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    TMTC3 transmembrane O-mannosyltransferase targeting cadherins 3 [ Homo sapiens (human) ]

    Gene ID: 160418, updated on 10-Dec-2024

    Summary

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    Official Symbol
    TMTC3provided by HGNC
    Official Full Name
    transmembrane O-mannosyltransferase targeting cadherins 3provided by HGNC
    Primary source
    HGNC:HGNC:26899
    See related
    Ensembl:ENSG00000139324 MIM:617218; AllianceGenome:HGNC:26899
    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
    LIS8; SMILE
    Summary
    This gene encodes a protein that belongs to the transmembrane and tetratricopeptide repeat-containing protein family. [provided by RefSeq, May 2010]
    Expression
    Ubiquitous expression in skin (RPKM 6.6), esophagus (RPKM 5.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TMTC3 in Genome Data Viewer
    Location:
    12q21.32
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (88142307..88199887)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (88124249..88181842)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (88536084..88593664)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902977 Neighboring gene transmembrane protein 38A pseudogene Neighboring gene MPRA-validated peak1864 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6699 Neighboring gene RNA, 5S ribosomal pseudogene 364 Neighboring gene centrosomal protein 290 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:88535951-88536454 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:88621606-88622152 Neighboring gene suppressyn-like Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:88637506-88638084 Neighboring gene MPRA-validated peak1868 silencer Neighboring gene MPRA-validated peak1869 silencer Neighboring gene uncharacterized LOC124902978 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6701 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6702 Neighboring gene MPRA-validated peak1870 silencer

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. A Novel ER Stress Mediator TMTC3 Promotes Squamous Cell Carcinoma Progression by Activating GRP78/PERK Signaling Pathway. Yuan H, et al. Int J Biol Sci, 2022. PMID 35982901, Free PMC Article
    2. Biallelic Mutations in TMTC3, Encoding a Transmembrane and TPR-Containing Protein, Lead to Cobblestone Lissencephaly. Jerber J, et al. Am J Hum Genet, 2016 Nov 3. PMID 27773428, Free PMC Article
    3. The involvement of SMILE/TMTC3 in endoplasmic reticulum stress response. Racapé M, et al. PLoS One, 2011. PMID 21603654, Free PMC Article
    4. The deep infiltrating endometriosis tissue has lower T-cadherin, E-cadherin, progesterone receptor and oestrogen receptor than endometrioma tissue. Biyik I, et al. Taiwan J Obstet Gynecol, 2021 Nov. PMID 34794738
    5. 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. Eisenhaber B, et al. Biol Direct, 2021 Jan 12. PMID 33436046, Free PMC Article

    See all (62) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A Novel ER Stress Mediator TMTC3 Promotes Squamous Cell Carcinoma Progression by Activating GRP78/PERK Signaling Pathway.
      Title: A Novel ER Stress Mediator TMTC3 Promotes Squamous Cell Carcinoma Progression by Activating GRP78/PERK Signaling Pathway.
    2. The deep infiltrating endometriosis tissue has lower T-cadherin, E-cadherin, progesterone receptor and oestrogen receptor than endometrioma tissue.
      Title: The deep infiltrating endometriosis tissue has lower T-cadherin, E-cadherin, progesterone receptor and oestrogen receptor than endometrioma tissue.
    3. 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.
    4. O-mannosylation pathway dedicated to cadherins/ protocadherins orchestrated by the four TMTC1-4 genes
      Title: Discovery of an O-mannosylation pathway selectively serving cadherins and protocadherins.
    5. SMILE is a novel transgene specifying both bronchial smooth muscle and lung alveolar myofibroblast lineages, contributing to the understanding of the biological control of the development of these cells.
      Title: mSmile is necessary for bronchial smooth muscle and alveolar myofibroblast development.
    6. that SMILE is involved in the endoplasmic reticulum stress response, by modulating proteasome activity and XBP-1 transcript expression. This function of SMILE may influence immune cell behavior in the context of transplantation.
      Title: The involvement of SMILE/TMTC3 in endoplasmic reticulum stress response.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Lissencephaly 8
    MedGen: C4310646 OMIM: 617255 GeneReviews: Not available
    		not available

    EBI GWAS Catalog

    Description
    Clozapine-induced agranulocytosis is associated with rare HLA-DQB1 and HLA-B alleles.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ90492, DKFZp686C0968, DKFZp686M1969, DKFZp686O2342, DKFZp686O22167

    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 positive regulation of proteasomal protein catabolic process 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 
    involved_in response to endoplasmic reticulum stress IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    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
    		 PubMed 
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    protein O-mannosyl-transferase TMTC3
    Names
    transmembrane and TPR repeat-containing protein 3
    transmembrane and tetratricopeptide repeat containing 3
    NP_001353503.1
    NP_001353508.1
    NP_001353509.1
    NP_001353512.1
    NP_861448.2

    NCBI Reference Sequences (RefSeq)

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    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_021187.1 RefSeqGene

      Range
      5012..62592
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001366574.1 → NP_001353503.1  protein O-mannosyl-transferase TMTC3 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC087865, AC091516, AC127901, KF455688
      UniProtKB/TrEMBL
      B4DZ55
      Conserved Domains (3) summary
      sd00006
      Location:470 → 497
      TPR; TPR repeat [structural motif]
      pfam08409
      Location:199 → 271
      DUF1736; Domain of unknown function (DUF1736)
      cl26002
      Location:375 → 742
      TPR_11; TPR repeat

    2. NM_001366579.1 → NP_001353508.1  protein O-mannosyl-transferase TMTC3 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC087865, AC091516, AC127901
      UniProtKB/TrEMBL
      B4DZ55
      Conserved Domains (3) summary
      sd00006
      Location:457 → 484
      TPR; TPR repeat [structural motif]
      pfam08409
      Location:186 → 258
      DUF1736; Domain of unknown function (DUF1736)
      cl26002
      Location:362 → 729
      TPR_11; TPR repeat

    3. NM_001366580.1 → NP_001353509.1  protein O-mannosyl-transferase TMTC3 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC087865, AC091516, AC127901, KF455688
      UniProtKB/TrEMBL
      B4DZ55
      Conserved Domains (3) summary
      sd00006
      Location:441 → 468
      TPR; TPR repeat [structural motif]
      pfam08409
      Location:170 → 242
      DUF1736; Domain of unknown function (DUF1736)
      cl26002
      Location:346 → 713
      TPR_11; TPR repeat

    4. NM_001366583.1 → NP_001353512.1  protein O-mannosyl-transferase TMTC3 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC087865, AC091516, AC127901
      Conserved Domains (3) summary
      sd00006
      Location:299 → 326
      TPR; TPR repeat [structural motif]
      pfam08409
      Location:28 → 100
      DUF1736; Domain of unknown function (DUF1736)
      cl26002
      Location:204 → 571
      TPR_11; TPR repeat

    5. NM_181783.4 → NP_861448.2  protein O-mannosyl-transferase TMTC3 isoform 1

      See identical proteins and their annotated locations for NP_861448.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AK290436, BC117175, BG287027, BX538169, CR737828, CR749309, CR933632
      Consensus CDS
      CCDS9032.1
      UniProtKB/TrEMBL
      B4DZ55
      Related
      ENSP00000266712.6, ENST00000266712.11
      Conserved Domains (3) summary
      sd00006
      Location:530 → 557
      TPR; TPR repeat [structural motif]
      pfam08409
      Location:259 → 331
      DUF1736; Domain of unknown function (DUF1736)
      cl26002
      Location:435 → 802
      TPR_11; TPR repeat

    RNA

    1. NR_159381.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC087865, AC091516, AC127901, AK310375

    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
      88142307..88199887
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      88124249..88181842
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6ZXV5.2 GenPept UniProtKB/Swiss-Prot:Q6ZXV5

    Gene LinkOut

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

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