TMC2 transmembrane channel like 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TMC2provided by HGNC
Official Full Name: transmembrane channel like 2provided by HGNC
Primary source: HGNC:HGNC:16527
See related: Ensembl:ENSG00000149488 MIM:606707; AllianceGenome:HGNC:16527
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: C20orf145
Summary: 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]
Expression: Low expression observed in reference dataset See more
Orthologs: mouse all
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Genomic context

Location:: 20p13

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
110	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (2536573..2643580)
110	current	T2T-CHM13v2.0 (GCF_009914755.1)	20	NC_060944.1 (2566964..2674040)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (2517219..2624226)

Chromosome 20 - NC_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

But the great majority of evidence is consistent with these TMCs as pore-forming subunits of the long-sought hair-cell transduction channel. [review]
Title: Are TMCs the Mechanotransduction Channels of Vertebrate Hair Cells?
Autozygosity by descent analysis of 2 markers bordering the TMC2 gene allowed us to rule out its association with deafness within these families.
Title: TMC1 but not TMC2 is responsible for autosomal recessive nonsyndromic hearing impairment in Tunisian families.

Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

074WA9 (e-PCR)
- UniSTS:82177

Z94495 (e-PCR)
- UniSTS:13345

AL034535 (e-PCR)
- UniSTS:94241

AL034506 (e-PCR)
- UniSTS:94258

L18426 (e-PCR)
- UniSTS:34648

G35510 (e-PCR)
- UniSTS:44150

Z94349 (e-PCR)
- UniSTS:75697

DXS7958 (e-PCR)
- UniSTS:154365

Homology

Homologs of the TMC2 gene: The TMC2 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 309 organisms have orthologs with human gene TMC2
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables mechanosensitive ion channel activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables molecular_function	ND No biological Data available more info
enables voltage-gated calcium channel activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed

Process	Evidence Code	Pubs
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	PubMed
involved_in detection of mechanical stimulus involved in sensory perception of sound	IMP Inferred from Mutant Phenotype more info	PubMed
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	PubMed

Component	Evidence Code	Pubs
is_active_in cellular_component	ND No biological Data available more info
located_in 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 2

Names: transmembrane cochlear-expressed gene 2; transmembrane cochlear-expressed protein 2

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

NG_042834.1 RefSeqGene

Range

4967..111974

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_080751.3 → NP_542789.2 transmembrane channel-like protein 2

See identical proteins and their annotated locations for NP_542789.2

Status: REVIEWED

Source sequence(s)

AL049712

Consensus CDS

CCDS13029.2

UniProtKB/Swiss-Prot

Q8TDI7, Q9BYN5

Related

ENSP00000351732.1, ENST00000358864.2

Conserved Domains (1) summary

pfam07810
Location:579 → 685

TMC; TMC domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000020.11 Reference GRCh38.p14 Primary Assembly

Range

2536573..2643580

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005260660.5 → XP_005260717.1 transmembrane channel-like protein 2 isoform X1

Conserved Domains (2) summary

pfam05672
Location:95 → 187

MAP7; MAP7 (E-MAP-115) family

pfam07810
Location:604 → 710

TMC; TMC domain