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

Gene ID: 117531, updated on 7-Apr-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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Location:
9q21.13
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (72521608..72838297)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (84672507..84989215)
105.20220307 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
  • 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. GABA signaling triggered by TMC-1/Tmc delays neuronal aging by inhibiting the PKC pathway in C. elegans. Wu J, et al. Sci Adv, 2022 Dec 21. PMID 36542715, Free PMC Article
  2. A novel splicing variant in the TMC1 gene causes non-syndromic hearing loss in a Chinese family. Zeng B, et al. Chin Med J (Engl), 2022 Nov 5. PMID 35089886, Free PMC Article
  3. Prevalence and clinical features of autosomal dominant and recessive TMC1-associated hearing loss. Nishio SY, et al. Hum Genet, 2022 Apr. PMID 34523024, Free PMC Article
  4. Identification of TMC1 as a relatively common cause for nonsyndromic hearing loss in the Saudi population. Ramzan K, et al. Am J Med Genet B Neuropsychiatr Genet, 2020 Apr. PMID 31854501
  5. Next-generation sequencing reveals a novel pathological mutation in the TMC1 gene causing autosomal recessive non-syndromic hearing loss in an Iranian kindred. Sadeghian L, et al. Int J Pediatr Otorhinolaryngol, 2019 Sep. PMID 31176026

See all (59) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. New Tmc1 Deafness Mutations Impact Mechanotransduction in Auditory Hair Cells.
    Title: New Tmc1 Deafness Mutations Impact Mechanotransduction in Auditory Hair Cells.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. We suggest that KCNQ1, expression of which is not thought to overlap with TMC1 in hair cells, is a proxy partner bearing structural elements or a sequence motif reminiscent of a true in vivo TMC1 hair cell partner.
    Title: KCNQ1 rescues TMC1 plasma membrane expression but not mechanosensitive channel activity.
Submit: New GeneRIF Correction See all GeneRIFs (44)

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 mechanosensitive monoatomic ion channel activity IBA
Inferred from Biological aspect of Ancestor
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 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_2023_10

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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