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] See more...

Aliases for TMC1 Gene

Aliases for TMC1 Gene

  • Transmembrane Channel Like 1 2 3 5
  • Transmembrane Cochlear-Expressed Protein 1 3 4
  • Transmembrane Channel-Like Protein 1 3 4
  • Transmembrane, Cochlear Expressed, 1 2 3
  • DFNA36 3
  • DFNB11 3
  • DFNB7 3

External Ids for TMC1 Gene

Previous HGNC Symbols for TMC1 Gene

  • DFNA36
  • DFNB7
  • DFNB11

Previous GeneCards Identifiers for TMC1 Gene

  • GC09P066275
  • GC09P067087
  • GC09P068801
  • GC09P070688
  • GC09P070593
  • GC09P072366
  • GC09P074326
  • GC09P074211
  • GC09P075137
  • GC09P044959

Summaries for TMC1 Gene

Entrez Gene Summary for TMC1 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, 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]

GeneCards Summary for TMC1 Gene

TMC1 (Transmembrane Channel Like 1) is a Protein Coding gene. Diseases associated with TMC1 include Deafness, Autosomal Recessive 7 and Deafness, Autosomal Dominant 36. Gene Ontology (GO) annotations related to this gene include voltage-gated calcium channel activity. An important paralog of this gene is TMC2.

UniProtKB/Swiss-Prot Summary for TMC1 Gene

  • Probable ion channel required for the normal function of cochlear hair cells.

Gene Wiki entry for TMC1 Gene

Additional gene information for TMC1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TMC1 Gene

Genomics for TMC1 Gene

GeneHancer (GH) Regulatory Elements for TMC1 Gene

Promoters and enhancers for TMC1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09J072611 Promoter/Enhancer 0.5 EPDnew FANTOM5 500.2 +90.2 90192 0.1 TMC1 lnc-ZFAND5-3 lnc-GDA-6 lnc-GDA-5
GH09J072521 Enhancer 0.3 ENCODE 500.7 +0.3 345 0.4 ZBTB33 MG828757 TMC1 LOC101927234 RF01210-396 lnc-TMC1-1
GH09J072575 Promoter/Enhancer 1.2 Ensembl ENCODE 21.8 +57.8 57767 7.4 TCF12 JUND FOS PHB2 ZNF10 CUX1 MYC EP300 NCOR1 NEUROD1 lnc-GDA-5 TMC1 ZFAND5 LINC01474 LOC101927191 lnc-ZFAND5-5 piR-55985-201
GH09J072553 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 18 +35.1 35080 7.4 TCF12 USF1 JUND FOS TCF7 CUX1 MYC TOE1 CTBP1 EP300 TMC1 LINC01474 ZFAND5 LOC101927191 lnc-ZFAND5-5 piR-33804-151 lnc-TMC1-1
GH09J072592 Promoter/Enhancer 0.9 Ensembl ENCODE 21.5 +71.7 71747 1.5 CTCF REST RAD21 TRIM22 SMC3 FOXA2 ZNF207 GATA3 FOXA1 ZNF654 TMC1 ZFAND5 LINC01474 piR-50437-664 piR-55985-201 lnc-GDA-5
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TMC1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TMC1

Top Transcription factor binding sites by QIAGEN in the TMC1 gene promoter:
  • AP-1
  • Cdc5
  • CUTL1
  • E47
  • En-1
  • Gfi-1
  • Hand1
  • Hlf
  • POU6F1 (c2)
  • Sox5

Genomic Locations for TMC1 Gene

Genomic Locations for TMC1 Gene
chr9:72,521,608-72,838,291
(GRCh38/hg38)
Size:
316,684 bases
Orientation:
Plus strand
chr9:75,136,717-75,451,267
(GRCh37/hg19)
Size:
314,551 bases
Orientation:
Plus strand

Genomic View for TMC1 Gene

Genes around TMC1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TMC1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TMC1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TMC1 Gene

Proteins for TMC1 Gene

  • Protein details for TMC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8TDI8-TMC1_HUMAN
    Recommended name:
    Transmembrane channel-like protein 1
    Protein Accession:
    Q8TDI8
    Secondary Accessions:
    • A8MVZ2
    • B1AM91

    Protein attributes for TMC1 Gene

    Size:
    760 amino acids
    Molecular mass:
    87768 Da
    Quaternary structure:
    • Interacts with TOMT. The interaction of TMC1 and TMC2 with TOMT is required for the transportation of TMC1/2 into the stereocilia of hair cells. Interacts (via N-terminus) with both isoforms CD1 and CD3 of PCDH15.
    SequenceCaution:
    • Sequence=BAC05351.1; Type=Erroneous termination; Note=Truncated C-terminus.; Evidence={ECO:0000305}; Sequence=BAC05351.1; Type=Frameshift; Evidence={ECO:0000305};

neXtProt entry for TMC1 Gene

Post-translational modifications for TMC1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for TMC1 Gene

Domains & Families for TMC1 Gene

Gene Families for TMC1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Potential drug targets
  • Predicted membrane proteins
  • Transporters

Protein Domains for TMC1 Gene

Blocks:
  • TMC
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for TMC1 Gene

GenScript: Design optimal peptide antigens:
  • TMC1 protein (A4FU59_HUMAN)
  • TMC1 protein (A4FUA6_HUMAN)
  • TMC1 protein (A5D8Y1_HUMAN)
  • TMC1 protein (Q3MI88_HUMAN)
  • Transmembrane cochlear-expressed protein 1 (TMC1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8TDI8

UniProtKB/Swiss-Prot:

TMC1_HUMAN :
  • Belongs to the TMC family.
Family:
  • Belongs to the TMC family.
genes like me logo Genes that share domains with TMC1: view

Function for TMC1 Gene

Molecular function for TMC1 Gene

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

Phenotypes From GWAS Catalog for TMC1 Gene

Gene Ontology (GO) - Molecular Function for TMC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005216 ion channel activity IBA 21873635
GO:0005245 voltage-gated calcium channel activity IBA 21873635
GO:0008381 mechanosensitive ion channel activity IBA 21873635
genes like me logo Genes that share ontologies with TMC1: view
genes like me logo Genes that share phenotypes with TMC1: view

Human Phenotype Ontology for TMC1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for TMC1 Gene

MGI Knock Outs for TMC1:
  • Tmc1 Tmc1<tm1.1Ajg>

Animal Model Products

CRISPR Products

miRNA for TMC1 Gene

miRTarBase miRNAs that target TMC1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for TMC1 Gene

Localization for TMC1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TMC1 Gene

Cell membrane; Multi-pass membrane protein. Note=Localized to the stereocilia of the cochlear hair cells. {ECO:0000250 UniProtKB:Q8R4P5}.

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 TMC1 gene
Compartment Confidence
plasma membrane 4
extracellular 2
cytoskeleton 1
mitochondrion 1
peroxisome 1
nucleus 1
endoplasmic reticulum 1
cytosol 1

Gene Ontology (GO) - Cellular Components for TMC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0005887 integral component of plasma membrane IEA --
GO:0009897 external side of plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with TMC1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for TMC1 Gene

Pathways & Interactions for TMC1 Gene

PathCards logo

SuperPathways for TMC1 Gene

No Data Available

Interacting Proteins for TMC1 Gene

;

Gene Ontology (GO) - Biological Process for TMC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006811 ion transport IEA --
GO:0007605 sensory perception of sound IEA --
GO:0050910 detection of mechanical stimulus involved in sensory perception of sound IBA 21873635
GO:0060005 vestibular reflex IBA 21873635
GO:0060117 auditory receptor cell development IEA --
genes like me logo Genes that share ontologies with TMC1: view

No data available for Pathways by source and SIGNOR curated interactions for TMC1 Gene

Drugs & Compounds for TMC1 Gene

No Compound Related Data Available

Transcripts for TMC1 Gene

mRNA/cDNA for TMC1 Gene

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

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TMC1 Gene

No ASD Table

Relevant External Links for TMC1 Gene

GeneLoc Exon Structure for
TMC1

Expression for TMC1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TMC1 Gene

mRNA differential expression in normal tissues according to GTEx for TMC1 Gene

This gene is overexpressed in Esophagus - Mucosa (x7.4), Brain - Spinal cord (cervical c-1) (x4.2), Testis (x4.1), and Bladder (x4.0).

Protein differential expression in normal tissues from HIPED for TMC1 Gene

This gene is overexpressed in Vitreous humor (22.3), Colon muscle (21.2), Stomach (7.6), Breast (7.3), and Heart (6.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for TMC1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TMC1

SOURCE GeneReport for Unigene cluster for TMC1 Gene:

Hs.670211

mRNA Expression by UniProt/SwissProt for TMC1 Gene:

Q8TDI8-TMC1_HUMAN
Tissue specificity: Detected in fetal cochlea, and at low levels in placenta and testis.

Evidence on tissue expression from TISSUES for TMC1 Gene

  • Nervous system(4.2)
  • Lung(2.7)
  • Blood(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for TMC1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • nervous
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • head
  • inner ear
  • middle ear
  • outer ear
  • skull
Thorax:
  • heart
  • heart valve
Limb:
  • forearm
General:
  • peripheral nerve
  • peripheral nervous system
genes like me logo Genes that share expression patterns with TMC1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Protein tissue co-expression partners for TMC1 Gene

Orthologs for TMC1 Gene

This gene was present in the common ancestor of animals.

Orthologs for TMC1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TMC1 31 30
  • 99.39 (n)
OneToOne
cow
(Bos Taurus)
Mammalia TMC1 31 30
  • 91.74 (n)
OneToOne
dog
(Canis familiaris)
Mammalia TMC1 31 30
  • 90.56 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Tmc1 30
  • 89.78 (n)
mouse
(Mus musculus)
Mammalia Tmc1 17 31 30
  • 88.61 (n)
oppossum
(Monodelphis domestica)
Mammalia TMC1 31
  • 88 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TMC1 31
  • 80 (a)
OneToOne
chicken
(Gallus gallus)
Aves TMC1 31 30
  • 72.45 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TMC1 31
  • 65 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tmc1 30
  • 69.58 (n)
zebrafish
(Danio rerio)
Actinopterygii tmc1 31 30
  • 66.67 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG3280 31
  • 14 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea T13G4.3 32
  • 34 (a)
B0416.1 32
  • 31 (a)
tmc-1 31
  • 19 (a)
ManyToMany
tmc-2 31
  • 19 (a)
ManyToMany
Species where no ortholog for TMC1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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 squirt (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 TMC1 Gene

ENSEMBL:
Gene Tree for TMC1 (if available)
TreeFam:
Gene Tree for TMC1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TMC1: view image

Paralogs for TMC1 Gene

Paralogs for TMC1 Gene

(2) SIMAP similar genes for TMC1 Gene using alignment to 5 proteins:

  • TMC1_HUMAN
  • A4FU59_HUMAN
  • A4FUA6_HUMAN
  • A5D8Y1_HUMAN
  • Q3MI88_HUMAN
genes like me logo Genes that share paralogs with TMC1: view

Variants for TMC1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TMC1 Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
4106 Pathogenic: Deafness, autosomal recessive 7 72,648,665(+) G/T SPLICE_DONOR_VARIANT
560914 Pathogenic: Deafness 72,789,302(+) G/A NONSENSE
560915 Pathogenic: Deafness 72,816,175(+) C/G MISSENSE_VARIANT
562098 Pathogenic: Deafness, autosomal recessive 7 72,789,236(+) C/G NONSENSE
594638 Uncertain Significance: not provided 72,830,498(+) C/T MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for TMC1 Gene

Structural Variations from Database of Genomic Variants (DGV) for TMC1 Gene

Variant ID Type Subtype PubMed ID
esv1000190 CNV insertion 20482838
esv2652527 CNV insertion 19546169
esv2738550 CNV deletion 23290073
esv3304582 CNV mobile element insertion 20981092
esv3305925 CNV mobile element insertion 20981092
esv3309405 CNV mobile element insertion 20981092
esv3324047 CNV duplication 20981092
esv3397704 CNV insertion 20981092
esv3402158 CNV insertion 20981092
esv3412301 CNV insertion 20981092
esv3431397 CNV insertion 20981092
esv3544912 CNV deletion 23714750
esv3620640 CNV loss 21293372
esv3620641 CNV loss 21293372
esv3620643 CNV loss 21293372
esv3620644 CNV loss 21293372
esv3620645 CNV loss 21293372
esv3891682 CNV loss 25118596
nsv1048501 CNV loss 25217958
nsv1128497 CNV deletion 24896259
nsv1133117 OTHER inversion 24896259
nsv1140996 CNV deletion 24896259
nsv1140997 CNV deletion 24896259
nsv416490 CNV insertion 16902084
nsv472123 CNV novel sequence insertion 20440878
nsv527600 CNV loss 19592680
nsv614611 CNV loss 21841781
nsv831619 CNV loss 17160897
nsv831620 CNV loss 17160897
nsv972400 CNV duplication 23825009
nsv972760 CNV duplication 23825009

Variation tolerance for TMC1 Gene

Residual Variation Intolerance Score: 24.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.48; 91.05% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TMC1 Gene

Human Gene Mutation Database (HGMD)
TMC1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TMC1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TMC1 Gene

Disorders for TMC1 Gene

MalaCards: The human disease database

(37) MalaCards diseases for TMC1 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search TMC1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

TMC1_HUMAN
  • Deafness, autosomal dominant, 36 (DFNA36) [MIM:606705]: A form of non-syndromic 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 bilateral hearing loss, and begins at 5-10 years of age. It progresses to profound deafness within 10-15 years. {ECO:0000269 PubMed:11850618, ECO:0000269 PubMed:25388789}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Deafness, autosomal recessive, 7 (DFNB7) [MIM:600974]: A form of non-syndromic 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. {ECO:0000269 PubMed:11850618}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for TMC1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with TMC1: view

No data available for Genatlas for TMC1 Gene

Publications for TMC1 Gene

  1. Dominant and recessive deafness caused by mutations of a novel gene, TMC1, required for cochlear hair-cell function. (PMID: 11850618) Kurima K … Griffith AJ (Nature genetics 2002) 2 3 4 23 54
  2. Novel TMC1 structural and splice variants associated with congenital nonsyndromic deafness in a Sudanese pedigree. (PMID: 15605408) Meyer CG … Horstmann RD (Human mutation 2005) 3 23 41 54
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41 54
  4. A novel mutation adjacent to the Bth mouse mutation in the TMC1 gene makes this mouse an excellent model of human deafness at the DFNA36 locus. (PMID: 20447146) Yang T … Smith RJ (Clinical genetics 2010) 3 23 54
  5. Mutations in TMC1 contribute significantly to nonsyndromic autosomal recessive sensorineural hearing loss: a report of five novel mutations. (PMID: 19187973) Sirmaci A … Tekin M (International journal of pediatric otorhinolaryngology 2009) 3 23 54

Products for TMC1 Gene

Sources for TMC1 Gene