TMC1 Gene
protein-coding GIFtS: 53
GCID: GC09P075137
|
|
transmembrane channel-like 1(Previous names: transmembrane, cochlear expressed, 1 )
(Previous symbols: DFNA36, DFNB7, DFNB11)
| |
Aliases
for TMC1 gene
(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 11 2 | | Transmembrane, Cochlear Expressed, 11 2 | | DFNA361 2 5 | | Transmembrane Cochlear-Expressed Protein 12 3 | | DFNB111 2 5 | | Transmembrane Channel-Like Protein 12 | | DFNB71 2 5 | | |
Export aliases for TMC1 gene to outside databasesPrevious GC identifers: GC09P066275 GC09P067087 GC09P068801 GC09P070688 GC09P070593 GC09P072366 GC09P074326 GC09P074211 GC09P044959 |
Summaries
for TMC1 gene(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 TMC1:
This gene is considered a member of a gene family predicted to encode transmembrane proteins. The specific function ofthis gene is unknown; however, it is known to be required for normal function of cochlear hair cells. Mutations inthis gene have been associated with progressive postlingual hearing loss and profound prelingual deafness. (providedby RefSeq, Jul 2008)
UniProtKB/Swiss-Prot: TMC1_HUMAN, Q8TDI8Function: Probable ion channel required for the normal function of cochlear hair cells (By similarity)
Gene Wiki entry for TMC1
|
Genomic Views
for TMC1 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 69),
Regulatory elements and Epigenetics data according to
QIAGEN,
SABiosciences, and/or
SwitchGear Genomics)
About This Section
| RefSeq DNA sequence:- NC_000009.11 NC_018920.1 NT_008470.19
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the TMC1 gene promoter:
Sox5 AP-1 CUTL1 POU6F1 (c2) Cdc5 E47 Gfi-1 Hand1 Hlf En-1
Other transcription factors
Search SABiosciences Chromatin IP Primers for TMC1
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat TMC1 |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 9q21.12 Ensembl cytogenetic band: 9q21.13 HGNC cytogenetic band: 9q21TMC1 Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc information about chromosome 9 GeneLoc Exon Structure GeneLoc location for GC09P075137: view genomic region
(about GC identifiers)
Start:
|
75,136,717 bp from pter |
End:
|
75,451,267 bp from pter |
Size:
|
314,551 bases |
Orientation:
|
plus strand |
|
Proteins
for TMC1 gene
(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: TMC1_HUMAN, Q8TDI8 (See
protein sequence)Recommended Name: Transmembrane channel-like protein 1 Size: 760 amino acids; 87768 Da
Subcellular location: Membrane; Multi-pass membrane protein (Potential)
Sequence caution: Sequence=BAC05351.1; Type=Erroneous termination; Positions=744; Note=Translated as Arg;Sequence=BAC05351.1; Type=Frameshift; Positions=588;
Secondary accessions: A8MVZ2 B1AM91Explore the universe of human proteins at neXtProt for TMC1: NX_Q8TDI8
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q8TDI8
TMC1 Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins: NP_619636.2
ENSEMBL proteins: ENSP00000297784 ENSP00000341433 ENSP00000379538
Human Recombinant Protein Products for TMC1:
Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0009897 | external side of plasma membrane |
IEA | -- | | GO:0016021 | integral to membrane |
IEA | -- | | GO:0032426 | stereocilium bundle tip |
IEA | -- |
TMC1 for ontologies About GeneDecksing
TMC1 Antibody Products:
Assay Products for TMC1: |
Protein
Domains /
Families
for TMC1 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
TMC1 for domains About GeneDecksing
1 InterPro domain/family:Graphical View of Domain Structure for InterPro Entry Q8TDI8ProtoNet protein and cluster: Q8TDI8 1 Blocks protein family: IPB012496 TMC
UniProtKB/Swiss-Prot: TMC1_HUMAN, Q8TDI8Similarity: Belongs to the TMC family |
Function
for TMC1 gene
(According to 1UniProtKB,
Genatlas,
LifeMap Discovery™,
IUBMB, and/or
2DME,
Human phenotypes from GenomeRNAi,
Animal models from MGI Mar 06 2013,
inGenious Targeting Laboratory,
bound targets from SABiosciences,
miRNA Gene Targets from miRTarBase,
shRNA from
OriGene,
Sirion Biotech,
RNAi from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
microRNA from QIAGEN,
Gene Editing from DNA2.0,
Sirion Biotech,
Clones from EMD Millipore,
OriGene,
SwitchGear Genomics,
GenScript,
Sino Biological,
DNA2.0,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
Sirion Biotech,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
|
Molecular Function:
UniProtKB/Swiss-Prot Summary: TMC1_HUMAN, Q8TDI8Function: Probable ion channel required for the normal function of cochlear hair cells (By similarity)Phenotypes:
2 GenomeRNAi human phenotypes for TMC1:
5 MGI mutant phenotypes (inferred from 6 alleles ) (MGI details for Tmc1):
TMC1 for phenotypes About GeneDecksing
Animal Models:
Clone
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OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for TMC1
OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
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| |  | GenScript: all cDNA clones in your preferred vector: TMC1 (NM_138691) | |  | Browse Sino Biological Human cDNA Clones | |  | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for TMC1 | |  | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat TMC1 |
In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TMC1 |
|
Pathways & Interactions
for TMC1 gene
(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 TMC1
5 Interacting proteins for TMC1 (Q8TDI83) via UniProtKB, MINT, STRING, and/or I2DAbout this table
Gene Ontology (GO): 4 biological process terms (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0007605 | sensory perception of sound |
-- | -- | | GO:0050910 | detection of mechanical stimulus involved in sensory perception of sound |
IEA | -- | | GO:0060005 | vestibular reflex |
IEA | -- | | GO:0060117 | auditory receptor cell development |
IEA | -- |
TMC1 for ontologies About GeneDecksing
|
Drugs & Compounds
for TMC1 gene(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 Tocris compounds for TMC1
Search CenterWatch for drugs/clinical trials and news about TMC1
|
Transcripts
for TMC1 gene(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,
Sirion Biotech,
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 TMC1 gene: NM_138691.2 Unigene Cluster for TMC1: Transmembrane channel-like 1 Hs.670211 [show with all ESTs]Unigene Representative Sequence: AF4175787 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000297784(uc010moz.1 uc004aiz.1) ENST00000497073 ENST00000492418
ENST00000486417 ENST00000469455 ENST00000340019(uc004aja.1 uc004ajb.1 uc004ajc.1 uc010mpa.1)
ENST00000396237
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for TMC1 (see all 3)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for TMC1
OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling
| | | GenScript: all cDNA clones in your preferred vector: TMC1 (NM_138691) | | | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for TMC1 | | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat TMC1 |
Additional cDNA sequence: AF417578.1 AK098607.1 AK307461.1 BC103955.1 BC103956.1 BC114380.1 BC114449.1 BC141860.1 3 DOTS entries: DT.97764636 DT.100013271 DT.75136370 11 AceView cDNA sequences: NM_138691 AF417578 BP370498 AW295808 AI686465 AI699911 AK098607 BX093725 BG150313 AI336832 BF214797
GeneLoc Exon Structure
|
Expression
for TMC1 gene
(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
| TMC1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: CTGGCCAATT
About this image
See TMC1 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for TMC1
SOURCE GeneReport for Unigene cluster: Hs.670211
UniProtKB/Swiss-Prot: TMC1_HUMAN, Q8TDI8Tissue specificity: Detected in fetal cochlea, and at low levels in placenta and testis
SABiosciences Custom PCR Arrays for TMC1
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for TMC1
Browse OriGene validated miRNA SYBR primer pairs
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Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TMC1 |
Orthologs
for TMC1 gene
(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 TMC1 gene from 5/16 species (see all 16) About this table
| Organism |
Taxonomic
classification |
Gene |
Description |
Human
Similarity |
Orthology
Type |
Details |
chicken
(Gallus gallus) |
Aves |
TMC11 |
transmembrane channel-like 1 |
70.42(n)
68.06(a) |
|
427255 NM_001006580.1 NP_001006580.1 |
lizard
(Anolis carolinensis) |
Reptilia |
TMC16 |
-- |
64(a) |
1 ↔ 1 |
2(47993071-48060703) |
zebrafish
(Danio rerio) |
Actinopterygii |
LOC5672371 |
novel protein similar to vertebrate transmembrane channel more |
64.56(n)
63.6(a) |
|
567237 XM_690529.3 XP_695621.3 |
fruit fly
(Drosophila melanogaster) |
Insecta |
CG32806 |
-- |
13(a) |
1 → many |
3L(9596701-9607009) |
worm
(Caenorhabditis elegans) |
Secernentea |
T13G4.33 |
-- |
34(a)
(best of 2) |
|
X(1202384-1212051) -- |
ENSEMBL Gene Tree for TMC1 (if available)
TreeFam Gene Tree for TMC1 (if available) |
Paralogs
for TMC1 gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| Paralogs for TMC1 gene
- TMC72 TMC32 TMC22 TMC82 TMC52 TMC62 TMC42
2 SIMAP similar genes for TMC1 using alignment to 5 protein entries: TMC1_HUMAN (see all proteins):TMC2 TMC3
TMC1 for paralogs About GeneDecksing
|
Genomic Variants
for TMC1 gene(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
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical
significance | Chr 9 pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
|---|
HapMap Linkage Disequilibrium report for TMC1 (75136717 - 75386717 bp, first 250kb of TMC1)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 9 variations for TMC1
7 CNVs: 96113 83061 96114 96118 96117 96116 83059
2 Indels: 100664 83060
Human Gene Mutation Database (HGMD): TMC1
Locus Specific Mutation Databases (LSDB): TMC1
| SABiosciences Cancer Mutation PCR Assays |
| | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing TMC1 |
|
Disorders
/ Diseases
for TMC1 gene
(in which this Gene is Involved, According to MalaCards,
OMIM, UniProtKB,
the University of Copenhagen DISEASES
database, Novoseek,
Genatlas, GeneTests,
GAD,
HuGE Navigator,
and/or TGDB.)
About This Section
|
TMC1 for disorders About GeneDecksing
OMIM gene information: 606706
OMIM disorders: 600974 606705
UniProtKB/Swiss-Prot: TMC1_HUMAN, Q8TDI8
Defects in TMC1 are the cause of deafness autosomal dominant type 36 (DFNA36) [MIM:606705]. DFNA36 is a formof sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear,the nerve pathways to the brain, or the area of the brain that receives sound information. DFNA36 is a bilateralhearing loss, and begins at 5-10 years of age. It progresses to profound deafness within 10-15 years Defects in TMC1 are the cause of deafness autosomal recessive type 7 (DFNB7) [MIM:600974]; also known asautosomal recessive neurosensory deafness type 11 (DFNB11). This hearing loss is congenital and profound
9  diseases for TMC1: About MalaCardshearing loss deafness, autosomal dominant 36 deafness, autosomal recessive 7 enlarged vestibular aqueduct
epidermodysplasia verruciformis sensorineural hearing loss toxic megacolon nonsyndromic deafness
megacolon
3 diseases from the University of Copenhagen DISEASES database for TMC1:Nonsyndromic deafness Sensorineural hearing loss Toxic megacolon 3 Novoseek disease relationships for TMC1 gene About this table
Human Genome Epidemiology (HuGE) Navigator: TMC1 (3 documents)
Export disorders for TMC1 gene to outside databases
|
Publications
for TMC1 gene (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 TMC1 gene, integrated from 9 sources (see all 27):
(articles sorted by number of sources associating them with TMC1) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- 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)
- Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
- Beethoven, a mouse model for dominant, progressive hearing loss DFNA36. (PubMed id 11850623)1, 3 Vreugde S....Steel K.P. (2002)
- Mutation analysis of TMC1 identifies four new mutations and suggests an additional deafness gene at loci DFNA36 and DFNB7/11. (PubMed id 18616530)1, 9 Hilgert N....Van Camp G. (2008)
- Identities, frequencies and origins of TMC1 mutations causing DFNB7/B11 deafness in Pakistan. (PubMed id 17877751)1, 9 Kitajiri S.I....Griffith A.J. (2007)
- Novel TMC1 structural and splice variants associated with congenital nonsyndromic deafness in a Sudanese pedigree. (PubMed id 15605408)1, 9 Meyer C.G....Horstmann R.D. (2005)
- Four novel TMC1 (DFNB7/DFNB11) mutations in Turkish patients with congenital autosomal recessive nonsyndromic hearing loss. (PubMed id 16287143)1, 9 Kalay E....Kremer H. (2005)
- Mutations in TMC1 contribute significantly to nonsyndromic autosomal recessive sensorineural hearing loss: a report of five novel mutations. (PubMed id 19187973)1, 9 Sirmaci A....Tekin M. (2009)
- Amino acid 572 in TMC1: hot spot or critical functional residue for dominant mutations causing hearing impairment. (PubMed id 19180119)1, 9 Hilgert N....Van Camp G. (2009)
- A novel mutation adjacent to the Bth mouse mutation i n the TMC1 gene makes this mouse an excellent model of human deafness at the DF NA36 locus. (PubMed id 20447146)1, 9 Yang T....Smith R.J. (2010)
|
External Searches for TMC1 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing TMC1 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing TMC1 gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing TMC1 gene(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
|
| Name | Description |
| PharmGKB entry for TMC1 | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| Patent Information for TMC1 gene:
Search GeneIP for patents involving TMC1
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for TMC1 gene(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, LifeMap BioReagents, and Sirion Biotech, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or
Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory)
About This Section
|
 | |
 | |
 |
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| | | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TMC1 |
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