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Aliases for TMTC3 Gene

Aliases for TMTC3 Gene

  • Transmembrane And Tetratricopeptide Repeat Containing 3 2 3 5
  • Transmembrane And TPR Repeat-Containing Protein 3 3
  • Protein SMILE 4
  • SMILE 3
  • LIS8 3

External Ids for TMTC3 Gene

Previous GeneCards Identifiers for TMTC3 Gene

  • GC12P087042
  • GC12P088536
  • GC12P085603

Summaries for TMTC3 Gene

Entrez Gene Summary for TMTC3 Gene

  • This gene encodes a protein that belongs to the transmembrane and tetratricopeptide repeat-containing protein family. [provided by RefSeq, May 2010]

GeneCards Summary for TMTC3 Gene

TMTC3 (Transmembrane And Tetratricopeptide Repeat Containing 3) is a Protein Coding gene. Diseases associated with TMTC3 include Lissencephaly 8 and Lissencephaly. An important paralog of this gene is TMTC4.

UniProtKB/Swiss-Prot for TMTC3 Gene

  • Involved in the positive regulation of proteasomal protein degradation in the endoplasmic reticulum (ER), and the control of ER stress response.

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TMTC3 Gene

Genomics for TMTC3 Gene

Regulatory Elements for TMTC3 Gene

Enhancers for TMTC3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH12G088297 1.7 FANTOM5 Ensembl ENCODE dbSUPER 9.3 +157.3 157344 3.8 PKNOX1 FOXA2 YY1 GATA2 CBX5 FOS JUNB TBX21 ZNF592 MAFF TMTC3 C12orf29 LOC101929554 GC12P088431
GH12G088241 1 Ensembl ENCODE 10.5 +100.3 100300 1.7 JUN BHLHE40 MAX USF2 CEBPB JUNB EP300 ZBTB40 FOSL1 JUND TMTC3 LOC101929554 GC12P088431
GH12G088144 1 Ensembl ENCODE 10.3 +3.2 3194 2.6 PKNOX1 FEZF1 CHD7 ZNF316 SCRT2 PRDM10 NFE2 ZBTB20 RFX1 HLF CEP290 TMTC3 C12orf29 PIR56802
GH12G088034 1.1 ENCODE 9.1 -106.3 -106280 2.4 HDGF PKNOX1 MLX CREB3L1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 CEP290 TMTC3 C12orf50 RNA5SP364
GH12G088181 0.8 ENCODE 11.4 +39.7 39706 1.0 PKNOX1 FEZF1 CEBPG ZNF2 ZNF316 GATA3 SCRT2 ZSCAN5C TRIM24 MAFK TMTC3 CEP290 PIR56802
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around TMTC3 on UCSC Golden Path with GeneCards custom track

Promoters for TMTC3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000054892 5 2200 HDGF PKNOX1 MLX CREB3L1 ARNT ZFP64 WRNIP1 ARID4B SIN3A DMAP1

Genomic Location for TMTC3 Gene

Chromosome:
12
Start:
88,142,296 bp from pter
End:
88,199,887 bp from pter
Size:
57,592 bases
Orientation:
Plus strand

Genomic View for TMTC3 Gene

Genes around TMTC3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TMTC3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TMTC3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TMTC3 Gene

Proteins for TMTC3 Gene

  • Protein details for TMTC3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6ZXV5-TMTC3_HUMAN
    Recommended name:
    Transmembrane and TPR repeat-containing protein 3
    Protein Accession:
    Q6ZXV5
    Secondary Accessions:
    • Q5CZ86
    • Q5H9T6
    • Q68DQ6
    • Q68DX0
    • Q7Z332
    • Q8NC50

    Protein attributes for TMTC3 Gene

    Size:
    915 amino acids
    Molecular mass:
    104009 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAC11325.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for TMTC3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TMTC3 Gene

Post-translational modifications for TMTC3 Gene

  • Ubiquitination at isoforms=2460 and posLast=738738
  • Glycosylation at Asn117, Asn494, isoforms=2541, and posLast=844844
  • Modification sites at PhosphoSitePlus

Other Protein References for TMTC3 Gene

Antibody Products

  • Abcam antibodies for TMTC3
  • Santa Cruz Biotechnology (SCBT) Antibodies for TMTC3

No data available for DME Specific Peptides for TMTC3 Gene

Domains & Families for TMTC3 Gene

Gene Families for TMTC3 Gene

Suggested Antigen Peptide Sequences for TMTC3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q6ZXV5

UniProtKB/Swiss-Prot:

TMTC3_HUMAN :
  • Belongs to the TMTC family.
Family:
  • Belongs to the TMTC family.
genes like me logo Genes that share domains with TMTC3: view

Function for TMTC3 Gene

Molecular function for TMTC3 Gene

UniProtKB/Swiss-Prot Function:
Involved in the positive regulation of proteasomal protein degradation in the endoplasmic reticulum (ER), and the control of ER stress response.

Gene Ontology (GO) - Molecular Function for TMTC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with TMTC3: view
genes like me logo Genes that share phenotypes with TMTC3: view

Animal Model Products

CRISPR Products

miRNA for TMTC3 Gene

miRTarBase miRNAs that target TMTC3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for TMTC3 Gene

Localization for TMTC3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TMTC3 Gene

Membrane; Multi-pass membrane protein. Endoplasmic reticulum. Note=In odontoblast cultures, it colocalizes with PDIA3 in the endoplasmic reticulum. {ECO:0000269 PubMed:21603654}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TMTC3 gene
Compartment Confidence
endoplasmic reticulum 5
cytoskeleton 2
plasma membrane 1

Gene Ontology (GO) - Cellular Components for TMTC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IDA 21603654
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with TMTC3: view

Pathways & Interactions for TMTC3 Gene

SuperPathways for TMTC3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for TMTC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0034976 response to endoplasmic reticulum stress IMP 21603654
GO:1901800 positive regulation of proteasomal protein catabolic process IMP 21603654
genes like me logo Genes that share ontologies with TMTC3: view

No data available for Pathways by source and SIGNOR curated interactions for TMTC3 Gene

Transcripts for TMTC3 Gene

Unigene Clusters for TMTC3 Gene

Transmembrane and tetratricopeptide repeat containing 3:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for TMTC3 Gene

No ASD Table

Relevant External Links for TMTC3 Gene

GeneLoc Exon Structure for
TMTC3
ECgene alternative splicing isoforms for
TMTC3

Expression for TMTC3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TMTC3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TMTC3 Gene

This gene is overexpressed in Nasal epithelium (26.5), Breast (17.2), and Cervix (8.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for TMTC3 Gene



NURSA nuclear receptor signaling pathways regulating expression of TMTC3 Gene:

TMTC3

SOURCE GeneReport for Unigene cluster for TMTC3 Gene:

Hs.331268

Evidence on tissue expression from TISSUES for TMTC3 Gene

  • Nervous system(4.3)
  • Intestine(4.2)
genes like me logo Genes that share expression patterns with TMTC3: view

Primer Products

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for TMTC3 Gene

Orthologs for TMTC3 Gene

This gene was present in the common ancestor of animals.

Orthologs for TMTC3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TMTC3 34 35
  • 99.78 (n)
dog
(Canis familiaris)
Mammalia TMTC3 34 35
  • 93.29 (n)
cow
(Bos Taurus)
Mammalia TMTC3 34 35
  • 92.38 (n)
rat
(Rattus norvegicus)
Mammalia Tmtc3 34
  • 86.67 (n)
oppossum
(Monodelphis domestica)
Mammalia TMTC3 35
  • 86 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Tmtc3 34 16 35
  • 85.54 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia TMTC3 35
  • 83 (a)
OneToOne
chicken
(Gallus gallus)
Aves TMTC3 34 35
  • 78.44 (n)
lizard
(Anolis carolinensis)
Reptilia TMTC3 35
  • 84 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.10499 34
zebrafish
(Danio rerio)
Actinopterygii tmtc3 34 35
  • 66.45 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010599 34
  • 56.36 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG4050 34 35
  • 53.84 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 42 (a)
OneToOne
Species where no ortholog for TMTC3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for TMTC3 Gene

ENSEMBL:
Gene Tree for TMTC3 (if available)
TreeFam:
Gene Tree for TMTC3 (if available)

Paralogs for TMTC3 Gene

Paralogs for TMTC3 Gene

(3) SIMAP similar genes for TMTC3 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with TMTC3: view

Variants for TMTC3 Gene

Sequence variations from dbSNP and Humsavar for TMTC3 Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type
VAR_077900 Lissencephaly 8 (LIS8) [MIM:617255]
VAR_077901 Lissencephaly 8 (LIS8) [MIM:617255]
rs1057517696 Pathogenic 88,188,872(+) TAGGA(-/A)GAACT reference, frameshift-variant
rs1057517697 Pathogenic 88,195,521(+) ACAAA(C/T)AATTA reference, stop-gained
rs1057517698 Pathogenic 88,148,318(+) AAGAT(A/G)GCTAA reference, missense

Structural Variations from Database of Genomic Variants (DGV) for TMTC3 Gene

Variant ID Type Subtype PubMed ID
nsv1132853 CNV insertion 24896259
nsv483111 CNV loss 15286789
nsv807 CNV deletion 18451855
nsv826471 CNV loss 20364138
nsv826472 CNV gain 20364138

Variation tolerance for TMTC3 Gene

Residual Variation Intolerance Score: 11.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.91; 74.35% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for TMTC3 Gene

Human Gene Mutation Database (HGMD)
TMTC3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TMTC3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TMTC3 Gene

Disorders for TMTC3 Gene

MalaCards: The human disease database

(5) MalaCards diseases for TMTC3 Gene - From: ClinVar, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
lissencephaly 8
  • lis8
lissencephaly
pachygyria
  • broad gyri of cerebrum
cobblestone lissencephaly
walker-warburg syndrome
  • cerebroocular dysplasia-muscular dystrophy syndrome
- elite association - COSMIC cancer census association via MalaCards
Search TMTC3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

TMTC3_HUMAN
  • Lissencephaly 8 (LIS8) [MIM:617255]: A form of lissencephaly, a disorder of cortical development characterized by agyria or pachygyria and disorganization of the clear neuronal lamination of normal six-layered cortex. LIS8 patients manifest delayed psychomotor development, intellectual disability with poor or absent speech, early-onset refractory seizures, hypotonia, cortical gyral abnormalities, and hypoplasia of the corpus callosum, brainstem and cerebellum. LIS8 inheritance is autosomal recessive. {ECO:0000269 PubMed:27773428}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for TMTC3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
TMTC3
genes like me logo Genes that share disorders with TMTC3: view

No data available for Genatlas for TMTC3 Gene

Publications for TMTC3 Gene

  1. The involvement of SMILE/TMTC3 in endoplasmic reticulum stress response. (PMID: 21603654) RacapAc M. … Brouard S. (PLoS ONE 2011) 3 4 64
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  4. Biallelic Mutations in TMTC3, Encoding a Transmembrane and TPR-Containing Protein, Lead to Cobblestone Lissencephaly. (PMID: 27773428) Jerber J. … Gleeson J.G. (Am. J. Hum. Genet. 2016) 4 64
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3 64

Products for TMTC3 Gene

Sources for TMTC3 Gene

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