    5. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)1, 2 Deloukas P....Rogers J. (2001)
    6. Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production. (PubMed id 21408207)1 Chung S.A....Criswell L.A. (2011)
    7. TMC1 but not TMC2 is responsible for autosomal recessive nonsyndromic hearing impairment in Tunisian families. (PubMed id 18259073)1 Tlili A....Masmoudi S. (2008)
    8. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
    9. 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. (2003)
    10. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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)
    About This Section
    Entrez Gene: 117532 HGNC: 16527 AceView: TMC2 Ensembl:ENSG00000149488 euGenes: HUgn117532
    ECgene: TMC2 H-InvDB: TMC2

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    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.)
    About This Section
    Patent Information for TMC2 gene:
    Search GeneIP for patents involving TMC2

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     GenScript Custom Purified and Recombinant Proteins Services for TMC2 GenScript cDNA clones with any tag delivered in your preferred vector for TMC2
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     TMC2 Proteins, Antibodies, CLIAs, and ELISAs
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     SwitchGear 3'UTR luciferase reporter plasmids for TMC2
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     Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat TMC2
           
    GeneCards Homepage - Last full update: 18 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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