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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
    mouse all
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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)

    Genotypes

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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