Basic information ----------------------------------------------------------------------------------------------------------------- Date of creation: December 18, 2017 Version: BioMuta 3.0 Summary ------------------------------------------------------------------------------------------------------------------- These tables were generated as part of the supporting information to accompany submission of the manuscript titled "Loss and Gain of N-linked Glycosylation Sequons due to Single-nucleotide Variation in Cancer.The manuscript describes the subset of somatic-only LOG and GOG variants that appear across at least three cancer types in the below table. This table contains 41 somatic variants predicted to cause a gain of the consensus NXS/T motif at that position in at least three cancer types. These variants include ONLY those somatic variants WITHOUT germline variants occurring at the same positions occurring in three or more cancers. Column name Description ================ ================================================================================== UniProtKB_AC UniProtKB/Swiss-Prot Accession Gene_name Gene name Protein_name Protein name as reported by UniProt Sequence_Length Length of protein in amino acids Signal_Peptide_Existence Describes if a signal peptide is reported for that protein in UniProt Signal_Peptide_Position Reports the annotated signal peptide position if Signal_Peptide_Existence is "Y" Cellular_component Relevant cellular component keyword(s) associated with the protein in UniProt Motif_position Position of the "N" in the identified NXS/T sequon Subsequence Four-residue sequence about the NXS/T sequon beginning with the "N" Prediction Predicted effect of variant; all should be gain_of_glycosylation Domain Domain mapping to the position, if reported Secondary_Structure Secondary structure mapping to the position, if reported Mutation_Position Position of the altered residue Reference Reference amino acid Variation Altered amino acid resulting from nsSNV Genomic_Variation Position of nucleotide variation within the coding frame Minor_Allele_Frequency MAF retrieved through Annovar during annotation associated with that position in dbSNP Source_Freq Frequency of samples containing this variant call by source PolyPhen2_Prediction Functional prediction reported by PolyPhen2 software; can be possibly damaging, probably damaging, or benign Cancer_Type Disease ontology ID (DOID) and label of cancers associated with samples containing this variant Data_Source Primary source of data from which variant calls were obtained Patient_ID Patient ID from primary source, when available PMID PubMed article ID for associated literature, when available HGMD_Disease Diseases associated with this variant in HGMD, when available HGMD_PMID PubMed article ID corresponding to publication reporting disease association in HGMD, when available NetNGlycMotif Four-residue sequence including NXS/T motif reported by NetNGlyc NetNGlycPrediction Likelihood of actual glycosylation at the sequon, as reported by NetNGlyc