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

Gene ID: 160335, updated on 2-Nov-2024

Summary

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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; AllianceGenome:HGNC:25440
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
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Genomic context

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See TMTC2 in Genome Data Viewer
Location:
12q21.31
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (82686906..83134866)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (82666441..83114534)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (83080685..83528645)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene KIAA1586 pseudogene Neighboring gene uncharacterized LOC107984487 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:83043817-83045016 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4686 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6691 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6692 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4687 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4688 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4689 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:83150061-83150605 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:83251535-83252512 Neighboring gene NANOG hESC enhancer GRCh37_chr12:83397660-83398161 Neighboring gene RNA, U6 small nuclear 977, pseudogene Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:83467822-83469021 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:83591168-83591841 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:83604635-83605269 Neighboring gene ribosomal protein L6 pseudogene 25 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:83694145-83694645 Neighboring gene NANOG hESC enhancer GRCh37_chr12:83726841-83727342 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:83826060-83826560 Neighboring gene uncharacterized LOC105369874

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 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. Polymorphism rs7961953 in TMTC2 gene is not associated with primary open-angle glaucoma in a Saudi cohort. Kondkar AA, et al. Ophthalmic Genet, 2019 Feb. PMID 30729851
  2. Association of TMTC2 With Human Nonsyndromic Sensorineural Hearing Loss. Runge CL, et al. JAMA Otolaryngol Head Neck Surg, 2016 Sep 1. PMID 27311106, Free PMC Article
  3. Genome-wide association of hypoxia-inducible factor (HIF)-1alpha and HIF-2alpha DNA binding with expression profiling of hypoxia-inducible transcripts. Mole DR, et al. J Biol Chem, 2009 Jun 19. PMID 19386601, Free PMC Article
  4. Three susceptible loci associated with primary open-angle glaucoma identified by genome-wide association study in a Japanese population. Nakano M, et al. Proc Natl Acad Sci U S A, 2009 Aug 4. PMID 19625618, Free PMC Article
  5. Metastasizing Pleomorphic Adenoma: Recurrent PLAG1/HMGA2 Rearrangements and Identification of a Novel HMGA2-TMTC2 Fusion. Wasserman JK, et al. Am J Surg Pathol, 2019 Aug. PMID 31094927

See all (32) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Conserved sequence motifs in human TMTC1, TMTC2, TMTC3, and TMTC4, new O-mannosyltransferases from the GT-C/PMT clan, are rationalized as ligand binding sites.
    Title: Conserved sequence motifs in human TMTC1, TMTC2, TMTC3, and TMTC4, new O-mannosyltransferases from the GT-C/PMT clan, are rationalized as ligand binding sites.
  2. Polymorphism rs7961953 in TMTC2 gene is not associated with primary open-angle glaucoma.
    Title: Polymorphism rs7961953 in TMTC2 gene is not associated with primary open-angle glaucoma in a Saudi cohort.
  3. Metastasizing pleomorphic adenomas with recurrent PLAG1/HMGA2 gene rearrangements and a novel HMGA2-TMTC2 fusion.
    Title: Metastasizing Pleomorphic Adenoma: Recurrent PLAG1/HMGA2 Rearrangements and Identification of a Novel HMGA2-TMTC2 Fusion.
  4. A previously uncharacterized gene, TMTC2, has been identified as a candidate for causing progressive sensorineural hearing loss in humans. This finding identifies a novel locus that causes autosomal dominant SNHL.
    Title: Association of TMTC2 With Human Nonsyndromic Sensorineural Hearing Loss.
  5. findings provide an important link between aneuploidy and the stress pathways activated by Aurora B inhibition and also support the use of Aurora B inhibitors in combination therapy for treatment of cancer.
    Title: TMTC1 and TMTC2 are novel endoplasmic reticulum tetratricopeptide repeat-containing adapter proteins involved in calcium homeostasis.
  6. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  7. TMTC2 expression induced by HIF-2alpha.
    Title: Genome-wide association of hypoxia-inducible factor (HIF)-1alpha and HIF-2alpha DNA binding with expression profiling of hypoxia-inducible transcripts.
  8. Clinical trial and genome-wide association study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Molecular genetics of successful smoking cessation: convergent genome-wide association study results.
  9. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: Three susceptible loci associated with primary open-angle glaucoma identified by genome-wide association study in a Japanese population.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

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

HIV-1 interactions

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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

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • DKFZp762A217

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables dolichyl-phosphate-mannose-protein mannosyltransferase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables mannosyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in calcium ion homeostasis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein O-linked mannosylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein O-linked mannosylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
  
is_active_in endoplasmic reticulum membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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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
XP_047284352.1
XP_054227192.1
XP_054227193.1
XP_054227194.1

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_001320321.2 → NP_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/TrEMBL
    B7Z639
    Conserved Domains (7) summary
    sd00006
    Location:282 → 310
    TPR; TPR repeat [structural motif]
    pfam00515
    Location:534 → 567
    TPR_1; Tetratricopeptide repeat
    pfam07719
    Location:364 → 393
    TPR_2; Tetratricopeptide repeat
    pfam08409
    Location:2 → 73
    DUF1736; Domain of unknown function (DUF1736)
    pfam13414
    Location:248 → 309
    TPR_11; TPR repeat
    pfam13424
    Location:312 → 389
    TPR_12; Tetratricopeptide repeat
    pfam14559
    Location:510 → 577
    TPR_19; Tetratricopeptide repeat

  2. NM_001320322.2 → NP_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)
    AC091214, BC098572, CA424966
    Consensus CDS
    CCDS81717.1
    UniProtKB/TrEMBL
    F8VSH2
    Related
    ENSP00000448292.1, ENST00000548305.5
    Conserved Domains (4) summary
    sd00006
    Location:493 → 521
    TPR; TPR repeat [structural motif]
    pfam00515
    Location:493 → 520
    TPR_1; Tetratricopeptide repeat
    pfam08409
    Location:247 → 318
    DUF1736; Domain of unknown function (DUF1736)
    pfam13414
    Location:493 → 554
    TPR_11; TPR repeat

  3. NM_152588.3 → NP_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
    B2RCU7, Q8N2K8, Q8N394
    UniProtKB/TrEMBL
    A0A0B4J253
    Related
    ENSP00000322300.3, ENST00000321196.8
    Conserved Domains (7) summary
    sd00006
    Location:527 → 555
    TPR; TPR repeat [structural motif]
    pfam00515
    Location:779 → 812
    TPR_1; Tetratricopeptide repeat
    pfam07719
    Location:609 → 638
    TPR_2; Tetratricopeptide repeat
    pfam08409
    Location:247 → 318
    DUF1736; Domain of unknown function (DUF1736)
    pfam13414
    Location:493 → 554
    TPR_11; TPR repeat
    pfam13424
    Location:557 → 634
    TPR_12; Tetratricopeptide repeat
    pfam14559
    Location:755 → 822
    TPR_19; Tetratricopeptide repeat

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    82686906..83134866
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017018884.3 → XP_016874373.1  protein O-mannosyl-transferase TMTC2 isoform X1

    UniProtKB/TrEMBL
    A0A0B4J253
    Conserved Domains (3) summary
    COG0457
    Location:364 → 595
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:410 → 438
    TPR; TPR repeat [structural motif]
    pfam08409
    Location:130 → 201
    DUF1736; Domain of unknown function (DUF1736)

  2. XM_047428396.1 → XP_047284352.1  protein O-mannosyl-transferase TMTC2 isoform X2

    Related
    ENST00000551915.5

  3. XM_024448863.2 → XP_024304631.1  protein O-mannosyl-transferase TMTC2 isoform X1

    UniProtKB/TrEMBL
    A0A0B4J253
    Conserved Domains (3) summary
    COG0457
    Location:364 → 595
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:410 → 438
    TPR; TPR repeat [structural motif]
    pfam08409
    Location:130 → 201
    DUF1736; Domain of unknown function (DUF1736)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    82666441..83114534
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054371218.1 → XP_054227193.1  protein O-mannosyl-transferase TMTC2 isoform X1

  2. XM_054371219.1 → XP_054227194.1  protein O-mannosyl-transferase TMTC2 isoform X2

  3. XM_054371217.1 → XP_054227192.1  protein O-mannosyl-transferase TMTC2 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N394.1 GenPept UniProtKB/Swiss-Prot:Q8N394

Gene LinkOut

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