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    TMCO1 transmembrane and coiled-coil domains 1 [ Homo sapiens (human) ]

    Gene ID: 54499, updated on 17-Jun-2024

    Summary

    Official Symbol
    TMCO1provided by HGNC
    Official Full Name
    transmembrane and coiled-coil domains 1provided by HGNC
    Primary source
    HGNC:HGNC:18188
    See related
    Ensembl:ENSG00000143183 MIM:614123; AllianceGenome:HGNC:18188
    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
    PCIA3; TMCC4; CFSMR1; HP10122; PNAS-136
    Summary
    This locus encodes a transmembrane protein. Mutations at this locus have been associated with craniofacial dysmorphism, skeletal anomalies, and cognitive disability. Mutations at this locus have also been associated with open angle glaucoma blindness. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jan 2012]
    Expression
    Ubiquitous expression in colon (RPKM 19.0), thyroid (RPKM 18.0) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See TMCO1 in Genome Data Viewer
    Location:
    1q24.1
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (165724291..165768922, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (165070667..165115003, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (165693528..165738159, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene aldehyde dehydrogenase 9 family member A1 Neighboring gene ribosomal protein L21 pseudogene 27 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:165667608-165668190 Neighboring gene carbonic anhydrase 14 pseudogene Neighboring gene MPRA-validated peak437 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2021 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:165737716-165738392 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:165738393-165739068 Neighboring gene TMCO1 antisense RNA 1 Neighboring gene ribosomal protein L26 pseudogene 12

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Craniofacial dysmorphism, skeletal anomalies, and impaired intellectual development 1
    MedGen: C5677021 OMIM: 213980 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    Common genetic determinants of intraocular pressure and primary open-angle glaucoma.
    EBI GWAS Catalog
    Common variants near ABCA1, AFAP1 and GMDS confer risk of primary open-angle glaucoma.
    EBI GWAS Catalog
    Genome-wide analysis of multi-ancestry cohorts identifies new loci influencing intraocular pressure and susceptibility to glaucoma.
    EBI GWAS Catalog
    Genome-wide association study and meta-analysis of intraocular pressure.
    EBI GWAS Catalog
    Genome-wide association study identifies susceptibility loci for open angle glaucoma at TMCO1 and CDKN2B-AS1.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables calcium channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables ribosome binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in Golgi membrane IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
     
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of multi-pass translocon complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    calcium load-activated calcium channel
    Names
    CLAC channel
    Ca(2+) load-activated Ca(2+) channel
    GEL complex subunit TMCO1
    putative membrane protein
    transmembrane and coiled-coil domain-containing protein 1
    transmembrane and coiled-coil domains 4
    xenogeneic cross-immune protein PCIA3

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_032004.1 RefSeqGene

      Range
      5055..47128
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001256164.1NP_001243093.1  calcium load-activated calcium channel isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses two alternate in-frame splice sites in the 5' coding region, compared to variant 1. This results in a shorter protein (isoform b), compared to isoform a.
      Source sequence(s)
      AI379550, AK316080, AL451074, BP257387
      UniProtKB/Swiss-Prot
      B2REA0, J9JIE6, O75545, Q9BZS3, Q9BZU8, Q9UM00
      Related
      ENSP00000480514.1, ENST00000612311.4
      Conserved Domains (1) summary
      pfam01956
      Location:45182
      DUF106; Integral membrane protein DUF106
    2. NM_001256165.1NP_001243094.1  calcium load-activated calcium channel isoform c

      See identical proteins and their annotated locations for NP_001243094.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in the 5' coding region and uses a downstream start codon, compared to variant 1. The encoded isoform (c) has a shorter and distinct N-terminus, compared to isoform a.
      Source sequence(s)
      AI379550, AK298614, AK316080, AL451074
      UniProtKB/TrEMBL
      B7Z591, J3KS45
      Related
      ENSP00000462300.1, ENST00000481278.5
      Conserved Domains (1) summary
      pfam01956
      Location:11153
      DUF106; Integral membrane protein DUF106
    3. NM_019026.6NP_061899.3  calcium load-activated calcium channel isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AF070626, AL451074
      Consensus CDS
      CCDS1251.3
      Related
      ENSP00000356856.6, ENST00000367881.11
      Conserved Domains (1) summary
      pfam01956
      Location:8165
      DUF106; Integral membrane protein DUF106

    RNA

    1. NR_045818.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate splice site in the 5' terminal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AI379550, AK316080, AL451074, BP257387

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      165724291..165768922 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      165070667..165115003 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001366129.1: Suppressed sequence

      Description
      NM_001366129.1: This RefSeq was removed because it is redundant with another RefSeq.