Aliases for TMC3 Gene

Aliases for TMC3 Gene

  • Transmembrane Channel Like 3 2 3 5
  • Transmembrane Channel-Like Protein 3 3 4
  • TMC3 5

External Ids for TMC3 Gene

Previous GeneCards Identifiers for TMC3 Gene

  • GC15M079192
  • GC15M079339
  • GC15M079410
  • GC15M081624
  • GC15M058383

Summaries for TMC3 Gene

GeneCards Summary for TMC3 Gene

TMC3 (Transmembrane Channel Like 3) is a Protein Coding gene. Diseases associated with TMC3 include Deafness, Autosomal Recessive 48 and Deafness, Autosomal Dominant 36. An important paralog of this gene is TMC2.

UniProtKB/Swiss-Prot Summary for TMC3 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TMC3 Gene

Genomics for TMC3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for TMC3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH15J081372 Promoter/Enhancer 0.7 EPDnew Ensembl ENCODE 611.5 +0.7 715 2.4 TMC3 ENSG00000273920 STARD5 TMC3-AS1
GH15J081291 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 10.8 +75.8 75831 14.7 SP1 CREB1 REST ZNF692 POLR2A BACH1 FOXA1 LARP7 STAT3 JUND IL16 piR-53038 piR-59520 TLNRD1 STARD5 TMC3 ENSG00000271725 piR-46911
GH15J081337 Enhancer 1.1 Ensembl ENCODE dbSUPER 19.4 +35.8 35812 2.4 PRDM10 ZNF629 ZNF692 PRDM1 ZIC2 SCRT2 SP2 ZNF639 CEBPB OSR2 TMC3 TMC3-AS1 STARD5 ENSG00000273920
GH15J081310 Promoter/Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 10.9 +60.6 60637 6.1 CREB1 ZBTB33 ZNF629 RELA IKZF2 POLR2A ZNF600 PKNOX1 ATF7 EED TLNRD1 TMC3 ENSG00000271725 STARD5 IL16 ENSG00000286488 piR-32839
GH15J081409 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE CraniofacialAtlas 11.4 -36.4 -36414 1.4 CEBPG CTCF REST RAD21 SCRT2 CEBPB ZNF335 SMC3 ZNF610 KLF17 TMC3-AS1 STARD5 TMC3 ENSG00000275995 piR-50748 MEX3B
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TMC3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TMC3

Top Transcription factor binding sites by QIAGEN in the TMC3 gene promoter:
  • COUP
  • COUP-TF1
  • Evi-1
  • HNF-1
  • HNF-1A
  • HNF-4alpha1
  • HNF-4alpha2
  • LCR-F1
  • YY1

Genomic Locations for TMC3 Gene

Genomic Locations for TMC3 Gene
43,126 bases
Minus strand
42,997 bases
Minus strand

Genomic View for TMC3 Gene

Genes around TMC3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TMC3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TMC3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TMC3 Gene

Proteins for TMC3 Gene

  • Protein details for TMC3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Transmembrane channel-like protein 3
    Protein Accession:
    Secondary Accessions:
    • A2RTY2
    • B2RXJ3
    • Q7Z405

    Protein attributes for TMC3 Gene

    1100 amino acids
    Molecular mass:
    125685 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAP78778.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Due to an insert of 27 undefined residues.; Evidence={ECO:0000305};

    Alternative splice isoforms for TMC3 Gene


neXtProt entry for TMC3 Gene

Post-translational modifications for TMC3 Gene

  • Glycosylation at Asn264
  • Modification sites at PhosphoSitePlus

Other Protein References for TMC3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for TMC3 Gene

Domains & Families for TMC3 Gene

Gene Families for TMC3 Gene

Protein Domains for TMC3 Gene

  • TMC

Suggested Antigen Peptide Sequences for TMC3 Gene

GenScript: Design optimal peptide antigens:
  • Transmembrane channel-like 3 (A2RTY2_HUMAN)
  • Transmembrane channel-like 3 (B2RXJ3_HUMAN)
  • Transmembrane channel-like protein 3 (TMC3_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the TMC family.
  • Belongs to the TMC family.
genes like me logo Genes that share domains with TMC3: view

Function for TMC3 Gene

Molecular function for TMC3 Gene

UniProtKB/Swiss-Prot Function:
Probable ion channel.

Phenotypes From GWAS Catalog for TMC3 Gene

Gene Ontology (GO) - Molecular Function for TMC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005216 ion channel activity IBA --
GO:0008381 mechanosensitive ion channel activity IBA 21873635
genes like me logo Genes that share ontologies with TMC3: view
genes like me logo Genes that share phenotypes with TMC3: view

Animal Model Products

CRISPR Products

miRNA for TMC3 Gene

miRTarBase miRNAs that target TMC3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TMC3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for TMC3 Gene

Localization for TMC3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TMC3 Gene

Membrane. Multi-pass membrane protein.

Subcellular locations from

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 TMC3 gene
Compartment Confidence
plasma membrane 4
cytosol 3
cytoskeleton 2
extracellular 1
nucleus 1
endoplasmic reticulum 1
golgi apparatus 0

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for TMC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005887 integral component of plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with TMC3: view

Pathways & Interactions for TMC3 Gene

PathCards logo

SuperPathways for TMC3 Gene

No Data Available

Interacting Proteins for TMC3 Gene

Gene Ontology (GO) - Biological Process for TMC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006811 ion transport IEA --
GO:0034220 ion transmembrane transport IEA --
genes like me logo Genes that share ontologies with TMC3: view

No data available for Pathways by source and SIGNOR curated interactions for TMC3 Gene

Drugs & Compounds for TMC3 Gene

No Compound Related Data Available

Transcripts for TMC3 Gene

mRNA/cDNA for TMC3 Gene

5 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TMC3

Alternative Splicing Database (ASD) splice patterns (SP) for TMC3 Gene

No ASD Table

Relevant External Links for TMC3 Gene

GeneLoc Exon Structure for

Expression for TMC3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TMC3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TMC3

SOURCE GeneReport for Unigene cluster for TMC3 Gene:


Evidence on tissue expression from TISSUES for TMC3 Gene

  • Heart(4)
  • Lung(4)
genes like me logo Genes that share expression patterns with TMC3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for TMC3 Gene

Orthologs for TMC3 Gene

This gene was present in the common ancestor of animals.

Orthologs for TMC3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia TMC3 30 31
  • 98.91 (n)
(Bos Taurus)
Mammalia TMC3 30 31
  • 84.36 (n)
(Canis familiaris)
Mammalia TMC3 30 31
  • 84.24 (n)
(Rattus norvegicus)
Mammalia Tmc3 30
  • 82.58 (n)
(Mus musculus)
Mammalia Tmc3 30 17 31
  • 82.52 (n)
(Ornithorhynchus anatinus)
Mammalia TMC3 31
  • 82 (a)
(Monodelphis domestica)
Mammalia TMC3 31
  • 70 (a)
(Gallus gallus)
Aves TMC3 30 31
  • 70.1 (n)
(Anolis carolinensis)
Reptilia TMC3 31
  • 48 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia tmc3 30
  • 65.65 (n)
(Danio rerio)
Actinopterygii TMC3 31
  • 54 (a)
Fruit Fly
(Drosophila melanogaster)
Insecta CG3280 31
  • 19 (a)
(Caenorhabditis elegans)
Secernentea tmc-2 31
  • 28 (a)
tmc-1 31
  • 27 (a)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 53 (a)
Species where no ortholog for TMC3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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 TMC3 Gene

Gene Tree for TMC3 (if available)
Gene Tree for TMC3 (if available)
Evolutionary constrained regions (ECRs) for TMC3: view image

Paralogs for TMC3 Gene

Paralogs for TMC3 Gene

(2) SIMAP similar genes for TMC3 Gene using alignment to 2 proteins:

  • H0YK69_HUMAN
genes like me logo Genes that share paralogs with TMC3: view

Variants for TMC3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TMC3 Gene

SNP ID Clinical significance and condition Chr 15 pos Variation AA Info Type
rs150843673 Benign: not specified 81,332,588(-) G/T NONSENSE
rs11636318 - p.Cys893Tyr
rs4417518 - p.Asp1099Asn
rs7497202 - p.Val196Ile
rs8031046 - p.Arg1012Lys

Additional dbSNP identifiers (rs#s) for TMC3 Gene

Structural Variations from Database of Genomic Variants (DGV) for TMC3 Gene

Variant ID Type Subtype PubMed ID
nsv1048106 CNV gain 25217958
nsv1048788 CNV loss 25217958
nsv1054305 CNV gain 25217958
nsv1108970 CNV deletion 24896259
nsv520339 CNV loss 19592680

Variation tolerance for TMC3 Gene

Residual Variation Intolerance Score: 92.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.98; 84.08% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TMC3 Gene

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

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TMC3 Gene

Disorders for TMC3 Gene

MalaCards: The human disease database

(5) MalaCards diseases for TMC3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
deafness, autosomal recessive 48
  • dfnb48
deafness, autosomal dominant 36
  • dfna36
deafness, autosomal recessive 7
  • dfnb7
epidermodysplasia verruciformis 1
  • epidermodysplasia verruciformis, susceptibility to, 1
autosomal dominant nonsyndromic deafness
  • autosomal dominant deafness
- elite association - COSMIC cancer census association via MalaCards
Search TMC3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for TMC3

genes like me logo Genes that share disorders with TMC3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TMC3 Gene

Publications for TMC3 Gene

  1. 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 4 23
  2. TMC and EVER genes belong to a larger novel family, the TMC gene family encoding transmembrane proteins. (PMID: 12812529) Keresztes G … Heller S (BMC genomics 2003) 2 3 4
  3. Analysis of the DNA sequence and duplication history of human chromosome 15. (PMID: 16572171) Zody MC … Nusbaum C (Nature 2006) 3 4
  4. The intracellular NADH level regulates atrophic nonunion pathogenesis through the CtBP2-p300-Runx2 transcriptional complex. (PMID: 30585266) Zhang W … Wang K (International journal of biological sciences 2018) 3
  5. Large-scale genome-wide association studies and meta-analyses of longitudinal change in adult lung function. (PMID: 24983941) Tang W … Cassano PA (PloS one 2014) 3

Products for TMC3 Gene

Sources for TMC3 Gene