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TMC4 transmembrane channel like 4 [ Homo sapiens (human) ]

Gene ID: 147798, updated on 5-Mar-2024

Summary

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Official Symbol
TMC4provided by HGNC
Official Full Name
transmembrane channel like 4provided by HGNC
Primary source
HGNC:HGNC:22998
See related
Ensembl:ENSG00000167608 MIM:617181; AllianceGenome:HGNC:22998
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
Predicted to enable mechanosensitive ion channel activity. Predicted to be involved in ion transmembrane transport. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in duodenum (RPKM 27.9), colon (RPKM 25.4) and 14 other tissues See more
Orthologs
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Genomic context

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Location:
19q13.42
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (54160108..54173160, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (57240374..57253360, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (54663846..54676854, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene CCR4-NOT transcription complex subunit 3 Neighboring gene uncharacterized LOC102724273 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:54662792-54663461 Neighboring gene leukocyte receptor cluster member 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:54676977-54677793 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:54677794-54678609 Neighboring gene membrane bound O-acyltransferase domain containing 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54683683-54684198 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:54684199-54684714 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:54684715-54685229 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54687509-54688008 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:54692762-54693444 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:54693445-54694126 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:54695049-54695250 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54696095-54696610 Neighboring gene tRNA splicing endonuclease subunit 34 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:54704113-54704783 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54709694-54710202 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54710710-54711217 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54711218-54711724 Neighboring gene ribosomal protein S9

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. Lack of evidence supporting a role of TMC4-rs641738 missense variant-MBOAT7- intergenic downstream variant-in the Susceptibility to Nonalcoholic Fatty Liver Disease. Sookoian S, et al. Sci Rep, 2018 Mar 23. PMID 29572551, Free PMC Article
  2. The MBOAT7-TMC4 Variant rs641738 Increases Risk of Nonalcoholic Fatty Liver Disease in Individuals of European Descent. Mancina RM, et al. Gastroenterology, 2016 May. PMID 26850495, Free PMC Article
  3. Characterization of the transmembrane channel-like (TMC) gene family: functional clues from hearing loss and epidermodysplasia verruciformis. Kurima K, et al. Genomics, 2003 Sep. PMID 12906855
  4. TMC and EVER genes belong to a larger novel family, the TMC gene family encoding transmembrane proteins. Keresztes G, et al. BMC Genomics, 2003 Jun 17. PMID 12812529, Free PMC Article
  5. Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Denoeud F, et al. Genome Res, 2007 Jun. PMID 17567994, Free PMC Article

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. This study explored the role of rs641738 C/T located in TMC4 exon 1 (p.Gly17Glu) and 500 bases- downstream of MBOAT7 gene (TMC4/MBOAT7), in the genetic risk for developing nonalcoholic fatty liver disease (NAFLD). No evidence was found of association between rs641738 and either NAFLD (Cochran-Armitage test for trend, p = 0.529) or the disease severity (p = 0.61).
    Title: Lack of evidence supporting a role of TMC4-rs641738 missense variant-MBOAT7- intergenic downstream variant-in the Susceptibility to Nonalcoholic Fatty Liver Disease.
  2. Report no association between the TMC4 rs641738 variant and the development and severity of NAFLD in individuals of European descent.
    Title: The MBOAT7-TMC4 Variant rs641738 Increases Risk of Nonalcoholic Fatty Liver Disease in Individuals of European Descent.
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
An atlas of genetic influences on human blood metabolites.
EBI GWAS Catalog

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC39329

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables mechanosensitive monoatomic ion channel activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in monoatomic ion transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in extracellular exosome HDA PubMed 
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
transmembrane channel-like protein 4
Names
testicular tissue protein Li 204

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.

mRNA and Protein(s)

  1. NM_001145303.3 → NP_001138775.2  transmembrane channel-like protein 4 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AA578987, AC245052, AY236492, BC025323, BQ082417, BU680152
    Consensus CDS
    CCDS46174.1
    UniProtKB/TrEMBL
    A0A087WT65, A0A0G2JPL6
    Related
    ENSP00000477627.1, ENST00000617472.4
    Conserved Domains (1) summary
    pfam07810
    Location:480 → 558
    TMC; TMC domain

  2. NM_144686.4 → NP_653287.2  transmembrane channel-like protein 4 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame segment in the 5' coding region compared to variant 1. The resulting isoform (2) is shorter but has the same N- and C-termini compared to isoform 1.
    Source sequence(s)
    AA578987, AC245052, AY236492, BC025323, BQ082417, BU680152
    Consensus CDS
    CCDS12882.1
    UniProtKB/TrEMBL
    A0A087WVI4, A0A0G2JMM6
    Related
    ENSP00000479458.1, ENST00000619895.5
    Conserved Domains (1) summary
    pfam07810
    Location:474 → 552
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    54160108..54173160 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011526486.3 → XP_011524788.1  transmembrane channel-like protein 4 isoform X1

    Conserved Domains (1) summary
    pfam07810
    Location:320 → 398
    TMC; TMC domain

RNA

  1. XR_935741.3 RNA Sequence

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NW_003571054.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    134958..147932 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054329665.1 → XP_054185640.1  transmembrane channel-like protein 4 isoform X1

RNA

  1. XR_008485656.1 RNA Sequence

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NW_003571055.2 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    134959..147968 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330144.1 → XP_054186119.1  transmembrane channel-like protein 4 isoform X2

  2. XM_054330143.1 → XP_054186118.1  transmembrane channel-like protein 4 isoform X1

RNA

  1. XR_008485690.1 RNA Sequence

Reference GRCh38.p14 ALT_REF_LOCI_3

Genomic

  1. NW_003571056.2 Reference GRCh38.p14 ALT_REF_LOCI_3

    Range
    134959..147968 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330457.1 → XP_054186432.1  transmembrane channel-like protein 4 isoform X3

  2. XM_054330456.1 → XP_054186431.1  transmembrane channel-like protein 4 isoform X1

RNA

  1. XR_008485695.1 RNA Sequence

Reference GRCh38.p14 ALT_REF_LOCI_4

Genomic

  1. NW_003571057.2 Reference GRCh38.p14 ALT_REF_LOCI_4

    Range
    134959..147968 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330710.1 → XP_054186685.1  transmembrane channel-like protein 4 isoform X4

  2. XM_054330709.1 → XP_054186684.1  transmembrane channel-like protein 4 isoform X1

RNA

  1. XR_008485701.1 RNA Sequence

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

  1. NW_003571058.2 Reference GRCh38.p14 ALT_REF_LOCI_5

    Range
    134959..147968 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330941.1 → XP_054186916.1  transmembrane channel-like protein 4 isoform X5

  2. XM_054330940.1 → XP_054186915.1  transmembrane channel-like protein 4 isoform X1

RNA

  1. XR_008485705.1 RNA Sequence

Reference GRCh38.p14 ALT_REF_LOCI_6

Genomic

  1. NW_003571059.2 Reference GRCh38.p14 ALT_REF_LOCI_6

    Range
    134959..147968 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054331219.1 → XP_054187194.1  transmembrane channel-like protein 4 isoform X6

  2. XM_054331218.1 → XP_054187193.1  transmembrane channel-like protein 4 isoform X1

RNA

  1. XR_008485712.1 RNA Sequence

Reference GRCh38.p14 ALT_REF_LOCI_7

Genomic

  1. NW_003571060.1 Reference GRCh38.p14 ALT_REF_LOCI_7

    Range
    134959..147938 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054331491.1 → XP_054187466.1  transmembrane channel-like protein 4 isoform X1

RNA

  1. XR_008485719.1 RNA Sequence

Reference GRCh38.p14 ALT_REF_LOCI_8

Genomic

  1. NW_003571061.2 Reference GRCh38.p14 ALT_REF_LOCI_8

    Range
    134959..147968 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054333530.1 → XP_054189505.1  transmembrane channel-like protein 4 isoform X7

  2. XM_054333529.1 → XP_054189504.1  transmembrane channel-like protein 4 isoform X1

RNA

  1. XR_008485848.1 RNA Sequence

Reference GRCh38.p14 ALT_REF_LOCI_9

Genomic

  1. NT_187693.1 Reference GRCh38.p14 ALT_REF_LOCI_9

    Range
    134959..147968 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054333628.1 → XP_054189603.1  transmembrane channel-like protein 4 isoform X8

  2. XM_054333627.1 → XP_054189602.1  transmembrane channel-like protein 4 isoform X1

RNA

  1. XR_008485853.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    57240374..57253360 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054319880.1 → XP_054175855.1  transmembrane channel-like protein 4 isoform X9

  2. XM_054319879.1 → XP_054175854.1  transmembrane channel-like protein 4 isoform X1

RNA

  1. XR_008485087.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q7Z404.3 GenPept UniProtKB/Swiss-Prot:Q7Z404

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