Gene Gene information from NCBI Gene database.
Entrez ID 160418
Gene name Transmembrane O-mannosyltransferase targeting cadherins 3
Gene symbol TMTC3
Synonyms (NCBI Gene)
LIS8SMILE
Chromosome 12
Chromosome location 12q21.32
Summary This gene encodes a protein that belongs to the transmembrane and tetratricopeptide repeat-containing protein family. [provided by RefSeq, May 2010]
SNPs SNP information provided by dbSNP.
6
SNP ID Visualize variation Clinical significance Consequence
rs754200057 C>G,T Pathogenic 5 prime UTR variant, missense variant, intron variant, non coding transcript variant, coding sequence variant
rs768546704 C>A,T Likely-pathogenic Coding sequence variant, stop gained, synonymous variant, non coding transcript variant
rs1057517696 A>- Pathogenic Frameshift variant, non coding transcript variant, coding sequence variant
rs1057517697 C>T Pathogenic Non coding transcript variant, stop gained, coding sequence variant
rs1057517698 G>A Pathogenic Intron variant, non coding transcript variant, missense variant, initiator codon variant
miRNA miRNA information provided by mirtarbase database.
1122
miRTarBase ID miRNA Experiments Reference
MIRT020400 hsa-miR-29c-3p Sequencing 20371350
MIRT020906 hsa-miR-155-5p Proteomics 18668040
MIRT022084 hsa-miR-128-3p Sequencing 20371350
MIRT024869 hsa-miR-215-5p Microarray 19074876
MIRT026736 hsa-miR-192-5p Microarray 19074876
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
15
GO ID Ontology Definition Evidence Reference
GO:0000030 Function Mannosyltransferase activity IBA
GO:0004169 Function Dolichyl-phosphate-mannose-protein mannosyltransferase activity IEA
GO:0004169 Function Dolichyl-phosphate-mannose-protein mannosyltransferase activity IMP 28973932
GO:0005515 Function Protein binding IPI 25416956
GO:0005783 Component Endoplasmic reticulum IBA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
617218 26899 ENSG00000139324
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q6ZXV5
Protein name Protein O-mannosyl-transferase TMTC3 (EC 2.4.1.109) (Protein SMILE) (Transmembrane O-mannosyltransferase targeting cadherins 3) (Transmembrane and tetratricopeptide repeat-containing 3)
Protein function Transfers mannosyl residues to the hydroxyl group of serine or threonine residues. The 4 members of the TMTC family are O-mannosyl-transferases dedicated primarily to the cadherin superfamily, each member seems to have a distinct role in decorat
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF08409 DUF1736 258 331 Domain of unknown function (DUF1736) Family
PF13432 TPR_16 450 508 Family
PF13181 TPR_8 528 562 Tetratricopeptide repeat Repeat
PF13431 TPR_17 585 618 Repeat
PF13181 TPR_8 669 702 Tetratricopeptide repeat Repeat
PF13174 TPR_6 704 736 Tetratricopeptide repeat Repeat
PF13181 TPR_8 737 771 Tetratricopeptide repeat Repeat
Sequence
MANINLKEITLIVGVVTACYWNSLFCGFVFDDVSAILDNKDLHPSTPLKTLFQNDFWGTP
MSEERSHKSYRPLTVLTFRLNYLLSELKPMSYHLLNMIFHAVVSVIFLKVCKLFLDNKSS
VIASLLFAVHPIHTEAVTGVVGRAELLSSIFFLAAFLSYTRSKGPDNSIIWTPIALTVFL
VAVATLCKEQGITVVGICCVYEVFIAQGYTLPLLCTTAGQFLRGKGSIPFSMLQTLVKLI
VLMFSTLLLVVIRVQVIQSQLPVFTRFDNPAAVSPTPTRQLTFNYLLPVNAWLLLNPSEL
CCDWTMGTIPLIESLLDIRNLATFTFFCFLG
MLGVFSIRYSGDSSKTVLMALCLMALPFI
PASNLFFPVGFVVAERVLYVPSMGFCILVAHGWQKISTKSVFKKLSWICLSMVILTHSLK
TFHRNWDWESEYTLFMSALKVNKNNAKLWNNVGHALENEKNFERALKYFLQATHVQPDDI
GAHMNVGRTYKNLNRTKEAEESYMMAKS
LMPQIIPGKKYAARIAPNHLNVYINLANLIRA
NESRLEEADQLYRQAISMRPDF
KQAYISRGELLLKMNKPLKAKEAYLKALELDRNNADLW
YNLAIVHIELKEPNEALK
KNFNRALELNPKHKLALFNSAIVMQESGEVKLRPEARKRLLS
YINEEPLDANGYFNLGMLAMDDKKDNEAEIWMKKAIKLQADFRSALFNLALLYSQTAKEL
KALPILEELLRYYPDH
IKGLILKGDILMNQKKDILGAKKCFERILEMDPSNVQGKHNLCV
VYFEEKDLLKAERCLLETLALAPHEEYIQRHLNIVRDKISSSSFIEPIFPTSKISSVEGK
KIPTESVKEIRGESRQTQIVKTSDNKSQSKSNKQLGKNGDEETPHKTTKDIKEIEKKRVA
ALKRLEEIERILNGE
Sequence length 915
Interactions View interactions
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
11
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Lissencephaly 8 Likely pathogenic; Pathogenic rs746894544, rs2041490074, rs2501965282, rs2501978087, rs1057517696, rs1057517697, rs1057519417, rs754200057, rs1057517698, rs768546704 RCV001824204
RCV004784021
RCV003493246
RCV003989233
RCV000412494
View all (5 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
COBBLESTONE LISSENCEPHALY WITHOUT MUSCULAR OR OCULAR INVOLVEMENT Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
GLIOMA GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
LISSENCEPHALY CTD, Disgenet
CTD, Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
MACROGYRIA Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Agyria Agyria CTD_human_DG
★☆☆☆☆
Found in Text Mining only
Aortic Aneurysm Aortic Aneurysm HPO_DG
★☆☆☆☆
Found in Text Mining only
Aortic Valve Insufficiency Aortic Valve Insufficiency HPO_DG
★☆☆☆☆
Found in Text Mining only
Astigmatism Astigmatism BEFREE 31710370
★☆☆☆☆
Found in Text Mining only
Breast Carcinoma Breast Carcinoma BEFREE 30413519
★☆☆☆☆
Found in Text Mining only
Breast Neoplasms Breast neoplasm Pubtator 33503040 Associate
★☆☆☆☆
Found in Text Mining only
Carcinoma Squamous Cell Squamous cell carcinoma Pubtator 35982901 Associate
★☆☆☆☆
Found in Text Mining only
Cerebellar Diseases Cerebellar diseases Pubtator 27773428 Associate
★☆☆☆☆
Found in Text Mining only
Cobblestone Lissencephaly Cobblestone Lissencephaly BEFREE 27773428, 28973161, 31851597
★☆☆☆☆
Found in Text Mining only
Cobblestone Lissencephaly Cobblestone Lissencephaly GENOMICS_ENGLAND_DG 27773428
★☆☆☆☆
Found in Text Mining only