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    TMC1 transmembrane channel like 1 [ Homo sapiens (human) ]

    Gene ID: 117531, updated on 3-Nov-2024

    Summary

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    Official Symbol
    TMC1provided by HGNC
    Official Full Name
    transmembrane channel like 1provided by HGNC
    Primary source
    HGNC:HGNC:16513
    See related
    Ensembl:ENSG00000165091 MIM:606706; AllianceGenome:HGNC:16513
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    DFNB7; DFNA36; DFNB11
    Summary
    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]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    mouse all
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    Genomic context

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    See TMC1 in Genome Data Viewer
    Location:
    9q21.13
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (72521608..72838297)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (84672507..84989215)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (75136524..75453213)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein S12 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28459 Neighboring gene Sharpr-MPRA regulatory region 9116 Neighboring gene uncharacterized LOC105376080 Neighboring gene uncharacterized LOC101927234 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:75139667-75140228 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:75140229-75140790 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28460 Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28461 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:75166586-75167086 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:75172238-75173437 Neighboring gene uncharacterized LOC101927191 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28462 Neighboring gene ribosomal protein S20 pseudogene 24 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:75295411-75296186 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:75299935-75300148 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28463 Neighboring gene RPS27A pseudogene 15 Neighboring gene uncharacterized LOC124902181 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:75472952-75474151 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:75477204-75478403 Neighboring gene long intergenic non-protein coding RNA 1474

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Progressive sensorineural hearing loss and normal vestibular function in a Dutch DFNB7/11 family with a novel mutation in TMC1. de Heer AM, et al. Audiol Neurootol, 2011. PMID 21252500
    2. Recessive mutations of TMC1 associated with moderate to severe hearing loss. Imtiaz A, et al. Neurogenetics, 2016 Apr. PMID 26879195, Free PMC Article
    3. Exome sequencing identifies a mutation in TMC1 as a novel cause of autosomal recessive nonsyndromic hearing loss. Hu J, et al. J Transl Med, 2016 Jan 28. PMID 26822030, Free PMC Article
    4. A novel mutation in the TMC1 gene causes non-syndromic hearing loss in a Moroccan family. Bakhchane A, et al. Gene, 2015 Dec 10. PMID 26226225
    5. Targeted gene capture and massively parallel sequencing identify TMC1 as the causative gene in a six-generation Chinese family with autosomal dominant hearing loss. Gao X, et al. Am J Med Genet A, 2015 Oct. PMID 26079994, Free PMC Article

    See all (62) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Heterozygous variants in transmembrane channel-like 1 gene cause autosomal recessive nonsyndromic hearing loss.
      Title: Heterozygous variants in transmembrane channel-like 1 gene cause autosomal recessive nonsyndromic hearing loss.
    2. Novel autosomal dominant TMC1 variants linked to hearing loss: insight into protein-lipid interactions.
      Title: Novel autosomal dominant TMC1 variants linked to hearing loss: insight into protein-lipid interactions.
    3. A novel splicing variant in the TMC1 gene causes non-syndromic hearing loss in a Chinese family.
      Title: A novel splicing variant in the TMC1 gene causes non-syndromic hearing loss in a Chinese family.
    4. GABA signaling triggered by TMC-1/Tmc delays neuronal aging by inhibiting the PKC pathway in C. elegans.
      Title: GABA signaling triggered by TMC-1/Tmc delays neuronal aging by inhibiting the PKC pathway in C. elegans.
    5. Prevalence and clinical features of autosomal dominant and recessive TMC1-associated hearing loss.
      Title: Prevalence and clinical features of autosomal dominant and recessive TMC1-associated hearing loss.
    6. New Tmc1 Deafness Mutations Impact Mechanotransduction in Auditory Hair Cells.
      Title: New Tmc1 Deafness Mutations Impact Mechanotransduction in Auditory Hair Cells.
    7. Compound Heterozygous Mutations in TMC1 and MYO15A Are Associated with Autosomal Recessive Nonsyndromic Hearing Loss in Two Chinese Han Families.
      Title: Compound Heterozygous Mutations in TMC1 and MYO15A Are Associated with Autosomal Recessive Nonsyndromic Hearing Loss in Two Chinese Han Families.
    8. Novel homozygous variants in the TMC1 and CDH23 genes cause autosomal recessive nonsyndromic hearing loss.
      Title: Novel homozygous variants in the TMC1 and CDH23 genes cause autosomal recessive nonsyndromic hearing loss.
    9. Identification of TMC1 as a relatively common cause for nonsyndromic hearing loss in the Saudi population.
      Title: Identification of TMC1 as a relatively common cause for nonsyndromic hearing loss in the Saudi population.
    10. Deafness mutation D572N of TMC1 destabilizes TMC1 expression by disrupting LHFPL5 binding.
      Title: Deafness mutation D572N of TMC1 destabilizes TMC1 expression by disrupting LHFPL5 binding.
    Submit: New GeneRIF Correction See all GeneRIFs (45)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of transmembrane channel-like 1 (TMC1) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium channel activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables mechanosensitive monoatomic ion channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables mechanosensitive monoatomic ion channel activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables voltage-gated calcium channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in auditory receptor cell development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in calcium ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in detection of mechanical stimulus involved in sensory perception of sound IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of calcium ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in vestibular reflex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in external side of plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in stereocilium ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in stereocilium tip IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    transmembrane channel-like protein 1
    Names
    transmembrane cochlear-expressed protein 1
    transmembrane, cochlear expressed, 1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_008213.1 RefSeqGene

      Range
      4808..321497
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_138691.3 → NP_619636.2  transmembrane channel-like protein 1

      See identical proteins and their annotated locations for NP_619636.2

      Status: REVIEWED

      Source sequence(s)
      AF417578, AL162416, AL591662, BC114449, HY031448
      Consensus CDS
      CCDS6643.1
      UniProtKB/Swiss-Prot
      A8MVZ2, B1AM91, Q8TDI8
      UniProtKB/TrEMBL
      Q3MI88
      Related
      ENSP00000297784.6, ENST00000297784.10
      Conserved Domains (1) summary
      pfam07810
      Location:520 → 626
      TMC; TMC domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      72521608..72838297
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017014256.2 → XP_016869745.1  transmembrane channel-like protein 1 isoform X1

      UniProtKB/TrEMBL
      Q3MI88

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      84672507..84989215
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054361949.1 → XP_054217924.1  transmembrane channel-like protein 1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TDI8.2 GenPept UniProtKB/Swiss-Prot:Q8TDI8

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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