{ "bcoid": "GLY_000526", "title": "Disease Names", "description": "", "filename": "protein_disease_names.csv", "filetype": "csv", "categories": { "molecule": "Protein", "tags": "Disease Names", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "0011078...", "mondo..." ], [ "0011078...", "mondo..." ] ], "headers": [ "xref_id...", "xref_key..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "xref_id" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "name_type" }, { "type": "string", "label": "name" }, { "type": "string", "label": "description" } ], [ "0011078", "mondo", "recommended_name", "anterior chamber cleavage disorder, cerebellar hypoplasia, hypothyroidism, and tracheal stenosis", "" ], [ "0011078", "mondo", "synonym", "anterior chamber cleavage disorder, cerebellar hypoplasia, hypothyroidism, and tracheal stenosis", "" ], [ "0011078", "mondo", "synonym", "Jung Wolff back Stahl syndrome", "" ], [ "0011079", "mondo", "recommended_name", "rhizomelic dysplasia, Patterson-Lowry type", "Rhizomelic dysplasia, Patterson-Lowry type is a rare primary bone dysplasia characterized by short stature, severe rhizomelic shortening of the upper limbs associated with specific malformations of humeri (including marked widening and flattening of proximal metaphyses, medial flattening of the proximal epiphyses, and lateral bowing with medial cortical thickening of the proximal diaphyses), marked coxa vara with dysplastic femoral heads and brachimetacarpalia." ], [ "0011079", "mondo", "synonym", "rhizomelic dysplasia, Patterson-Lowry type", "" ], [ "0011079", "mondo", "synonym", "Patterson-Lowry rhizomelic dysplasia", "" ], [ "0011079", "mondo", "synonym", "Patterson Lowry syndrome", "" ], [ "0011079", "mondo", "synonym", "rhizomelic dysplasia Patterson Lowry type", "" ], [ "0011070", "mondo", "recommended_name", "van Maldergem syndrome 1", "Any van Maldergem syndrome in which the cause of the disease is a mutation in the DCHS1 gene." ], [ "0011070", "mondo", "synonym", "DCHS1 van Maldergem syndrome", "" ], [ "0011070", "mondo", "synonym", "Van Maldergem syndrome type 1", "" ], [ "0011070", "mondo", "synonym", "VAN Maldergem syndrome 1; VMLDS1", "" ], [ "0011070", "mondo", "synonym", "van Maldergem syndrome 1", "" ], [ "0011070", "mondo", "synonym", "VMLDS1", "" ], [ "0011070", "mondo", "synonym", "van Maldergem syndrome caused by mutation in DCHS1", "" ], [ "0011070", "mondo", "synonym", "Cerebrofacioarticular syndrome", "" ], [ "0011071", "mondo", "recommended_name", "hereditary thrombocytopenia with normal platelets-hematological cancer predisposition syndrome", "Familial platelet disorder with predisposition to acute myelogenous leukemia (FPD/AML) is characterised by moderate thrombocytopenia, abnormal platelet function and the propensity to develop myeloid malignancies, in particular AML." ], [ "0011071", "mondo", "synonym", "asprin-like platelet disorder", "" ], [ "0011071", "mondo", "synonym", "familial platelet disorder with associated myeloid malignancy", "" ], [ "0011071", "mondo", "synonym", "platelet disorder, aspirin-like", "" ], [ "0011071", "mondo", "synonym", "FPS/AML syndrome", "" ], [ "0011071", "mondo", "synonym", "FPDMM", "" ], [ "0011071", "mondo", "synonym", "FPD/AML syndrome", "" ], [ "0011071", "mondo", "synonym", "familial thrombocytopenia with propensity to acute myelogenous leukemia", "" ], [ "0011071", "mondo", "synonym", "platelet disorder, familial, with associated myeloid malignancy", "" ], [ "0011071", "mondo", "synonym", "platelet disorder, familial, with associated myeloid malignancy; FPDMM", "" ], [ "0011071", "mondo", "synonym", "familial platelet syndrome with predisposition to acute myelogenous leukemia", "" ], [ "0011071", "mondo", "synonym", "thrombocytopenia, familial, with propensity to acute myelogenous leukemia", "" ], [ "0011072", "mondo", "recommended_name", "NIDDM2", "" ], [ "0011072", "mondo", "synonym", "NIDDM2", "" ], [ "0011072", "mondo", "synonym", "noninsulin-dependent diabetes mellitus 2", "" ], [ "0011072", "mondo", "synonym", "diabetes mellitus, noninsulin-dependent, 2", "" ], [ "0011072", "mondo", "synonym", "diabetes mellitus, noninsulin-dependent, 2; NIDDM2", "" ], [ "0011073", "mondo", "recommended_name", "diabetes mellitus, transient neonatal, 1", "" ], [ "0011073", "mondo", "synonym", "diabetes mellitus, transient neonatal, 1", "" ], [ "0011073", "mondo", "synonym", "Dmtn", "" ], [ "0011073", "mondo", "synonym", "Tndm", "" ], [ "0011073", "mondo", "synonym", "diabetes mellitus, transient neonatal, type 1", "" ], [ "0011073", "mondo", "synonym", "Tndm1", "" ], [ "0011074", "mondo", "recommended_name", "autosomal dominant nonsyndromic deafness 7", "An autosomal dominant nonsyndromic deafness that is characterized by progressive high-tone hearing loss and has_material_basis_in variation in the chromosome region 1q21-q23." ], [ "0011074", "mondo", "synonym", "DFNA7", "" ], [ "0011074", "mondo", "synonym", "deafness, autosomal dominant 7", "" ], [ "0011074", "mondo", "synonym", "autosomal dominant nonsyndromic deafness type 7", "" ], [ "0011074", "mondo", "synonym", "autosomal dominant deafness 7", "" ], [ "0011074", "mondo", "synonym", "deafness, autosomal dominant 7; DFNA7", "" ], [ "0011075", "mondo", "recommended_name", "retinitis pigmentosa 18", "Any retinitis pigmentosa in which the cause of the disease is a mutation in the PRPF3 gene." ], [ "0011075", "mondo", "synonym", "retinitis pigmentosa 18; RP18", "" ], [ "0011075", "mondo", "synonym", "retinitis pigmentosa type 18", "" ], [ "0011075", "mondo", "synonym", "retinitis pigmentosa caused by mutation in PRPF3", "" ], [ "0011075", "mondo", "synonym", "RP 18", "" ], [ "0011075", "mondo", "synonym", "PRPF3 retinitis pigmentosa", "" ], [ "0011075", "mondo", "synonym", "RP18", "" ], [ "0011075", "mondo", "synonym", "retinitis pigmentosa 18", "" ], [ "0011076", "mondo", "recommended_name", "myofibrillar myopathy 1", "Desminopathy is a rare genetic skeletal muscle disease characterized by abnormal chimeric aggregates of desmin and other cytoskeletal proteins and granulofilamentous material at the ultrastructural level in muscle biopsies and variable clinical/ myopathological features, age of disease onset and rate of disease progression. Patients present with bilateral skeletal muscle weakness that starts in distal leg muscles and spreads proximally, sometimes involving trunk, neck flexors and facial muscles and often cardiomyopathy manifested by conduction blocks, arrhythmias, chronic heart failure, and sometimes tachyarrhythmia. Weakness eventually leads to wheelchair dependence. Respiratory insufficiency can be a major cause of disability and death, beginning with nocturnal hyperventilation with oxygen desaturation and progressing to daytime respiratory failure." ], [ "0011076", "mondo", "synonym", "cardiomyopathy, dilated, with conduction defect and muscular dystrophy", "" ], [ "0011076", "mondo", "synonym", "arrhythmogenic right ventricular dysplasia, familial, 7, formerly", "" ], [ "0011076", "mondo", "synonym", "IBM1", "" ], [ "0011076", "mondo", "synonym", "arrhythmogenic right ventricular cardiomyopathy 7", "" ], [ "0011076", "mondo", "synonym", "cardiomyopathy, dilated, 1F and limb-girdle muscular dystrophy type 1D", "" ], [ "0011076", "mondo", "synonym", "CMD1F and LGMD1D, formerly", "" ], [ "0011076", "mondo", "synonym", "myopathy, myofibrillar, type 1", "" ], [ "0011076", "mondo", "synonym", "arrhythmogenic right ventricular dysplasia, familial, 7", "" ], [ "0011076", "mondo", "synonym", "myopathy, myofibrillar, 1", "" ], [ "0011076", "mondo", "synonym", "desmin-related myopathy with arrhythmogenic right ventricular cardiomyopathy", "" ], [ "0011076", "mondo", "synonym", "myofibrillar myopathy type 1", "" ], [ "0011076", "mondo", "synonym", "desmin-related myofibrillar myopathy", "" ], [ "0011076", "mondo", "synonym", "myofibrillar myopathy (disease) caused by mutation in DES", "" ], [ "0011076", "mondo", "synonym", "myopathy, myofibrillar, desmin-related", "" ], [ "0011076", "mondo", "synonym", "desminopathy", "" ], [ "0011076", "mondo", "synonym", "desminopathy, primary", "" ], [ "0011076", "mondo", "synonym", "MFM1", "" ], [ "0011076", "mondo", "synonym", "myopathy, myofibrillar, 1; MFM1", "" ], [ "0011076", "mondo", "synonym", "inclusion body myopathy 1, autosomal dominant, formerly", "" ], [ "0011076", "mondo", "synonym", "CMD1F and LGMD1D", "" ], [ "0011076", "mondo", "synonym", "DES myofibrillar myopathy (disease)", "" ], [ "0011076", "mondo", "synonym", "myofibrillar myopathy with arrhythmogenic right ventricular cardiomyopathy", "" ], [ "0011076", "mondo", "synonym", "cardiomyopathy, dilated, 1F and limb-girdle muscular dystrophy type 1D, formerly", "" ], [ "0011076", "mondo", "synonym", "arrhythmogenic right ventricular cardiomyopathy 7, formerly", "" ], [ "0011076", "mondo", "synonym", "desmin-related myopathy", "" ], [ "0011076", "mondo", "synonym", "inclusion body myopathy 1, autosomal dominant", "" ], [ "0011077", "mondo", "recommended_name", "microcephaly, corpus callosum dysgenesis, and cleft lip/palate", "" ], [ "0011077", "mondo", "synonym", "microcephaly, corpus callosum dysgenesis, and cleft lip/palate", "" ], [ "0011077", "mondo", "synonym", "microcephaly, facial clefting, and preaxial polydactyly", "" ], [ "0011077", "mondo", "synonym", "microcephaly, corpus callosum dysgenesis and cleft lip-palate", "" ] ] }, "readme": "Name\n - Disease Names\n\nVersion\n - 1.11.2\n\nCreated on\n - 2020-08-19T14:13:07.626533\n\nModified on\n - 2020-08-19T14:15:31.389234\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 - \n\nChecksum\n - \n\nUsability Domain\n - \n - \n\nExecution Domain\n Scripts\n\n Software Prerequisites\n\nI/O Domain\n Output Subdomain\n Name: protein_disease_names.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.11.2/reviewed/protein_disease_names.csv\n Name: protein_disease_names.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.11.2/reviewed/protein_disease_names.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/protein_disease_names.csv" }