{ "bcoid": "GLY_000225", "title": "Human Protein Glycosylation Diseases", "description": "The Human Diseases dataset contains list of human [taxid:9606] diseases as described by OMIM and Monarch ...", "filename": "human_protein_disease_glyco.csv", "filetype": "csv", "categories": { "species": "Homo sapiens", "molecule": "Protein", "tags": "Diseases_Glyco", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P20933-1...", "protein_xref..." ], [ "Q9BT22-1...", "protein_xref..." ] ], "headers": [ "uniprotkb_ca...", "xref_key..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "gene_symbol" }, { "type": "string", "label": "disease_aliases" }, { "type": "string", "label": "mondo_disease_name" }, { "type": "string", "label": "mondo_label" }, { "type": "string", "label": "mondo_id" }, { "type": "string", "label": "pmid" } ], [ "P20933-1", "protein_xref_mondo", "8830", "AGA", "aspartylglucosaminuria, aspartylglucosaminidase deficiency, glycosylasparaginase deficiency, aspartylglycosaminuria", "Aspartylglucosaminuria", "Aspartylglucosaminuria", "MONDO:0008830", "" ], [ "Q9BT22-1", "protein_xref_mondo", "12052", "ALG1", "CDG1K, congenital disorder of glycosylation type Ik, mannosyltransferase 1 deficiency, CDG syndrome type Ik, congenital disorder of glycosylation type 1k, CDG-Ik, carbohydrate deficient glycoprotein syndrome type Ik", "ALG1-CDG", "ALG1-CDG", "MONDO:0012052", "26430078" ], [ "Q2TAA5-1", "protein_xref_mondo", "13349", "ALG11", "CDG-Ip, Congenital Disorder of Glycosylation, Type Ip", "ALG11-CDG", "ALG11-CDG", "MONDO:0013349", "" ], [ "Q9BV10-1", "protein_xref_mondo", "11783", "ALG12", "Congenital disorder of glycosylation, type Ig, CDG-Ig", "ALG12-CDG", "ALG12-CDG", "MONDO:0011783", "" ], [ "Q9NP73-1", "protein_xref_mondo", "10472", "ALG13", "CDG-Is, Congenital Disorder of Glycosylation, Type Is", "ALG13-CDG", "ALG13-CDG", "MONDO:0010472", "" ], [ "Q96F25-1", "protein_xref_mondo", "14542", "ALG14", "ALG14 congenital myasthenic syndrome, congenital myasthenic syndrome type 15, myasthenic syndrome, congenital, type 15, congenital myasthenic syndrome caused by mutation in ALG14, CMS15, congenital myasthenic syndrome 15 without tubular aggregates", "ALG14-CMS", "congenital myasthenic syndrome 15", "MONDO:0014542", "" ], [ "Q9H553-1", "protein_xref_mondo", "11933", "ALG2", "CDG-Ii, Congenital disorder of glycosylation, type Ii", "ALG2-CDG", "ALG2-CDG", "MONDO:0011933", "" ], [ "Q92685-1", "protein_xref_mondo", "10998", "ALG3", "CDG-Id, Congenital disorder of glycosylation, type Id", "ALG3-CDG", "ALG3-CDG", "MONDO:0010998", "" ], [ "Q9Y672-1", "protein_xref_mondo", "11291", "ALG6", "CDG-Ic, Congenital disorder of glycosylation, type Ic", "ALG6-CDG", "congenital disorder of glycosylation type 1C", "MONDO:0011291", "" ], [ "Q9BVK2-1", "protein_xref_mondo", "11969", "ALG8", "Congenital disorder of glycosylation, type Ih, CDG-Ih", "ALG8-CDG", "ALG8-CDG", "MONDO:0011969", "" ], [ "Q9H6U8-1", "protein_xref_mondo", "12117", "ALG9", "CDG-IL, Congenital disorder of glycosylation, type IL", "ALG9-CDG", "ALG9-CDG", "MONDO:0012117", "" ], [ "P15289-1", "protein_xref_mondo", "18868", "ARSA", "MLD, arylsulfatase A deficiency, sulfatide lipoidosis, Scholz cerebral sclerosis, deficiency of cerebroside-sulfatase", "Metachromatic leukodystrophy", "metachromatic leukodystrophy", "MONDO:0018868", "" ], [ "P15848-1", "protein_xref_mondo", "9661", "ARSB", "MPS VI, Maroteaux-Lamy syndrome", "Mucopolysaccharidosis VI", "mucopolysaccharidosis type 6", "MONDO:0009661", "" ], [ "Q13510-1", "protein_xref_mondo", "9218", "ASAH1", "Acid Ceramidase Deficiency", "Farber Lipogranulomatosis", "Farber lipogranulomatosis", "MONDO:0009218", "" ], [ "Q15904-1", "protein_xref_mondo", "10504", "ATP6AP1", "immunodeficiency 47, IMD47immunodeficiency type 47, primary immunodeficiency disease caused by mutation in ATP6AP1, immunodeficiency 47, IMD47, ATP6AP1 primary immunodeficiency disease", "ATP6AP1-CDG", "immunodeficiency 47", "MONDO:0010504", "" ], [ "O75787-1", "protein_xref_mondo", "10319", "ATP6AP2", "mental retardation, X-linked, syndromic, Hedera type, MRXE, MRXSH, X-linked mental retardation with epilepsy", "ATP6AP2-CDG", "syndromic X-linked intellectual disability Hedera type", "MONDO:0010319", "" ], [ "P38606-1", "protein_xref_mondo", "27451", "ATP6V1A", "cutis laxa, autosomal recessive, type IID, ARCL2D, autosomal recessive cutis laxa type IID, cutis laxa, autosomal recessive, type 2D", "ATP6V1A-CDG", "autosomal recessive cutis laxa type 2d", "MONDO:0027451", "" ], [ "P36543-1", "protein_xref_mondo", "27462", "ATP6V1E1", "autosomal recessive cutis laxa type IIC, ARCL2C, cutis laxa, autosomal recessive, type 2C, cutis laxa, autosomal recessive, type IIC, ARCL2C", "ATP6V1E1-CDG", "autosomal recessive cutis laxa type 2c", "MONDO:0027462", "" ], [ "Q9Y487-1", "protein_xref_mondo", "18163", "ATP6V0A2", "V-ATPase a2 subunit defect, Debre-Type cutis laxa, Cutis laxa, autosomal recessive, type IIA (ARCL2A), ATP6VOA2 defect (cutis laxa type II)", "ATP6VOA2-CDG", "Autosomal recessive cutis laxa type 2A", "MONDO:0018163", "" ], [ "Q8NCR0-1", "protein_xref_mondo", "14071", "B3GALNT2", "Congenital muscular dystrophy (MDDGA11)muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11, B3GALNT2 muscular dystrophy-dystroglycanopathy, type A, muscular dystrophy-dystroglycanopathy, type A caused by mutation in B3GALNT2", "B3GALNT2-CDG", "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11", "MONDO:0014071", "" ], [ "Q96L58-1", "protein_xref_mondo", "13019", "B3GALT6", "Brachyolmia 4 with mild epiphyseal and metaphyseal changes, SEMD, pakistani type", "Spondyloepimetaphyseal dysplasia, pakistani type", "spondyloepimetaphyseal dysplasia, Pakistani type", "MONDO:0013019", "" ], [ "Q6Y288-1", "protein_xref_mondo", "9856", "B3GLCT", "Peters-plus syndrome, Krause-Kivlin syndrome, Peters anomaly with short limb dwarfism", "B3GALTL-CDG", "ALG13-CDG", "MONDO:0009856", "" ], [ "O94766-1", "protein_xref_mondo", "9511", "B3GAT3", "multiple joint dislocations-short stature-craniofacial dysmorphism-congenital heart defects syndrome", "B3GAT3-CDG", "Larsen-like syndrome, B3GAT3 type", "MONDO:0009511", "" ], [ "Q6Y288-1", "protein_xref_mondo", "9856", "B3GLCT", "Peters anomaly-short limb dwarfism syndrome, Krause-van Schooneveld-Kivlin syndrome, Peters-plus syndrome, Krause-Kivlin syndrome, Peters anomaly with short limb dwarfism", "B3GLCT-CDG", "Peters plus syndrome", "MONDO:0009856", "" ], [ "Q00973-1", "protein_xref_mondo", "12213", "B4GALNT1", "autosomal recessive spastic paraplegia type 26, hereditary spastic paraplegia type 26, GM2 synthase deficiency, SPG26, autosomal recessive spastic paraplegia 26", "B4GALNT1-CDG", "hereditary spastic paraplegia 26", "MONDO:0012213", "" ], [ "P15291-1", "protein_xref_mondo", "11772", "B4GALT1", "CDG-IId, Congenital disorder of glycosylation, type IId", "B4GALT1-CDG", "B4GALT1-CDG", "MONDO:0011772", "" ], [ "Q9UBV7-1", "protein_xref_mondo", "7526", "B4GALT7", "Ehlers-Danlos syndrome, progeroid form, Ehlers-Danlos syndrome, progeroid type, 1, Galactosyltransferase 1 deficiency", "B4GALT7-CDG", "Ehlers-Danlos syndrome progeroid type", "MONDO:0007526", "" ], [ "O43505-1", "protein_xref_mondo", "14120", "B4GAT1", "MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH BRAIN AND EYE ANOMALIES), TYPE A, 13, MDDGA13", "B4GAT1-CDG", "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13", "MONDO:0014120", "" ], [ "Q96EU7-1", "protein_xref_mondo", "10381", "C1GALT1C1", "Tn syndrome (SOMATIC MUTATION), Galactosyltransferase Deficiency", "Tn polyagglutination syndrome, somatic (SOMATIC MUTATION)", "Tn Polyagglutination syndrome", "MONDO:0010381", "" ], [ "P27708-1", "protein_xref_mondo", "14647", "CAD", "epileptic encephalopathy, early infantile, 50, congenital disorder of glycosylation, type Iz, formerly, epileptic encephalopathy, early infantile, 50, EIEE50, congenital disorder of glycosylation, type Iz, EIEE50, congenital disorder of glycosylation, type Iz, CDG1Z", "CAD-CDG", "CAD-CDG", "MONDO:0014647", "" ], [ "Q96NT0-1", "protein_xref_mondo", "14789", "CCDC115", "carbohydrate deficient glycoprotein syndrome type IIo, CDG-IIo, CDG syndrome type IIo, CDG2O, congenital disorder of glycosylation type IIo, congenital disorder of glycosylation, type IIo, congenital disorder of glycosylation type 2o", "CCDC115-CDG", "CCDC115-CDG", "MONDO:0014789", "" ], [ "Q8NCH0-1", "protein_xref_mondo", "11142", "CHST14", "Adducted thumb and clubfoot syndrome", "Ehlers-Danlos syndrome, musculocontractural type", "Ehlers-Danlos syndrome, musculocontractural type", "MONDO:0011142", "" ], [ "Q7LGC8-1", "protein_xref_mondo", "7738", "CHST3", "chondrodysplasia with multiple dislocations, Kozlowski Celermajer tink syndrome, SDCD, CHST3 type, CHST3-Related skeletal dysplasia, chondrodysplasia with congenital joint dislocations, CHST3 type, spondyloepiphyseal dysplasia with congenital joint dyslocations, CHST3 type, spondyloepiphyseal dysplasia with congenital joint dislocations, Humerospinal dysostosis, Omani type, humero-spinal dysostosis with congenital heart disease, spondyloepiphyseal dysplasia", "CHST3-CDG", "spondyloepiphyseal dysplasia with congenital joint dislocations", "MONDO:0007738", "" ], [ "Q9GZX3-1", "protein_xref_mondo", "9020", "CHST6", "Macular corneal dystrophy Type II, Macular corneal dystrophy Type I", "Macular corneal dystrophy", "macular corneal dystrophy", "MONDO:0009020", "" ], [ "Q86X52-1", "protein_xref_mondo", "11533", "CHSY1", "TPBS", "Temtamy preaxial brachydactyly syndrome", "temtamy preaxial brachydactyly syndrome", "MONDO:0011533", "" ], [ "Q8WTW3-1", "protein_xref_mondo", "12637", "COG1", "Congenital disorder of glycosylation, type IIg, CDGII/COG1 Cerebrocostomandibular-like syndrome, CDG-IIg, COG1 deficiency", "COG1-CDG", "COG1-CDG", "MONDO:0012637", "" ], [ "Q14746-1", "protein_xref_mondo", "54559", "COG2", "CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIq, CDG2Q", "COG2-CDG", "congenital disorder of glycosylation, type IIq", "MONDO:0054559", "" ], [ "Q9H9E3-1", "protein_xref_mondo", "13281", "COG4", "Congenital disorder of glycosylation, type IIj, CDG-IIj", "COG4-CDG", "COG4-CDG", "MONDO:0013281", "" ], [ "Q9UP83-1", "protein_xref_mondo", "13325", "COG5", "Congenital disorder of glycosylation, type IIi, CDG-IIi", "COG5-CDG", "COG5-CDG", "MONDO:0013325", "" ], [ "Q9Y2V7-1", "protein_xref_mondo", "13810", "COG6", "CDG-IIL, Congenital Disorder of Glycosylation, Type IIL", "COG6-CDG", "COG6-CGD", "MONDO:0013810", "" ], [ "P83436-1", "protein_xref_mondo", "12118", "COG7", "Congenital disorder of glycosylation, type IIe, CDG-IIe", "COG7-CDG", "COG7-CDG", "MONDO:0012118", "" ], [ "Q96MW5-1", "protein_xref_mondo", "12635", "COG8", "CDG-IIh, COG8 deficiency, Congenital disorder of glycosylation, type IIh", "COG8-CDG", "COG8-CDG", "MONDO:0012635", "" ], [ "P10619-1", "protein_xref_mondo", "9737", "CTSA", "Combined deficiency of sialidase AND beta galactosidase", "Galactosialidosis", "galactosialidosis", "MONDO:0009737", "" ], [ "P39656-1", "protein_xref_mondo", "13789", "DDOST", "Congenital Disorder of Glycosylation, Type Ir, CDG-Ir", "DDOST-CDG", "DDOST-CDG", "MONDO:0013789", "" ], [ "Q86SQ9-1", "protein_xref_mondo", "13468", "DHDDS", "retinitis pigmentosa caused by mutation in DHDDS, RP59, DHDDS retinitis pigmentosa, retinitis pigmentosa type 59, retinitis pigmentosa 59", "DHDDS retinitis pigmentosa", "retinitis pigmentosa 59", "MONDO:0013468", "" ], [ "P11532-1", "protein_xref_mondo", "10679", "DMD", "Muscular dystrophy, pseudohypertrophic progressive, Duchenne type, DMD", "Duchenne muscular dystrophy", "Duchenne muscular dystrophy", "MONDO:0010679", "" ], [ "Q9UPQ8-1", "protein_xref_mondo", "12556", "DOLK", "CDG-Im, DK1-CDG, Dolichol kinase deficiency, Congenital disorder of glycosylation, type Im, DK1 deficiency", "DOLK-CDG", "congenital disorder of glycosylation type I", "MONDO:0012556", "" ], [ "Q9H3H5-1", "protein_xref_mondo", "11964", "DPAGT1", "CDG-Ij, Congenital disorder of glycosylation, type Ij", "DPAGT1-CDG", "DPAGT1-CDG", "MONDO:0011964", "" ], [ "O60762-1", "protein_xref_mondo", "12123", "DPM1", "CDG-Ie, Congenital disorder of glycosylation, type Ie", "DPM1-CDG", "congenital disorder of glycosylation type 1E", "MONDO:0012123", "" ], [ "O94777-1", "protein_xref_mondo", "14023", "DPM2", "CDG-Iu, CDG syndrome type Iu, carbohydrate deficient glycoprotein syndrome type Iu,congenital disorder of glycosylation type 1u, DPM2-CDG, CDG1U, CMD with intellectual disability and severe epilepsy, congenital disorder of glycosylation type Iu", "DMP2-CDG", "congenital muscular dystrophy with intellectual disability and severe epilepsy", "MONDO:0014023", "" ], [ "Q9P2X0-1", "protein_xref_mondo", "13049", "DPM3", "CDG-Io, Congenital Disorder of Glycosylation, Type Io", "DPM3-CDG", "DPM3-CDG", "MONDO:0013049", "" ], [ "Q9UL01-1", "protein_xref_mondo", "14236", "DSE", "Ehlers-Danlos syndrome, musculocontractural type 2, Ehlers-Danlos syndrome, musculocontractural type caused by mutation in DSE, DSE Ehlers-Danlos syndrome, musculocontractural type", "DSE Ehlers-Danlos syndrome", "Ehlers-Danlos syndrome, musculocontractural type 2", "MONDO:0014236", "" ], [ "Q5NDL2-1", "protein_xref_mondo", "14124", "EOGT", "Adams-Oliver syndrome type 4, EOGT Adams-Oliver syndrome, Adams-Oliver syndrome 4, Adams-Oliver syndrome caused by mutation in EOGT", "EOGT Adams-Oliver syndrome", "Adams-Oliver syndrome 4", "MONDO:0014124", "" ], [ "Q16394-1", "protein_xref_mondo", "5508", "EXT1", "Hereditary multiple osteochondromas (HMO), Hereditary multiple exostoses (HME), Multiple cartilaginous exostoses, Exostoses, multiple, type 2, Exostoses, multiple, type 1", "EXT1/EXT2-CDG", "Hereditary multiple osteochondromas", "MONDO:0005508", "" ], [ "Q93063-1", "protein_xref_mondo", "5508", "EXT2", "Hereditary multiple osteochondromas (HMO), Hereditary multiple exostoses (HME), Multiple cartilaginous exostoses, Exostoses, multiple, type 2, Exostoses, multiple, type 1", "EXT1/EXT2-CDG", "Hereditary multiple osteochondromas", "MONDO:0005508", "" ], [ "O43909-1", "protein_xref_mondo", "44312", "EXTL3", "ISDNA, IMMUNOSKELETAL dysplasia with neurodevelopmental abnormalities, ISDNA", "immunoskeletal dysplasia with neurodevelopmental abnormalities", "immunoskeletal dysplasia with neurodevelopmental abnormalities", "MONDO:0044312", "" ], [ "Q9H9S5-1", "protein_xref_mondo", "11688", "FKRP", "Muscular dystrophy, congenital, type 1C (MDC1C), Congenital muscular dystrophy type 1C (CMD1C), FKRP-CDG (cong. muscular dystrophy spectrum), Muscular dystrophy-dystroglycanopathy (Congenital with or without mental retardation), type B, 5 (MDDGB5)", "Muscular dystrophy, congenital, type 1C", "muscular dystrophy-dystroglycanopathy type B5", "MONDO:0011688", "" ], [ "Q9H9S5-1", "protein_xref_mondo", "11787", "FKRP", "Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 5 (MDDGC5), FKRP-CDG (cong. muscular dystrophy spectrum), Limb-girdle muscular dystrophy type 2I (LGMD2I)", "Muscular dystrophy, limb-girdle, type 2I", "autosomal recessive limb-girdle muscular dystrophy type 2I", "MONDO:0011787", "" ], [ "O75072-1", "protein_xref_mondo", "12704", "FKTN", "Dilated cardiomyopathy with mild or no proximal muscle weakness, Cardiomyopathy, dilated, 1X (CMD1X), FKTN-CDG (cong. muscular dystrophy spectrum)", "Cardiomyopathy, dilated, 1X", "dilated cardiomyopathy 1X", "MONDO:0012704", "" ], [ "O75072-1", "protein_xref_mondo", "9678", "FKTN", "Fukuyama congenital muscular dystrophy (FCMD), Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 4 (MDDGA4), FKTN-CDG (cong. muscular dystrophy spectrum)", "Fukuyama congenital muscular dystrophy", "Fukuyama congenital muscular dystrophy", "MONDO:0009678", "" ], [ "O75072-1", "protein_xref_mondo", "12699", "FKTN", "Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 4 (MDDGC4), Limb-girdle muscular dystrophy type 2M (LGMD2M), FKTN-CDG (cong. muscular dystrophy spectrum)", "Muscular dystrophy, limb-girdle, type 2M", "autosomal recessive limb-girdle muscular dystrophy type 2M", "MONDO:0012699", "" ], [ "P04066-1", "protein_xref_mondo", "9254", "FUCA1", "A-fucosidase deficiency, Alpha-L-fucosidase deficiency, alpha fucosidase deficiency, fucosidosis", "Fucosidosis", "Fucosidosis", "MONDO:0009254", "23676310" ], [ "Q9BYC5-1", "protein_xref_mondo", "60720", "FUT8", "CONGENITAL DISORDER OF glycosylation with defective fucosylation, CDGF, CDGF", "FUT8-CDG", "congenital disorder of glycosylation with defective fucosylation", "MONDO:0060720", "" ], [ "Q9BUM1-1", "protein_xref_mondo", "12930", "G6PC3", "SCN4, severe congenital neutropenia-pulmonary hypertension-superficial venous angiectasis syndrome, severe congenital neutropenia type 4, Dursun syndrome", "severe congenital neutropenia type 4", "autosomal recessive severe congenital neutropenia due to G6PC3 deficiency", "MONDO:0012930", "" ], [ "P10253-1", "protein_xref_mondo", "18485", "GAA", "GSD type II, Lysosomal alpha 1,4 Glucosidase Deficiency Disease", "Pompe disease", "glycogen storage disease due to acid maltase deficiency, late-onset", "MONDO:0018485", "23676310" ], [ "P54803-1", "protein_xref_mondo", "9499", "GALC", "Galactosylceramide beta-galactosidase deficiency, Leukodystrophy, globoid cell, Krabbe leukodystrophy, Globoid cell leukodystrophy", "Krabbe disease", "Krabbe disease", "MONDO:0009499", "" ], [ "P34059-1", "protein_xref_mondo", "9647", "GALNS", "MPS IVA, Galactosamine-6-sulphatase deficiency, Morquio's syndrome, classic form, Mucopolysaccharidosis type IVA", "Morquio syndrome A", "Morquio syndrome C", "MONDO:0009647", "" ], [ "Q14435-1", "protein_xref_mondo", "8897", "GALNT3", "Tumoral calcinosis, hyperphosphatemic, familial", "GALNT3-CDG", "hyperphosphatemic familial tumoral calcinosis", "MONDO:0008897", "" ], [ "Q14697-1", "protein_xref_mondo", "10916", "GANAB", "polycystic kidney disease type 3, Apkd3, GANAB autosomal dominant polycystic kidney disease, polycystic kidney disease, adult, type III, polycystic kidney disease 3, autosomal dominant polycystic kidney disease caused by mutation in GANAB, Pkd3", "GANAB-CDG", "polycystic kidney disease 3", "MONDO:0010916", "" ], [ "P04062-1", "protein_xref_mondo", "9265", "GBA", "non-neuronopathic form", "Gaucher disease, type I", "Gaucher disease type I", "MONDO:0009265", "23676311" ], [ "P04062-1", "protein_xref_mondo", "9266", "GBA", "acute neuronopathic Gaucher disease, infantile cerebral Gaucher disease, GD II, Gaucher's disease type II, Gaucher disease, acute neuronopathic type", "Gaucher disease, type II", "Gaucher disease type II", "MONDO:0009266", "23676312" ], [ "P04062-1", "protein_xref_mondo", "9267", "GBA", "neuronopathic form", "Gaucher disease, type III", "Gaucher disease type III", "MONDO:0009267", "23676313" ], [ "P04062-1", "protein_xref_mondo", "9268", "GBA", "neuronopathic form, cardiovascular form", "Gaucher disease, type IIIC", "Gaucher disease-ophthalmoplegia-cardiovascular calcification syndrome", "MONDO:0009268", "23676314" ], [ "Q06210-1", "protein_xref_mondo", "182", "GFPT1", "CMSTA1", "Myasthenia, congenital, with tubular aggregates 1", "congenital myasthenic syndrome with tubular aggregates", "MONDO:0000182", "" ], [ "P06280-1", "protein_xref_mondo", "10526", "GLA", "Alpha-galactosidase A deficiency", "Fabry disease", "Fabry disease", "MONDO:0010526", "" ], [ "P16278-1", "protein_xref_mondo", "9260", "GLB1", "Norman-Landing disease, infantile GM1 gangliosidosis", "GM1-gangliosidosis, type I", "GM1 gangliosidosis type 1", "MONDO:0009260", "23676310" ], [ "P16278-1", "protein_xref_mondo", "9261", "GLB1", "juvenile form, Derry syndrome", "GM1-gangliosidosis, type II", "GM1 gangliosidosis type 2", "MONDO:0009261", "" ], [ "P16278-1", "protein_xref_mondo", "9262", "GLB1", "adult form", "GM1-gangliosidosis, type III", "GM1 gangliosidosis type 3", "MONDO:0009262", "" ], [ "P16278-1", "protein_xref_mondo", "9647", "GLB1", "MPS IVB, Morquio-like syndrome, Mucopolysaccharidosis type IVB", "Morquio syndrome B", "Morquio syndrome C", "MONDO:0009647", "" ], [ "P17900-1", "protein_xref_mondo", "10099", "GM2A", "GM2-Gangliosidosis, B variant, GM2-gangliosidosis, type I, Hexosaminidase A deficiency", "Tay-Sachs disease", "Tay-Sachs disease AB variant", "MONDO:0010099", "" ], [ "Q96IJ6-1", "protein_xref_mondo", "14219", "GMPPA", "GMPPA-CDG, alacrima, achalasia, and mental retardation syndrome, AAMR, AAMR", "GMPPA-CDG", "alacrima, achalasia, and mental retardation syndrome", "MONDO:0014219", "" ], [ "Q9Y5P6-1", "protein_xref_mondo", "14140", "GMPPB", "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A14", "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A14", "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A14", "MONDO:0014140", "" ], [ "Q9Y223-1", "protein_xref_mondo", "11603", "GNE", "GNE-CDG (hereditary inclusion body myopathy), Inclusion body myopathy 2, autosomal recessive (IBM2), Hereditary inclusion body myopathy type 2 (HIBM2)", "Hereditary inclusion body myopathy type 2", "hereditary inclusion body myopathy type 4", "MONDO:0011603", "" ], [ "Q9Y223-1", "protein_xref_mondo", "11603", "GNE", "Nonaka myopathy (NM), Distal myopathy with rimmed vacuoles (DMRV), Distal myopathy, Nonaka type", "Nonaka myopathy", "GNE myopathy", "MONDO:0011603", "" ] ] }, "readme": "Name\n - Human Protein Glycosylation Diseases\n\nVersion\n - 1.11.2\n\nCreated on\n - 2019-09-06T14:06:38.953629\n\nModified on\n - 2022-01-19T11:34:45.226050\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Amanda Bell [amandab2140@gwu.edu], Jonathon Keeney [keeneyjg@gwu.edu], Millicent Quartey [mquartey@email.gwu.edu]\n\nAuthors\n - Maria Martin [martin@ebi.ac.uk], Preethi Vasudev [pvasudev@ebi.ac.uk], Jean-Philippe Gourdine [gourdine@ohsu.edu], Melissa Haendel [haendel@ohsu.edu]\n\nChecksum\n - \n\nUsability Domain\n - The Human Diseases dataset contains list of human [taxid:9606] diseases as described by OMIM and Monarch Initiative database. \n - Online Mendelian Inheritance in Man (OMIM) is a continuously updated catalog of human genes and genetic disorders and traits, with a particular focus on the gene-phenotype relationship. \n - The Monarch Initiative is focused primarily on phenotype-related resources and brings in data associated with those phenotypes so that the users can begin to make connections among other biological entities of interest. \n - If you are using this dataset please give proper attribution to OMIM, Monarch Initiative, EMBL-EBI-UniProt and GlyGen. \n\nDescription Domain\n Keywords\n - disease\n - HPO\n - OMIM\n - Congenital Disorders of Glycosylation (CDG)\n - Monarch Initiative\n\n Pipeline Steps\n - Step-1: The script extracts the glycosylation disease information from the human_protein_disease_glyco.csv that is compiled from human_glyco-phenotype_disease_curation_list_v12-18-74.csv. The script maps the UniProtKB accessions to the UniprotKB canonical accessions. \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: uniprot-proteome-homo-sapiens.nt\n URI: https://data.glygen.org/ln2wwwdata/source/uniprot-proteome-homo-sapiens.nt\n Name: human_protein_disease_glyco.csv\n URI: https://data.glygen.org/ln2wwwdata/compiled/human_protein_disease_glyco.csv\n Name: human_protein_masterlist.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/human_protein_masterlist.csv\n Output Subdomain\n Name: human_protein_disease_glyco.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/human_protein_disease_glyco.csv\n Name: human_protein_disease_glyco.stat.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/human_protein_disease_glyco.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"16\"\n Name: \"motif_start\"\n Description: \"\"\n Unique Values: \"23\"\n Name: \"filter_flags\"\n Description: \"Filter tags/flags assigned to the mutation entries that have passed the mutation filter criteria\"\n Unique Values: \"19\"\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: \"3\"\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: \"1\"\n Name: \"chr_pos\"\n Description: \"Chromosome Position of a gene\"\n Unique Values: \"19\"\n Name: \"chr_id\"\n Description: \"\"\n Unique Values: \"10\"\n Name: \"dbsnp_id\"\n Description: \"\"A reference SNP ID number\"\n Unique Values: \"19\"\n Name: \"evidence_ECO:0000313\"\n Description: \"A type of evidence that is imported information used in an automatic assertion\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"19\"\n Name: \"mim_id\"\n Description: \"Disease ID from the OMIM database\"\n Unique Values: \"1\"\n Name: \"description\"\n Description: \"\"\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: \"18\"\n Name: \"cytogenic_band\"\n Description: \"One of the subregions of a chromosome visible microscopically after special staining\"\n Unique Values: \"14\"\n Name: \"aa_pos\"\n Description: \"Position of the amino acid in canonical sequence of protein in the UniProtKB database\"\n Unique Values: \"18\"\n Name: \"ref_aa\"\n Description: \"Reference amino acid residue\"\n Unique Values: \"9\"\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: \"10\"\n Name: \"alt_motif\"\n Description: \"Altered motif\"\n Unique Values: \"24\"\n Name: \"disease_xrefs\"\n Description: \"\"\n Unique Values: \"1\"\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: \"is_known_glycoprotein\"\n Description: \"Yes or no flag to denote if a protein is experimentally proven glycoprotein\"\n Unique Values: \"1\"\n Name: \"alt_nt\"\n Description: \"Alternative nucleotide\"\n Unique Values: \"1\"\n Name: \"protein_name\"\n Description: \"Protein name in the UniProtKB\"\n Unique Values: \"16\"\n Name: \"disease_evidence_ECO:0000313\"\n Description: \"The evidence that could be a PMID or a ClinVar ID that associates disease with the variant\"\n Unique Values: \"1\"\n Name: \"effect\"\n Description: \"The effect on glycosylation or N-sequon due to variation at site of glycosylated amino acid.\"\n Unique Values: \"3\"\n Name: \"end_aa_pos\"\n Description: \"End position of the amino acid in the sequence of a protein in UniProtKB\"\n Unique Values: \"18\"\n Name: \"mutation_type\"\n Description: \"Denotes whether mutation was reported with reference to amino acid or nucleotide\"\n Unique Values: \"1\"\n Name: \"disease_description\"\n Description: \"The disease description and/or definition \"\n Unique Values: \"1\"\n Name: \"do_id\"\n Description: \"Disease Ontology identifier\"\n Unique Values: \"1\"\n Name: \"evidence_ECO:0000269\"\n Description: \"A type of experimental evidence that is used in a manual assertion. Usually the values are PMIDs\"\n Unique Values: \"1\"\n Name: \"ref_nt\"\n Description: \"Reference nucleotide\"\n Unique Values: \"4\"\n Name: \"disease\"\n Description: \"The disease name for the cell line\"\n Unique Values: \"1\"\n Name: \"alt_aa\"\n Description: \"Altered amino acid residue\"\n Unique Values: \"10\"\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: \"ref_motif\"\n Description: \"Reference motif\"\n Unique Values: \"20\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"2\"\n Name: \"minor_allelic_frequency\"\n Description: \"\"\n Unique Values: \"1\"\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: \"17\"\n Name: \"disease_evidence_ECO:0000269\"\n Description: \"The PMID evidence for the association of the disease with the variant.\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.11.2/reviewed/human_protein_disease_glyco.csv" }