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

Gene ID: 54499, updated on 7-Jun-2020

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
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; 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

Genomic context

See TMCO1 in Genome Data Viewer
Location:
1q24.1
Exon count:
7
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (165724291..165768922, complement)
105 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 carbonic anhydrase 14 pseudogene Neighboring gene uncharacterized LOC105371581 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 mental retardation syndrome
MedGen: C1859252 OMIM: 213980 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium channel activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
calcium channel activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
ER overload response IDA
Inferred from Direct Assay
more info
PubMed 
calcium ion transmembrane transport IDA
Inferred from Direct Assay
more info
PubMed 
cellular calcium ion homeostasis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endoplasmic reticulum calcium ion homeostasis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endoplasmic reticulum calcium ion homeostasis IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
Golgi membrane IEA
Inferred from Electronic Annotation
more info
 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 
integral component of endoplasmic reticulum membrane 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
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)

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
    5001..49632
    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/TrEMBL
    B7Z591
    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
    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 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AF070626, AL451074
    Consensus CDS
    CCDS1251.2
    Related
    ENSP00000375975.5, ENST00000392129.10
    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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    165724291..165768922 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.
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