{
    "bcoid": "GLY_000618",
    "title": "Mouse Germline Mutation Glycoeffect",
    "description": "The Mouse Germline Mutation GlycoEffect Dataset was derived from the Germline Mutation Dataset provided ...",
    "filename_list": "mouse_protein_mutation_germline_glycoeffect.csv",
    "filename": "mouse_protein_mutation_germline_glycoeffect.csv",
    "filetype": "csv",
    "categories": {
        "species": [
            "Mus musculus"
        ],
        "molecule": [
            "Protein"
        ],
        "tag": [
            "Germline Mutation Glycoeffect"
        ],
        "file_type": [
            "csv"
        ],
        "status": [
            "Reviewed"
        ],
        "scope": [
            "internal"
        ],
        "file_category": [
            "mutation_"
        ]
    },
    "minitable": {
        "content": [
            [
                "Q9R0X5-1...",
                "394..."
            ],
            [
                "Q9R0X5-1...",
                "394..."
            ]
        ],
        "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": "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": "protein_class"
                },
                {
                    "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"
                }
            ],
            [
                "Q9R0X5-1",
                "394",
                "rs229541962",
                "",
                "",
                "Xq",
                "X",
                "10062273",
                "T",
                "null",
                "D",
                "N",
                "394",
                "394",
                "",
                "missense",
                "",
                "",
                "0.27",
                "tolerated",
                "0",
                "",
                "",
                "",
                "protein_xref_dbsnp",
                "rs229541962",
                "",
                "",
                "Germline mutation passed 1 filters: n-glyco-sequon-gain (DLS->NLS).",
                "none",
                "yes",
                "394",
                "DLS",
                "NLS",
                "n-glyco-sequon-gain"
            ],
            [
                "Q9R0X5-1",
                "394",
                "rs229541962",
                "",
                "",
                "Xq",
                "X",
                "10062273",
                "T",
                "null",
                "D",
                "N",
                "394",
                "394",
                "",
                "missense",
                "",
                "",
                "0.27",
                "tolerated",
                "0",
                "",
                "",
                "",
                "protein_xref_eva",
                "rs229541962",
                "",
                "",
                "Germline mutation passed 1 filters: n-glyco-sequon-gain (DLS->NLS).",
                "none",
                "yes",
                "394",
                "DLS",
                "NLS",
                "n-glyco-sequon-gain"
            ]
        ]
    },
    "readme": "Name\n   - Mouse Germline Mutation Glycoeffect\n\nVersion\n   - v-2.12.1\n\nCreated on\n  - 2021-10-15T15:38:41.625772\n\nModified on\n   - 2025-03-11T20:34:25.116Z\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 Mouse Germline Mutation GlycoEffect Dataset was derived from the Germline Mutation Dataset provided by the European Bioinformatics Institute (EBI) and dbSNP for Mus musculus [TaxID: 10090]. 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-2.12.1/reviewed/glycan_masterlist.csv\n      Name: aadict.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/misc/aadict.csv\n   Output Subdomain\n      Name: mouse_protein_mutation_germline_glycoeffect.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/mouse_protein_mutation_germline_glycoeffect.csv\n      Name: mouse_protein_mutation_germline_glycoeffect.stat.csv\n      URI: https:/data.glygen.org/ln2releases/data/v-2.12.1/reviewed/mouse_protein_mutation_germline_glycoeffect.stat.csv\n\nFields\n      Name: \"uniprotkb_canonical_ac\"\"\n     Description: \"\"\n      Unique Values: \"4522\"",
    "downloadurl": "/ln2data/releases/data/v-2.12.1/reviewed/mouse_protein_mutation_germline_glycoeffect.csv"
}