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

Gene ID: 160418, updated on 27-Nov-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
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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: 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. 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
Compare labs

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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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

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