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TMTC2 transmembrane O-mannosyltransferase targeting cadherins 2 [ Homo sapiens (human) ]

Gene ID: 160335, updated on 15-Jun-2019

Summary

Official Symbol
TMTC2provided by HGNC
Official Full Name
transmembrane O-mannosyltransferase targeting cadherins 2provided by HGNC
Primary source
HGNC:HGNC:25440
See related
Ensembl:ENSG00000179104 MIM:615856
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
IBDBP1
Summary
The protein encoded by this gene is an integral membrane protein localized to the endoplasmic reticulum (ER). The encoded protein contains many tetratricopeptide repeats, sequences known for being involved in protein-protein interactions. This protein binds both the calcium uptake pump SERCA2B and the carbohydrate-binding chaperone calnexin, and it appears to play a role in calcium homeostasis in the ER. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2016]
Expression
Ubiquitous expression in brain (RPKM 7.5), gall bladder (RPKM 7.0) and 24 other tissues See more
Orthologs

Genomic context

See TMTC2 in Genome Data Viewer
Location:
12q21.31
Exon count:
13
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 12 NC_000012.12 (82686952..83134868)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (83080731..83528647)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene KIAA1586 pseudogene Neighboring gene uncharacterized LOC107984487 Neighboring gene RNA, U6 small nuclear 977, pseudogene Neighboring gene ribosomal protein L6 pseudogene 25 Neighboring gene uncharacterized LOC105369874

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 FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants.
NHGRI GWA Catalog
Genome-wide association study of antibody response to smallpox vaccine.
NHGRI GWA Catalog
Identification of candidate loci at 6p21 and 21q22 in a genome-wide association study of cardiac manifestations of neonatal lupus.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies identifies novel loci that influence cupping and the glaucomatous process.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Vif vif HIV-1 Vif upregulates the expression of transmembrane and tetratricopeptide repeat containing 2 (TMTC2) in Vif-expression T cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp762A217

Gene Ontology Provided by GOA

Function Evidence Code Pubs
dolichyl-phosphate-mannose-protein mannosyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
mannosyltransferase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
calcium ion homeostasis IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein O-linked mannosylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 
endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
PubMed 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
protein O-mannosyl-transferase TMTC2
Names
transmembrane and TPR repeat-containing protein 2
transmembrane and tetratricopeptide repeat containing 2
NP_001307250.1
NP_001307251.1
NP_689801.1
XP_016874373.1
XP_024304631.1

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.

mRNA and Protein(s)

  1. NM_001320321.2NP_001307250.1  protein O-mannosyl-transferase TMTC2 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate coding exon compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AC091214, AK299771, AL834509, BC071614
    UniProtKB/Swiss-Prot
    Q8N394
    UniProtKB/TrEMBL
    B7Z639
    Conserved Domains (7) summary
    sd00006
    Location:282310
    TPR; TPR repeat [structural motif]
    pfam00515
    Location:534567
    TPR_1; Tetratricopeptide repeat
    pfam07719
    Location:364393
    TPR_2; Tetratricopeptide repeat
    pfam08409
    Location:273
    DUF1736; Domain of unknown function (DUF1736)
    pfam13414
    Location:248309
    TPR_11; TPR repeat
    pfam13424
    Location:312389
    TPR_12; Tetratricopeptide repeat
    pfam14559
    Location:510577
    TPR_19; Tetratricopeptide repeat
  2. NM_001320322.1NP_001307251.1  protein O-mannosyl-transferase TMTC2 isoform 3 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (3) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    BC098572, CA424966
    Consensus CDS
    CCDS81717.1
    UniProtKB/TrEMBL
    F8VSH2
    Related
    ENSP00000448292.1, ENST00000548305.5
    Conserved Domains (4) summary
    sd00006
    Location:493521
    TPR; TPR repeat [structural motif]
    pfam00515
    Location:493520
    TPR_1; Tetratricopeptide repeat
    pfam08409
    Location:247318
    DUF1736; Domain of unknown function (DUF1736)
    pfam13414
    Location:493554
    TPR_11; TPR repeat
  3. NM_152588.3NP_689801.1  protein O-mannosyl-transferase TMTC2 isoform 1 precursor

    See identical proteins and their annotated locations for NP_689801.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC091214, AL834509, BC071614
    Consensus CDS
    CCDS9025.1
    UniProtKB/Swiss-Prot
    Q8N394
    Related
    ENSP00000322300.3, ENST00000321196.8
    Conserved Domains (7) summary
    sd00006
    Location:527555
    TPR; TPR repeat [structural motif]
    pfam00515
    Location:779812
    TPR_1; Tetratricopeptide repeat
    pfam07719
    Location:609638
    TPR_2; Tetratricopeptide repeat
    pfam08409
    Location:247318
    DUF1736; Domain of unknown function (DUF1736)
    pfam13414
    Location:493554
    TPR_11; TPR repeat
    pfam13424
    Location:557634
    TPR_12; Tetratricopeptide repeat
    pfam14559
    Location:755822
    TPR_19; Tetratricopeptide repeat

RefSeqs of Annotated Genomes: Homo sapiens 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_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    82686906..83134868
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017018884.2XP_016874373.1  protein O-mannosyl-transferase TMTC2 isoform X1

    Conserved Domains (3) summary
    COG0457
    Location:364595
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:410438
    TPR; TPR repeat [structural motif]
    pfam08409
    Location:131201
    DUF1736; Domain of unknown function (DUF1736)
  2. XM_024448863.1XP_024304631.1  protein O-mannosyl-transferase TMTC2 isoform X1

    Conserved Domains (3) summary
    COG0457
    Location:364595
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:410438
    TPR; TPR repeat [structural motif]
    pfam08409
    Location:131201
    DUF1736; Domain of unknown function (DUF1736)

RNA

  1. XR_001748601.1 RNA Sequence

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