Human Gene TMC1 (uc010mpa.1)
  Description: Homo sapiens transmembrane channel-like 1 (TMC1), mRNA.
RefSeq Summary (NM_138691): This gene is considered a member of a gene family predicted to encode transmembrane proteins. The specific function of this gene is unknown; however, it is known to be required for normal function of cochlear hair cells. Mutations in this gene have been associated with progressive postlingual hearing loss and profound prelingual deafness. [provided by RefSeq, Jul 2008]. ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000297784.10/ ENSP00000297784.6 RefSeq Select criteria :: based on manual assertion, conservation, expression ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr9:75,242,837-75,451,267 Size: 208,431 Total Exon Count: 18 Strand: +
Coding Region
   Position: hg19 chr9:75,355,111-75,451,007 Size: 95,897 Coding Exon Count: 15 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:75,242,837-75,451,267)mRNA (may differ from genome)Protein (636 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMalacardsMGI
OMIMPubMedTreefamUniProtKBWikipediaBioGrid CRISPR DB

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TMC1
CDC HuGE Published Literature: TMC1
Positive Disease Associations: monocyte chemoattractant protein 1 (66-77)
Related Studies:
  1. monocyte chemoattractant protein 1 (66-77)
    , , . [PubMed 0]

-  MalaCards Disease Associations
  MalaCards Gene Search: TMC1
Diseases sorted by gene-association score: deafness, autosomal dominant 36* (1250), deafness, autosomal recessive 7* (1250), nonsyndromic deafness* (174), nonsyndromic hearing loss and deafness* (121), autosomal dominant non-syndromic sensorineural deafness type dfna* (106), dfna36 nonsyndromic hearing loss and deafness* (100), dfnb 7/11 nonsyndromic hearing loss and deafness* (100), autosomal recessive non-syndromic sensorineural deafness type dfnb* (69), toxic megacolon (15), sensorineural hearing loss (11), epidermodysplasia verruciformis (10), autosomal dominant nonsyndromic deafness (8), auditory system disease (6), hodgkin's lymphoma, nodular sclerosis (6), deafness, autosomal recessive 30 (6), deafness, autosomal recessive 63 (6), autosomal recessive nonsyndromic deafness (6)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 0.61 RPKM in Testis
Total median expression: 3.93 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -103.20439-0.235 Picture PostScript Text
3' UTR -53.11260-0.204 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR012496 - TMC

Pfam Domains:
PF07810 - TMC domain

ModBase Predicted Comparative 3D Structure on A4FUA6
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0050910 detection of mechanical stimulus involved in sensory perception of sound

Cellular Component:
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AF417578 - Homo sapiens transmembrane channel-like protein 1 (TMC1) mRNA, complete cds.
AK307461 - Homo sapiens cDNA, FLJ97409.
BC141860 - Homo sapiens transmembrane channel-like 1, mRNA (cDNA clone IMAGE:40011719), partial cds.
BC103955 - Homo sapiens transmembrane channel-like 1, mRNA (cDNA clone IMAGE:40011715), partial cds.
BC103956 - Homo sapiens transmembrane channel-like 1, mRNA (cDNA clone IMAGE:40011718), partial cds.
BC114380 - Homo sapiens transmembrane channel-like 1, mRNA (cDNA clone IMAGE:40001409), partial cds.
BC114449 - Homo sapiens transmembrane channel-like 1, mRNA (cDNA clone IMAGE:40001405), with apparent retained intron.
BC156561 - Synthetic construct Homo sapiens clone IMAGE:100063243, MGC:190723 transmembrane channel-like 1 (TMC1) mRNA, encodes complete protein.
BC172523 - Synthetic construct Homo sapiens clone IMAGE:100069217, MGC:199228 transmembrane channel-like 1 (TMC1) mRNA, encodes complete protein.
JD147439 - Sequence 128463 from Patent EP1572962.
AK098607 - Homo sapiens cDNA FLJ25741 fis, clone TST05901.
JD371799 - Sequence 352823 from Patent EP1572962.
JD081685 - Sequence 62709 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A4FUA6, A4FUA6_HUMAN, BC114380, E9PEW6, NM_138691, NP_619636
UCSC ID: uc010mpa.1
RefSeq Accession: NM_138691
Protein: A4FUA6

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene TMC1:
deafness-overview (Genetic Hearing Loss Overview)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: BC114380.1
exon count: 18CDS single in 3' UTR: no RNA size: 2221
ORF size: 1911CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3787.50frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.