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Aliases for TMC2 Gene

Aliases for TMC2 Gene

  • Transmembrane Channel Like 2 2 3 5
  • Transmembrane Cochlear-Expressed Protein 2 3 4
  • C20orf145 3 4
  • Transmembrane Cochlear-Expressed Gene 2 3
  • Transmembrane Channel-Like Protein 2 3
  • Transmembrane, Cochlear Expressed, 2 2

External Ids for TMC2 Gene

Previous HGNC Symbols for TMC2 Gene

  • C20orf145

Previous GeneCards Identifiers for TMC2 Gene

  • GC20P002505
  • GC20P002512
  • GC20P002465

Summaries for TMC2 Gene

Entrez Gene Summary for TMC2 Gene

  • This gene encodes a transmembrane protein that is necesssary for mechanotransduction in cochlear hair cells of the inner ear. Mutations in this gene may underlie hereditary disorders of balance and hearing. [provided by RefSeq, Aug 2015]

GeneCards Summary for TMC2 Gene

TMC2 (Transmembrane Channel Like 2) is a Protein Coding gene. Diseases associated with TMC2 include Deafness, Autosomal Dominant 36 and Autosomal Dominant Nonsyndromic Deafness. Gene Ontology (GO) annotations related to this gene include voltage-gated calcium channel activity. An important paralog of this gene is TMC1.

UniProtKB/Swiss-Prot for TMC2 Gene

  • Probable ion channel required for the normal function of cochlear hair cells (PubMed:11850618). Component of the hair cells mechanotransduction (MET) machinery. Involved in mechanosensitive responses of the hair cells (By similarity).

Gene Wiki entry for TMC2 Gene

Additional gene information for TMC2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TMC2 Gene

Genomics for TMC2 Gene

GeneHancer (GH) Regulatory Elements for TMC2 Gene

Promoters and enhancers for TMC2 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
GH20J002536 Promoter 0.7 EPDnew 650.7 -0.1 -52 0.1 ZFHX2 EGR2 TMC2 LOC105372504 ZNF343
GH20J002507 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 11.6 -27.8 -27837 2.6 PKNOX1 FOXA2 ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 POLR2B ZNF766 ZNF343 ENSG00000256566 SNRPB TMC2 SNORD56 SNORD57 NOP56 ENSG00000228293 IDH3B GC20M002474
GH20J002626 Enhancer 0.7 ENCODE 14.2 +90.5 90484 1.1 ELF3 TFAP4 FOXA2 NFIB ZNF266 ZNF507 TEAD3 TFE3 TEAD1 NFIA SNRPB VPS16 ZNF343 TMC2 NOP56 UBOX5 IDH3B GC20P002902 LOC105372505 GC20M002600
GH20J002604 Enhancer 0.4 ENCODE 11.2 +67.7 67743 0.2 CBFA2T3 RCOR1 CHD2 TMC2 SNORD110 NOP56 SNORD86 SNORD57 SNORD56 GC20M002600 GC20P002902
GH20J002605 Enhancer 0.2 ENCODE 19 +68.1 68063 0.2 TMC2 SNORD110 NOP56 SNORD56 SNORD86 SNORD57 GC20M002600 GC20P002902
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TMC2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TMC2 gene promoter:
  • CUTL1
  • Pax-4a
  • Bach2
  • Pax-6
  • S8
  • Bach1
  • GATA-1
  • Pbx1a
  • Chx10
  • Nkx6-1

Genomic Locations for TMC2 Gene

Genomic Locations for TMC2 Gene
chr20:2,536,607-2,641,869
(GRCh38/hg38)
Size:
105,263 bases
Orientation:
Plus strand
chr20:2,517,253-2,622,430
(GRCh37/hg19)
Size:
105,178 bases
Orientation:
Plus strand

Genomic View for TMC2 Gene

Genes around TMC2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TMC2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TMC2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TMC2 Gene

Proteins for TMC2 Gene

  • Protein details for TMC2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8TDI7-TMC2_HUMAN
    Recommended name:
    Transmembrane channel-like protein 2
    Protein Accession:
    Q8TDI7
    Secondary Accessions:
    • Q5JXT0
    • Q5JXT1
    • Q6UWW4
    • Q6ZS41
    • Q8N9F3
    • Q9BYN2
    • Q9BYN3
    • Q9BYN4
    • Q9BYN5

    Protein attributes for TMC2 Gene

    Size:
    906 amino acids
    Molecular mass:
    102610 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=AAQ88976.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAC04423.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for TMC2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TMC2 Gene

Post-translational modifications for TMC2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for TMC2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for TMC2 Gene

Domains & Families for TMC2 Gene

Gene Families for TMC2 Gene

Protein Domains for TMC2 Gene

Blocks:
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for TMC2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8TDI7

UniProtKB/Swiss-Prot:

TMC2_HUMAN :
  • Belongs to the TMC family.
Family:
  • Belongs to the TMC family.
genes like me logo Genes that share domains with TMC2: view

Function for TMC2 Gene

Molecular function for TMC2 Gene

UniProtKB/Swiss-Prot Function:
Probable ion channel required for the normal function of cochlear hair cells (PubMed:11850618). Component of the hair cells mechanotransduction (MET) machinery. Involved in mechanosensitive responses of the hair cells (By similarity).

Phenotypes From GWAS Catalog for TMC2 Gene

Gene Ontology (GO) - Molecular Function for TMC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0005245 voltage-gated calcium channel activity IEA --
GO:0008381 mechanosensitive ion channel activity IEA --
genes like me logo Genes that share ontologies with TMC2: view
genes like me logo Genes that share phenotypes with TMC2: view

Animal Models for TMC2 Gene

MGI Knock Outs for TMC2:
  • Tmc2 Tmc2<tm1.1Ajg>

Animal Model Products

  • Taconic Biosciences Mouse Models for TMC2

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for TMC2 Gene

Localization for TMC2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TMC2 Gene

Cell membrane; Multi-pass membrane protein. Note=Localized to the stereocilia of the cochlear hair cells. {ECO:0000250 UniProtKB:Q8R4P4}.

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 TMC2 gene
Compartment Confidence
plasma membrane 5
nucleus 2

Gene Ontology (GO) - Cellular Components for TMC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0032426 stereocilium tip IEA --
genes like me logo Genes that share ontologies with TMC2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for TMC2 Gene

Pathways & Interactions for TMC2 Gene

No Data Available

Interacting Proteins for TMC2 Gene

Gene Ontology (GO) - Biological Process for TMC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006811 ion transport IEA --
GO:0050910 detection of mechanical stimulus involved in sensory perception of sound IEA,IMP 11850618
GO:0060005 vestibular reflex IEA --
GO:0070588 calcium ion transmembrane transport IEA --
GO:1903169 regulation of calcium ion transmembrane transport IEA --
genes like me logo Genes that share ontologies with TMC2: view

No data available for Pathways by source and SIGNOR curated interactions for TMC2 Gene

Drugs & Compounds for TMC2 Gene

No Compound Related Data Available

Transcripts for TMC2 Gene

mRNA/cDNA for TMC2 Gene

(2) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(5) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for TMC2 Gene

Transmembrane channel-like 2:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TMC2 Gene

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:

Relevant External Links for TMC2 Gene

GeneLoc Exon Structure for
TMC2
ECgene alternative splicing isoforms for
TMC2

Expression for TMC2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TMC2 Gene

mRNA differential expression in normal tissues according to GTEx for TMC2 Gene

This gene is overexpressed in Brain - Cerebellum (x16.0), Brain - Cerebellar Hemisphere (x15.1), and Pituitary (x6.6).

Protein differential expression in normal tissues from HIPED for TMC2 Gene

This gene is overexpressed in Plasma (63.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for TMC2 Gene



Protein tissue co-expression partners for TMC2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of TMC2 Gene:

TMC2

SOURCE GeneReport for Unigene cluster for TMC2 Gene:

Hs.352626

mRNA Expression by UniProt/SwissProt for TMC2 Gene:

Q8TDI7-TMC2_HUMAN
Tissue specificity: Detected in fetal cochlea.

Evidence on tissue expression from TISSUES for TMC2 Gene

  • Nervous system(4.1)
genes like me logo Genes that share expression patterns with TMC2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for TMC2 Gene

Orthologs for TMC2 Gene

This gene was present in the common ancestor of animals.

Orthologs for TMC2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TMC2 34 33
  • 99.04 (n)
OneToOne
dog
(Canis familiaris)
Mammalia TMC2 34 33
  • 89.51 (n)
OneToOne
cow
(Bos Taurus)
Mammalia TMC2 34 33
  • 89.11 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia TMC2 34
  • 86 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Tmc2 16 34 33
  • 84.46 (n)
rat
(Rattus norvegicus)
Mammalia Tmc2 33
  • 84.44 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia TMC2 34
  • 78 (a)
OneToOne
chicken
(Gallus gallus)
Aves TMC2 34 33
  • 71.43 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TMC2 34
  • 67 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100490320 33
  • 65.39 (n)
zebrafish
(Danio rerio)
Actinopterygii TMC2 (2 of 2) 34
  • 65 (a)
OneToMany
si:dkey-267i17.6 33
  • 62.51 (n)
TMC2 (1 of 2) 34
  • 58 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta CG3280 34
  • 16 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea T13G4.3 35
  • 37 (a)
B0416.1 35
  • 34 (a)
tmc-1 34
  • 22 (a)
ManyToMany
tmc-2 34
  • 22 (a)
ManyToMany
Species where no ortholog for TMC2 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 TMC2 Gene

ENSEMBL:
Gene Tree for TMC2 (if available)
TreeFam:
Gene Tree for TMC2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TMC2: view image

Paralogs for TMC2 Gene

Paralogs for TMC2 Gene

(2) SIMAP similar genes for TMC2 Gene using alignment to 1 proteins:

  • TMC2_HUMAN
genes like me logo Genes that share paralogs with TMC2: view

Variants for TMC2 Gene

Sequence variations from dbSNP and Humsavar for TMC2 Gene

SNP ID Clin Chr 20 pos Variation AA Info Type
rs1000014742 -- 2,596,127(+) G/A intron_variant
rs1000032109 -- 2,612,964(+) G/T intron_variant
rs1000036899 -- 2,638,735(+) AAAAAAAA/AAAAAAAAA genic_downstream_transcript_variant, intron_variant
rs1000186865 -- 2,577,100(+) G/A intron_variant
rs1000196614 -- 2,588,894(+) A/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for TMC2 Gene

Variant ID Type Subtype PubMed ID
dgv40e213 CNV gain 24956385
esv28094 CNV gain 19812545
esv32983 CNV gain 17666407
esv3644998 CNV gain 21293372
esv3645016 CNV loss 21293372
nsv1072096 CNV deletion 25765185
nsv470535 CNV gain 18288195
nsv476409 CNV novel sequence insertion 20440878
nsv585265 CNV loss 21841781

Variation tolerance for TMC2 Gene

Residual Variation Intolerance Score: 81.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.31; 76.63% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TMC2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TMC2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TMC2 Gene

Disorders for TMC2 Gene

MalaCards: The human disease database

(3) MalaCards diseases for TMC2 Gene - From: DISEASES

Disorder Aliases PubMed IDs
deafness, autosomal dominant 36
  • dfna36
autosomal dominant nonsyndromic deafness
  • autosomal dominant deafness
nonsyndromic deafness
  • nonsyndromic hearing loss
- elite association - COSMIC cancer census association via MalaCards
Search TMC2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for TMC2

genes like me logo Genes that share disorders with TMC2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TMC2 Gene

Publications for TMC2 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 22 58
  2. Characterization of the transmembrane channel-like (TMC) gene family: functional clues from hearing loss and epidermodysplasia verruciformis. (PMID: 12906855) Kurima K … Griffith AJ (Genomics 2003) 2 3 22 58
  3. Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production. (PMID: 21408207) Chung SA … Criswell LA (PLoS genetics 2011) 3 44 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 3 4 58

Products for TMC2 Gene

Sources for TMC2 Gene

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