{ "bcoid": "GLY_000308", "title": "Genomics England- Congenital Disorders of Glycosylation", "description": "The dataset provides Genes involved in the Congenital disorders of glycosylation from Genomics England ...", "filename": "human_protein_genomics_england_disease.csv", "filetype": "csv", "categories": { "species": "Homo sapiens", "molecule": "Protein", "tags": "Disease", "status": "Reviewed", "file_type": "csv", "scope": "internal" }, "minitable": { "content": [ [ "Q6Y288-1...", "B3GLCT..." ], [ "Q6Y288-1...", "B3GLCT..." ] ], "headers": [ "uniprotkb_ca...", "gene_name..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "gene_name" }, { "type": "string", "label": "hgnc_id" }, { "type": "string", "label": "mode_of_inheritance" }, { "type": "string", "label": "disease_name" }, { "type": "string", "label": "pmid" }, { "type": "string", "label": "mim_id" }, { "type": "string", "label": "doid" } ], [ "Q6Y288-1", "B3GLCT", "20207", "BIALLELIC, autosomal or pseudoautosomal", "Peters-plus syndrome", "16909395", "261540", "0080201" ], [ "Q6Y288-1", "B3GLCT", "20207", "BIALLELIC, autosomal or pseudoautosomal", "Peters-plus syndrome", "23889335", "261540", "0080201" ], [ "P15291-1", "B4GALT1", "924", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IId", "21920538", "607091", "0070256" ], [ "P15291-1", "B4GALT1", "924", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IId", "11901181", "607091", "0070256" ], [ "Q96NT0-1", "CCDC115", "28178", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIo", "26833332", "616828", "0070267" ], [ "Q7LGC8-1", "CHST3", "1971", "BIALLELIC, autosomal or pseudoautosomal", "Spondyloepiphyseal dysplasia with congenital joint dislocations", "20830804", "143095", "0050813" ], [ "Q9GZX3-1", "CHST6", "6938", "BIALLELIC, autosomal or pseudoautosomal", "Macular corneal dystrophy", "16568029", "217800", "2565" ], [ "Q86X52-1", "CHSY1", "17198", "BIALLELIC, autosomal or pseudoautosomal", "Temtamy preaxial brachydactyly syndrome", "24269551", "605282", "0050814" ], [ "Q86X52-1", "CHSY1", "17198", "BIALLELIC, autosomal or pseudoautosomal", "Temtamy preaxial brachydactyly syndrome", "21129727", "605282", "0050814" ], [ "Q8WTW3-1", "COG1", "6545", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIg", "", "611209", "0070259" ], [ "Q9H9E3-1", "COG4", "18620", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIj", "11980916", "613489", "0070262" ], [ "Q9H9E3-1", "COG4", "18620", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIj", "19494034", "613489", "0070262" ], [ "Q9H9E3-1", "COG4", "18620", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIj", "19651599", "613489", "0070262" ], [ "Q9H9E3-1", "COG4", "18620", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIj", "21185756", "613489", "0070262" ], [ "Q9UP83-1", "COG5", "14857", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIi", "11980916", "613612", "0070261" ], [ "Q9UP83-1", "COG5", "14857", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIi", "19690088", "613612", "0070261" ], [ "Q9UP83-1", "COG5", "14857", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIi", "23228021", "613612", "0070261" ], [ "Q9UP83-1", "COG5", "14857", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIi", "23430875", "613612", "0070261" ], [ "Q9UP83-1", "COG5", "14857", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIi", "28960046", "613612", "0070261" ], [ "Q9Y2V7-1", "COG6", "18621", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIl", "11980916", "614576", "0070264" ], [ "Q9Y2V7-1", "COG6", "18621", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIl", "26260076", "614576", "0070264" ], [ "P83436-1", "COG7", "18622", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIe", "11980916", "608779", "0070257" ], [ "P83436-1", "COG7", "18622", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIe", "15107842", "608779", "0070257" ], [ "Q96MW5-1", "COG8", "18623", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIh", "11980916", "611182", "0070260" ], [ "Q96MW5-1", "COG8", "18623", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIh", "17331980", "611182", "0070260" ], [ "Q96MW5-1", "COG8", "18623", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIh", "17220172", "611182", "0070260" ], [ "Q9H3H5-1", "DPAGT1", "2995", "BIALLELIC, autosomal or pseudoautosomal", " Myasthenic syndrome, congenital, 13, with tubular aggregates", "12872255", "614750", "0110676" ], [ "Q9H3H5-1", "DPAGT1", "2995", "BIALLELIC, autosomal or pseudoautosomal", " Myasthenic syndrome, congenital, 13, with tubular aggregates", "22304930", "614750", "0110676" ], [ "Q16394-1", "EXT1", "3512", "BIALLELIC, autosomal or pseudoautosomal", "Exostoses, multiple, type 1", "12417417", "133700", "206" ], [ "Q93063-1", "EXT2", "3513", "BOTH monoallelic and biallelic, autosomal or pseudoautosomal", " Exostoses, multiple, type 2", "12417417", "133701", "206" ], [ "Q9H9S5-1", "FKRP", "17997", "BIALLELIC, autosomal or pseudoautosomal", "Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 5", "27421908", "613153", "0050588" ], [ "Q9H9S5-1", "FKRP", "17997", "BIALLELIC, autosomal or pseudoautosomal", "Muscular dystrophy-dystroglycanopathy (congenital with or without mental retardation), type B, 5", "27421908", "606612", "0110635" ], [ "Q9H9S5-1", "FKRP", "17997", "BIALLELIC, autosomal or pseudoautosomal", "Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 5", "27421908", "607155", "0110299" ], [ "O75072-1", "FKTN", "3622", "BIALLELIC, autosomal or pseudoautosomal", "Muscular dystrophy-dystroglycanopathy (congenital without mental retardation), type B, 4", "27421908", "613152", "0050588" ], [ "O75072-1", "FKTN", "3622", "BIALLELIC, autosomal or pseudoautosomal", "Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 4", "27421908", "611588", "0110296" ], [ "Q14435-1", "GALNT3", "4125", "BIALLELIC, autosomal or pseudoautosomal", "Tumoral calcinosis, hyperphosphatemic, familial", "15133511", "211900", "0111063" ], [ "Q06210-1", "GFPT1", "4241", "BIALLELIC, autosomal or pseudoautosomal", "Myasthenia, congenital, 12, with tubular aggregates(Disorders of protein N-glycosylation) ", "23569079", "610542", "0110660" ], [ "Q9Y223-1", "GNE", "23657", "BIALLELIC, autosomal or pseudoautosomal", "Nonaka myopathy", "26721333", "605820", "3429" ], [ "O95461-1", "LARGE1", "6511", "BIALLELIC, autosomal or pseudoautosomal", "Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 6", "27421908", "613154", "0050588" ], [ "O95461-1", "LARGE1", "6511", "BIALLELIC, autosomal or pseudoautosomal", " Muscular dystrophy-dystroglycanopathy (congenital with mental retardation), type B, 6", "27421908", "608840", "0110637" ], [ "Q10469-1", "MGAT2", "7045", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIa", "19419693", "212066", "0070253" ], [ "Q13724-1", "MOGS", "24862", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIb", "4716661", "606056", "0070254" ], [ "Q13724-1", "MOGS", "24862", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIb", "24716661", "606056", "0070254" ], [ "Q13724-1", "MOGS", "24862", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIb", "20301507", "606056", "0070254" ], [ "Q13724-1", "MOGS", "24862", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIb", "26805780", "606056", "0070254" ], [ "Q96IV0-1", "NGLY1", "17646", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of deglycosylation", "", "615273", "0060728" ], [ "P36871-1", "PGM1", "8905", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of deglycosylation", "27206562", "615273", "0060728" ], [ "P37287-1", "PIGA", "8957", "X-LINKED: hemizygous mutation in males, biallelic mutations in females", "Multiple congenital anomalies-hypotonia-seizures syndrome 2", "25885527", "300868", "0080139" ], [ "O15305-1", "PMM2", "9115", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type Ia", "11058895", "212065", "5212" ], [ "O15305-1", "PMM2", "9115", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type Ia", "11409861", "212065", "5212" ], [ "O15305-1", "PMM2", "9115", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type Ia", "11875054", "212065", "5212" ], [ "Q8WZA1-1", "POMGNT1", "19139", "BIALLELIC, autosomal or pseudoautosomal", "Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 3", "27421908", "253280", "0050560" ], [ "Q8WZA1-1", "POMGNT1", "19139", "BIALLELIC, autosomal or pseudoautosomal", " Muscular dystrophy-dystroglycanopathy (limb-girdle), type C 3", "27421908", "613157", "0110292" ], [ "Q9Y6A1-1", "POMT1", "9202", "BIALLELIC, autosomal or pseudoautosomal", "Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 1", "27421908", "236670", "0050560" ], [ "Q9Y6A1-1", "POMT1", "9202", "BIALLELIC, autosomal or pseudoautosomal", " Muscular dystrophy-dystroglycanopathy (congenital with mental retardation), type B, 1", "27421908", "613155", "0050588" ], [ "Q9Y6A1-1", "POMT1", "9202", "BIALLELIC, autosomal or pseudoautosomal", " Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 1", "27421908", "609308", "0110297" ], [ "Q9UKY4-1", "POMT2", "19743", "BIALLELIC, autosomal or pseudoautosomal", "Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 2", "27421908", "613150", "0050588" ], [ "Q9UKY4-1", "POMT2", "19743", "BIALLELIC, autosomal or pseudoautosomal", " Muscular dystrophy-dystroglycanopathy (congenital with mental retardation), type B, 2", "27421908", "613156", "0050588" ], [ "Q9UKY4-1", "POMT2", "19743", "BIALLELIC, autosomal or pseudoautosomal", " Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 2", "27421908", "613158", "0110298" ], [ "Q15437-1", "SEC23B", "10702", "BOTH monoallelic and biallelic, autosomal or pseudoautosomal", "Dyserythropoietic anemia, congenital, type II", "22208203", "224100", "1338" ], [ "P78382-1", "SLC35A1", "11021", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIf,", "15576474", "603585", "0070258" ], [ "P78382-1", "SLC35A1", "11021", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIf,", "23873973", "603585", "0070258" ], [ "P78382-1", "SLC35A1", "11021", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIf,", "28856833", "603585", "0070258" ], [ "P78382-1", "SLC35A1", "11021", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIf,", "30115659", "603585", "0070258" ], [ "Q96A29-1", "SLC35C1", "20197", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIc", "11326280", "266265", "0070255" ], [ "Q96A29-1", "SLC35C1", "20197", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIc", "12476046", "266265", "0070255" ], [ "Q9C0K1-1", "SLC39A8", "20862", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIn", "26637979", "616721", "0070266" ], [ "Q9C0K1-1", "SLC39A8", "20862", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIn", "26637978", "616721", "0070266" ], [ "Q9HC07-1", "TMEM165", "30760", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIk", "27401145", "614727", "0070263" ], [ "Q9HC07-1", "TMEM165", "30760", "BIALLELIC, autosomal or pseudoautosomal", "Congenital disorder of glycosylation, type IIk", "22683087", "614727", "0070263" ] ] }, "readme": "Name\n - Genomics England- Congenital Disorders of Glycosylation\n\nVersion\n - 1.5.12\n\nCreated on\n - 2019-11-14T12:15:32.954297\n\nModified on\n - 2019-12-02T16:44:17.799023\n\nCreated by\n - Rahi Navelkar [rsn13@gwu.edu], Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu]\n\nAuthors\n - \n\nChecksum\n - \n\nUsability Domain\n - The dataset provides Genes involved in the Congenital disorders of glycosylation from Genomics England PanelApp ( PanelApp crowdsources expert knowledge to establish consensus diagnostic gene panels. Antonio Rueda Martin and Eleanor Williams, Rebecca E. Foulger, Sarah Leigh, Louise C. Daugherty, Olivia Niblock, Ivone U. S. Leong, Katherine R. Smith, Oleg Gerasimenko, Eik Haraldsdottir, Ellen Thomas, Richard H. Scott, Emma Baple, Arianna Tucci, Helen Brittain, Anna de Burca, Kristina Iba\u00f1ez, Dalia Kasperaviciute, Damian Smedley, Mark Caulfield, Augusto Rendon & Ellen M. McDonagh. Nat Genet (2019) doi:10.1038/s41588-019-0528-2)\n\nDescription Domain\n Keywords\n - Protein\n - UniProtKB Accession\n - Genomics England\n - Panel App\n\n Pipeline Steps\n - Step-1: The input file was downloaded from the Genomics England (https://panelapp.genomicsengland.co.uk/panels/25/) from panel \"Congenital disorders of glycosylation\". A python script was used to process the data. 1. Map the HGNC/gene symbol to UniProtKB canonical accessions from the GlyGen protein masterlist. 2. Only those gene-disease associations are considered where one of the source is \"Expert Review Green\". 3. The MIM ID (Mendelian Inheritance ID) from column \"Phenotypes\" is mapped to DOID (Disease Ontology ID) using input file 2.\n\nExecution Domain\n Scripts - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/make-protein-dataset.py\n\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: congenital_disorders_of_glycosylation.tsv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.12/source/congenital_disorders_of_glycosylation.tsv\n Name: protein_domap.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.12/reviwed/protein_domap.csv\n Output Subdomain\n Name: human_protein_genomics_england_disease.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.5.12/reviewed/human_protein_genomics_england_disease.csv\n Name: human_protein_genomics_england_disease.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.5.12/reviewed/human_protein_genomics_england_disease.stat.csv\n\nFields\n Name: \"doid\"\n Description: \"Disease Ontology identifier\"\n Unique Values: \"36\"\n Name: \"uniprotkb_canonical_ac\"\n Description: \"Accession assigned to the protein isoform chosen to be the canonical sequence to which all positional annotation refers in UniProtKB database\"\n Unique Values: \"35\"\n Name: \"mim_id\"\n Description: \"\"\n Unique Values: \"43\"\n Name: \"mode_of_inheritance\"\n Description: \"\"\n Unique Values: \"3\"\n Name: \"hgnc_id\"\n Description: \"Identifier in the HUGO Gene Nomenclature Committee (HGNC) database\"\n Unique Values: \"35\"\n Name: \"disease_name\"\n Description: \"\"\n Unique Values: \"43\"\n Name: \"pmid\"\n Description: \"NCBI PubMed database Identifier\"\n Unique Values: \"50\"\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: \"35\"", "downloadurl": "/ln2data/releases/data/v-1.5.12/reviewed/human_protein_genomics_england_disease.csv" }