{ "bcoid": "GLY_000619", "title": "Rat Germline Mutation Glycoeffect", "description": "The Rat Germline Mutation GlycoEffect Dataset was derived from the Germline Mutation Dataset provided ...", "filename_list": "rat_protein_mutation_germline_glycoeffect.csv", "filename": "rat_protein_mutation_germline_glycoeffect.csv", "filetype": "csv", "categories": { "species": [ "Rattus norvegicus" ], "molecule": [ "Protein" ], "tag": [ "Germline Mutation Glycoeffect" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "A0A096MJ28-1...", "1166..." ], [ "A0A096MJ28-1...", "1166..." ] ], "headers": [ "uniprotkb_ca...", "aa_pos..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "aa_pos" }, { "type": "string", "label": "gene_name" }, { "type": "string", "label": "protein_name" }, { "type": "string", "label": "dbsnp_id" }, { "type": "string", "label": "cosmic_id" }, { "type": "string", "label": "description" }, { "type": "string", "label": "cytogenic_band" }, { "type": "string", "label": "chr_id" }, { "type": "string", "label": "chr_pos" }, { "type": "string", "label": "ref_nt" }, { "type": "string", "label": "alt_nt" }, { "type": "string", "label": "ref_aa" }, { "type": "string", "label": "alt_aa" }, { "type": "string", "label": "begin_aa_pos" }, { "type": "string", "label": "end_aa_pos" }, { "type": "string", "label": "minor_allelic_frequency" }, { "type": "string", "label": "mutation_type" }, { "type": "string", "label": "polyphen_score" }, { "type": "string", "label": "polyphen_prediction" }, { "type": "string", "label": "sift_score" }, { "type": "string", "label": "sift_prediction" }, { "type": "string", "label": "somatic_status" }, { "type": "string", "label": "disease" }, { "type": "string", "label": "disease_description" }, { "type": "string", "label": "disease_xrefs" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "mim_id" }, { "type": "string", "label": "do_id" }, { "type": "string", "label": "filter_flags" }, { "type": "string", "label": "is_known_glycoprotein" }, { "type": "string", "label": "motif_start" }, { "type": "string", "label": "ref_motif" }, { "type": "string", "label": "alt_motif" }, { "type": "string", "label": "effect" } ], [ "A0A096MJ28-1", "1166", "Ints2", "Integrator complex subunit 2", "rs3321790180", "", "", "", "", "10chr", "10", "71033722", "T", "null", "H", "N", "1166", "1166", "", "missense", "", "", "0.43", "tolerated", "0", "", "", "", "", "", "protein_xref_dbsnp", "yes", "1166", "T", "null", "o-glyco-site-loss" ], [ "A0A096MJ28-1", "1166", "Ints2", "Integrator complex subunit 2", "rs3321790180", "", "", "", "", "10chr", "10", "71033722", "T", "null", "H", "N", "1166", "1166", "", "missense", "", "", "0.43", "tolerated", "0", "", "", "", "", "", "protein_xref_eva", "yes", "1166", "T", "null", "o-glyco-site-loss" ] ] }, "readme": "Name\n - Rat Germline Mutation Glycoeffect\n\nVersion\n - v-2.9.1\n\nCreated on\n - 2021-10-15T15:41:22.561828\n\nModified on\n - 2025-03-11T20:36:07.761Z\n\nCreated by\n - [jeetvora@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Luke Johnson [luke.johnson@email.gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Cyrus Au-Yeung [cyruschauyeung@gwu.edu], Kate Warner [k.warner1@gwu.edu]\n\nAuthors\n - \n\nChecksum\n - \n\nUsability Domain\n - The Rat Germline Mutation GlycoEffect Dataset was derived from the Germline Mutation Dataset provided by the European Bioinformatics Institute (EBI) and dbSNP for Rattus norvegicus [TaxID: 10116]. This dataset is processed from the Germline Mutation Dataset and is useful in context of glycosylation. The dataset, for a given germline mutation site, indicates whether the protein with the germline SNV is a known glycoprotein. Additionally, it provides reference and altered motifs for the mutated glycosylated site and assesses the impact of the SNV on glycosylation. The observed effects include the loss of known O- and N-glycosites and the gain of an N-sequon, which may introduce a new N-glycosylation site. The following headers have been added as part of this analysis: is_known_glycoprotein, motif_start, ref_motif, alt_motif, and effect.\n\nExecution Domain\n\n Software Prerequisites\n Name: Python\n Version: 2.7.5\n URI: https://www.python.org/download/releases/2.7.5/\n\nI/O Domain\n Input Subdomain\n Name: glycan_masterlist.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/glycan_masterlist.csv\n Name: rat_protein_mutation_germline.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/rat_protein_mutation_germline.csv\n Name: aadict.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/misc/aadict.csv\n Output Subdomain\n Name: rat_protein_mutation_germline_glycoeffect.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/rat_protein_mutation_germline_glycoeffect.csv\n Name: rat_protein_mutation_germline_glycoeffect.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.9.1/reviewed/rat_protein_mutation_germline_glycoeffect.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"63\"\n Name: \"aa_pos\"\n Description: \"Position of the amino acid in canonical sequence of protein in the UniProtKB database\"\n Unique Values: \"68\"\n Name: \"gene_name\"\n Description: \"\"Official gene name/symbol assigned to the gene. Human gene name/symbol are approved by the HUGO Gene Nomenclature Committee (HGNC) and mouse gene name are approved by the Mouse Genome Informatics (MGI)\"\n Unique Values: \"63\"\n Name: \"protein_name\"\n Description: \"Protein name in the UniProtKB\"\n Unique Values: \"66\"\n Name: \"dbsnp_id\"\n Description: \"\"A reference SNP ID number\"\n Unique Values: \"69\"\n Name: \"cosmic_id\"\n Description: \"Legacy mutation identifier (COSM) in Catalogue of Somatic Mutations in Cancer (COSMIC) represents existing COSM mutation identifiers. This identifier remains the same between different assemblies (GRCh37 and GRCh38). All the COSM ids at the same genomic location have been collapsed into one representative COSM id. These ids are maintained to help track existing mutations\"\n Unique Values: \"1\"\n Name: \"description\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"cytogenic_band\"\n Description: \"One of the subregions of a chromosome visible microscopically after special staining\"\n Unique Values: \"1\"\n Name: \"chr_id\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"chr_pos\"\n Description: \"Chromosome Position of a gene\"\n Unique Values: \"19\"\n Name: \"ref_nt\"\n Description: \"Reference nucleotide\"\n Unique Values: \"19\"\n Name: \"alt_nt\"\n Description: \"Alternative nucleotide\"\n Unique Values: \"69\"\n Name: \"ref_aa\"\n Description: \"Reference amino acid residue\"\n Unique Values: \"4\"\n Name: \"alt_aa\"\n Description: \"Altered amino acid residue\"\n Unique Values: \"1\"\n Name: \"begin_aa_pos\"\n Description: \"Start position of the amino acid in the sequence of a protein in UniProtKB\"\n Unique Values: \"11\"\n Name: \"end_aa_pos\"\n Description: \"End position of the amino acid in the sequence of a protein in UniProtKB\"\n Unique Values: \"13\"\n Name: \"minor_allelic_frequency\"\n Description: \"\"\n Unique Values: \"68\"\n Name: \"mutation_type\"\n Description: \"Denotes whether mutation was reported with reference to amino acid or nucleotide\"\n Unique Values: \"68\"\n Name: \"polyphen_score\"\n Description: \"The score assigned to a amino acid substitution by a tool called as PolyPhen (=Polymorphism Phenotyping) which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations. The PolyPhen score ranges from 0.0 (tolerated) to 1.0 (deleterious). Variants with scores of 0.0 are predicted to be benign. Values closer to 1.0 are more confidently predicted to be deleterious\"\n Unique Values: \"1\"\n Name: \"polyphen_prediction\"\n Description: \"\"The PolyPhen prediction values are - greater than 0.908 - \"\"Probably Damaging\"\"; greater than 0.446 and less than or equal to 0.908 - \"\"Possibly Damaging\"\"; less than or equal to 0.446 - \"\"Benign\"\"\"\n Unique Values: \"1\"\n Name: \"sift_score\"\n Description: \"SIFT predicts whether an amino acid substitution is likely to affect protein function based on sequence homology and the physico-chemical similarity between the alternate amino acids. The data we provide for each amino acid substitution is a score and a qualitative prediction (either 'tolerated' or 'deleterious'). The score is the normalized probability that the amino acid change is tolerated so scores nearer zero are more likely to be deleterious. The qualitative prediction is derived from this score such that substitutions with a score < 0.05 are called 'deleterious' and all others are called 'tolerated\"\n Unique Values: \"1\"\n Name: \"sift_prediction\"\n Description: \"The SIFT qualitative prediction is derived from this score such that substitutions with a score < 0.05 are called 'deleterious' and all others are called 'tolerated\"\n Unique Values: \"1\"\n Name: \"somatic_status\"\n Description: \"The status of the variant whether it is germline (somatic status =0) or somatic (somatic status =1) variant\"\n Unique Values: \"31\"\n Name: \"disease\"\n Description: \"The disease name for the cell line\"\n Unique Values: \"5\"\n Name: \"disease_description\"\n Description: \"The disease description and/or definition \"\n Unique Values: \"1\"\n Name: \"disease_xrefs\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"1\"\n Name: \"mim_id\"\n Description: \"Disease ID from the OMIM database\"\n Unique Values: \"1\"\n Name: \"do_id\"\n Description: \"Disease Ontology identifier\"\n Unique Values: \"1\"\n Name: \"filter_flags\"\n Description: \"Filter tags/flags assigned to the mutation entries that have passed the mutation filter criteria\"\n Unique Values: \"2\"\n Name: \"is_known_glycoprotein\"\n Description: \"Yes or no flag to denote if a protein is experimentally proven glycoprotein\"\n Unique Values: \"1\"\n Name: \"motif_start\"\n Description: \"\"\n Unique Values: \"71\"\n Name: \"ref_motif\"\n Description: \"Reference motif\"\n Unique Values: \"11\"\n Name: \"alt_motif\"\n Description: \"Altered motif\"\n Unique Values: \"14\"\n Name: \"effect\"\n Description: \"The effect on glycosylation or N-sequon due to variation at site of glycosylated amino acid.\"\n Unique Values: \"2\"", "downloadurl": "/ln2data/releases/data/v-2.9.1/reviewed/rat_protein_mutation_germline_glycoeffect.csv" }