{ "bcoid": "GLY_000463", "title": "Human Literature Mutations", "description": "The Human Literature Mutation dataset contains human [taxid:9606] mutation data extracted from literature ...", "filename": "human_protein_mutation_literature.csv", "filetype": "csv", "categories": { "species": "Homo sapiens", "molecule": "Protein", "tags": "Literature Mutations", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P31749-1...", "27515171..." ], [ "P18887-1...", "25245010..." ] ], "headers": [ "uniprotkb_ca...", "pmid..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "pmid" }, { "type": "string", "label": "entrez_id" }, { "type": "string", "label": "gene_mention" }, { "type": "string", "label": "doid" }, { "type": "string", "label": "do_name" }, { "type": "string", "label": "disease_mention" }, { "type": "string", "label": "mutation_type" }, { "type": "string", "label": "abstract_extraction" }, { "type": "string", "label": "sentence_number" }, { "type": "string", "label": "sentence_text" }, { "type": "string", "label": "extraction_method" }, { "type": "string", "label": "patient_control_counts" }, { "type": "string", "label": "is_meta" }, { "type": "string", "label": "is_review" }, { "type": "string", "label": "start_pos" }, { "type": "string", "label": "start_pos" }, { "type": "string", "label": "ref_aa" }, { "type": "string", "label": "alt_aa" } ], [ "P31749-1", "27515171", "207", "AKT1", "1612", "breast cancer", "breast cancer", "Amino acid", "Title", "0", "AKT1 (E17K) mutation profiling in breast cancer: prevalence, concurrent oncogenic alterations, and blood-based detection.", "", "600 samples", "1", "1", "17", "17", "E", "K" ], [ "P18887-1", "25245010", "7515", "XRCC1", "3070, 5076", "malignant glioma, mixed glioma", "glioma", "Amino acid", "Result", "7", "The frequency of Arg399Gln A allele was significant higher in glioma group than in healthy controls [38.7 vs 30.1%, OR=1.29 (1.11-1.49), P=0.001]; the frequencies of GA or AA genotypes were different in two groups (45.4 vs 38.2%, 16 vs 10.9%).", "", "368 patients, 346 controls", "1", "1", "399", "399", "R", "Q" ], [ "P18887-1", "25245010", "7515", "XRCC1", "3070, 5076", "malignant glioma, mixed glioma", "glioma", "Amino acid", "Conclusion", "8", "This study demonstrates that the rs25489 (Arg280His) and Arg399Gln (rs25487) polymorphisms in XRCC1 gene might influence the risk of developing glioma in Chinese population.", "ASSOC", "368 patients, 346 controls", "1", "1", "280", "280", "R", "H" ], [ "P18887-1", "25245010", "7515", "XRCC1", "3070, 5076", "malignant glioma, mixed glioma", "glioma", "Amino acid", "Conclusion", "8", "This study demonstrates that the rs25489 (Arg280His) and Arg399Gln (rs25487) polymorphisms in XRCC1 gene might influence the risk of developing glioma in Chinese population.", "ASSOC", "368 patients, 346 controls", "1", "1", "399", "399", "R", "Q" ], [ "O00255-1", "15754732", "4221", "MEN1", "305", "carcinoma", "carcinoma", "Amino acid", "Result", "6", "Somatic MEN1 mutations were detected in 6 of the 35 patients with a benign parathyroid lesion examined (17.1%), whereas no alterations were found in the carcinomas.", "MutFound", "95 cases, 4 carcinoma, 1 tumors", "1", "1", "89", "89", "L", "R" ], [ "P15056-1", "23526598", "673", "BRAF", "1909", "melanoma", "malignant melanoma", "Amino acid", "Title", "0", "A role for immunohistochemical detection of BRAF V600E prior to BRAF-inhibitor treatment of malignant melanoma?", "", "", "1", "1", "600", "600", "V", "E" ], [ "P00533-1", "28173668", "1956", "EGFR", "3910", "lung adenocarcinoma", "lung adenocarcinomas", "Amino acid", "Result", "8", "Among them, T790M mutation was found in 8 patients, L858R became G719X plus S768I mutation in one patient, and 19-del converted into wild-type in one other patient.", "MutFound", "8 patients, 15 patients, 1 patient, 5 patients, 20 patients", "1", "1", "790", "790", "T", "M" ], [ "P00533-1", "28173668", "1956", "EGFR", "3910", "lung adenocarcinoma", "lung adenocarcinomas", "Amino acid", "Conclusion", "9", "Conclusions: T790M mutation is the primary type of EGFR mutation in lung adenocarcinomas with acquired resistance to EGFR-TKIs therapy.", "", "8 patients, 15 patients, 1 patient, 5 patients, 20 patients", "1", "1", "790", "790", "T", "M" ], [ "P15056-1", "28329426", "673", "BRAF", "3969", "thyroid gland papillary carcinoma", "PTCs", "Amino acid", "Result", "9", "There was no significant difference in the presence of multifocality, thyroid capsular invasion, extrathyroid extension, BRAF V600E mutation, lymph node metastasis or distant metastasis between FDG-avid and non-FDG-avid PTCs.", "ASSOC", "", "1", "1", "600", "600", "V", "E" ], [ "P15056-1", "28329426", "673", "BRAF", "3969", "thyroid gland papillary carcinoma", "papillary thyroid carcinoma", "Amino acid", "Title", "0", "Clinicopathological characteristics including BRAF V600E mutation status and PET/CT findings in papillary thyroid carcinoma.", "", "", "1", "1", "600", "600", "V", "E" ], [ "Q16832-1", "28161936", "4921", "DDR2", "1749", "squamous cell carcinoma", "SCC", "Amino acid", "Result", "6", "RESULTS: We identified novel somatic mutations of DDR2 in two of the 100 SCC samples studied.", "MutFound", "100 samples", "1", "1", "595", "595", "L", "P" ], [ "P00533-1", "27655904", "1956", "EGFR", "3908", "lung non-small cell carcinoma", "NSCLC", "Amino acid", "Conclusion", "10", "Platinum-based doublet chemotherapy\u00a0\u00b1\u00a0bevacizumab was moderately effective, indicating the need for targeted therapies for patients with T790M mutation-positive NSCLC.", "", "141 patients", "1", "1", "790", "790", "T", "M" ], [ "P00533-1", "27655904", "1956", "EGFR", "3908", "lung non-small cell carcinoma", "NSCLC", "Amino acid", "Conclusion", "8", "CONCLUSIONS: This study reveals the treatment patterns and outcomes of NSCLC patients in Japan after detection of the T790M mutation.", "", "141 patients", "1", "1", "790", "790", "T", "M" ], [ "P00533-1", "27655904", "1956", "EGFR", "60888", "transient myeloproliferative syndrome", "MST", "Amino acid", "Title", "0", "Treatments and outcomes of advanced/recurrent non-small cell lung cancer harboring the EGFR T790M mutation: a retrospective observational study of 141 patients in Japan.", "MutFound", "141 patients", "1", "1", "790", "790", "T", "M" ], [ "P00533-1", "27655904", "1956", "EGFR", "60888", "transient myeloproliferative syndrome", "MST", "Amino acid", "Method", "4", "METHODS: We conducted a retrospective observational study at 23 sites in Japan, and 141 patients with T790M-positive advanced/recurrent NSCLC were identified from January 2008 to December 2014.", "MutFound", "141 patients", "1", "1", "790", "790", "T", "M" ], [ "P48735-1", "28325290", "3418", "IDH2", "9119", "acute myeloid leukemia", "AML", "Amino acid", "Conclusion", "5", "Using the IDH2 R140Q mutation as a model, we present a new effective methodology here using the RNA-guided clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system to reproduce or remove AML-associated mutations in or from human leukemic cells, respectively, via introduction of a DNA template at the endogenous gene locus via homologous recombination.", "", "50 patients", "1", "1", "140", "140", "R", "Q" ], [ "P31213-1", "17136762", "6716", "SRD5A2", "10283", "prostate cancer", "prostate cancer", "Amino acid", "Result", "8", "Carriers of the rarer A49T A allele were at a 60% higher risk of prostate cancer (OR = 1.60; 95% CI 1.09-2.36; p = 0.02) and 50% lower risk of vertex and frontal balding (p = 0.03) compared with men homozygous for the more common G allele.", "", "1 cancer, 736 controls, 827 cases", "1", "1", "49", "49", "A", "T" ], [ "P31213-1", "17136762", "6716", "SRD5A2", "10283", "prostate cancer", "prostate cancer", "Amino acid", "Introduction", "1", "Controversy exists over the significance of associations between the SRD5A2 (5alpha-reductase type 2) polymorphisms, A49T and V89L, and risk of prostate cancer.", "ASSOC", "1 cancer, 736 controls, 827 cases", "1", "1", "49", "49", "A", "T" ], [ "P31213-1", "17136762", "6716", "SRD5A2", "10283", "prostate cancer", "prostate cancer", "Amino acid", "Result", "10", "Our study provides evidence that the SRD5A2 A49T A variant is associated with an increased risk of prostate cancer, lower levels of circulating 3alpha-diolG and decreased risk of baldness.", "ASSOC", "1 cancer, 736 controls, 827 cases", "1", "1", "49", "49", "A", "T" ], [ "P04637-1", "22507745", "7157", "TP53", "1319", "brain cancer", "brain tumors", "Amino acid", "Result", "10", "Clinically relevant TP53 germline mutations were identified in three of the four patients (75%) with a family history of at least two LFS-linked cancers (breast, bone or soft tissue sarcoma, brain tumors or adrenocortical cancer); 1 of the 17 patients (6%) with a family history of breast cancer only, and 1 of the 62 patients (< 2%) with no family history of breast or LFS-linked cancers.", "MutFound", "2 individuals, 2 cancers, 2 patients, 1 cancers, 83 patients, 100 patients", "1", "1", "285", "285", "E", "K" ], [ "P04637-1", "22507745", "7157", "TP53", "660", "adrenal cortex cancer", "adrenocortical cancer", "Amino acid", "Result", "10", "Clinically relevant TP53 germline mutations were identified in three of the four patients (75%) with a family history of at least two LFS-linked cancers (breast, bone or soft tissue sarcoma, brain tumors or adrenocortical cancer); 1 of the 17 patients (6%) with a family history of breast cancer only, and 1 of the 62 patients (< 2%) with no family history of breast or LFS-linked cancers.", "MutFound", "2 individuals, 2 cancers, 2 patients, 1 cancers, 83 patients, 100 patients", "1", "1", "285", "285", "E", "K" ], [ "P04637-1", "22507745", "7157", "TP53", "1319", "brain cancer", "brain tumors", "Amino acid", "Result", "10", "Clinically relevant TP53 germline mutations were identified in three of the four patients (75%) with a family history of at least two LFS-linked cancers (breast, bone or soft tissue sarcoma, brain tumors or adrenocortical cancer); 1 of the 17 patients (6%) with a family history of breast cancer only, and 1 of the 62 patients (< 2%) with no family history of breast or LFS-linked cancers.", "MutFound", "2 individuals, 2 cancers, 2 patients, 1 cancers, 83 patients, 100 patients", "1", "1", "138", "138", "A", "V" ], [ "P04637-1", "22507745", "7157", "TP53", "660", "adrenal cortex cancer", "adrenocortical cancer", "Amino acid", "Result", "10", "Clinically relevant TP53 germline mutations were identified in three of the four patients (75%) with a family history of at least two LFS-linked cancers (breast, bone or soft tissue sarcoma, brain tumors or adrenocortical cancer); 1 of the 17 patients (6%) with a family history of breast cancer only, and 1 of the 62 patients (< 2%) with no family history of breast or LFS-linked cancers.", "MutFound", "2 individuals, 2 cancers, 2 patients, 1 cancers, 83 patients, 100 patients", "1", "1", "138", "138", "A", "V" ], [ "P00533-1", "27523899", "1956", "EGFR", "3908", "lung non-small cell carcinoma", "non small cell lung cancer", "Amino acid", "Title", "0", "[The relationship between EGFR-TKI-Resistant and T790M in non small cell lung cancer].", "", "", "1", "1", "790", "790", "T", "M" ], [ "P40238-1", "25970554", "4352", "Mpl", "2224", "essential thrombocythemia", "ET", "Amino acid", "Conclusion", "4", "Herein, we describe a Mpl W515K somatic mutation in a paediatric case of ET who presented with Budd-Chiari syndrome.", "", "", "1", "1", "515", "515", "W", "K" ], [ "P40238-1", "27519934", "4352", "MPL", "4971", "myelofibrosis", "myelofibrosis", "Amino acid", "Title", "0", "Concurrent MPL W515L and Y591D mutations in a patient with myelofibrosis.", "", "", "1", "1", "515", "515", "W", "L" ], [ "P40238-1", "27519934", "4352", "MPL", "4971", "myelofibrosis", "myelofibrosis", "Amino acid", "Title", "0", "Concurrent MPL W515L and Y591D mutations in a patient with myelofibrosis.", "", "", "1", "1", "591", "591", "Y", "D" ], [ "P00519-1", "25963192", "25", "Bcr-Abl", "8692", "myeloid leukemia", "myeloid leukemia", "Amino acid", "Title", "0", "CD-200 induces apoptosis and inhibits Bcr-Abl signaling in imatinib-resistant chronic myeloid leukemia with T315I mutation.", "", "", "1", "1", "315", "315", "T", "I" ], [ "Q86YC2-1", "28319063", "79728", "PALB2", "1612", "breast cancer", "breast cancer", "Amino acid", "Conclusion", "9", "Our findings establish L35P as the first pathogenic missense mutation in PALB2 and directly demonstrate the requirement of the PALB2-BRCA1 interaction for breast cancer suppression.", "", "1 carrier, 1 cancer", "1", "1", "35", "35", "L", "P" ], [ "P00995-1", "15764155", "6690", "SPINK1", "1793", "pancreatic cancer", "pancreatic cancer", "Amino acid", "Title", "0", "Mutations N34S and P55S of the SPINK1 gene in patients with chronic pancreatitis or pancreatic cancer and in healthy subjects: a report from Finland.", "", "188 cancer, 1 cancer, 188 tumour, 459 individuals", "1", "1", "34", "34", "N", "S" ], [ "P00995-1", "15764155", "6690", "SPINK1", "1793", "pancreatic cancer", "pancreatic cancer", "Amino acid", "Title", "0", "Mutations N34S and P55S of the SPINK1 gene in patients with chronic pancreatitis or pancreatic cancer and in healthy subjects: a report from Finland.", "", "188 cancer, 1 cancer, 188 tumour, 459 individuals", "1", "1", "55", "55", "P", "S" ], [ "P38398-1", "24078348", "672", "BRCA1", "2394", "ovarian cancer", "ovarian cancer", "Amino acid", "Result", "6", "RESULTS: The most common BRCA1/BRCA2 mutations were identified in 30 patients with ovarian cancer.", "MutFound", "30 cancer", "1", "1", "61", "61", "C", "G" ], [ "P18074-1", "18415712", "2068", "XPD", "1612, 3459", "breast cancer, breast carcinoma", "BC", "Amino acid", "Result", "4", "The genotype frequency for homozygote A/A in XPD exon 6 (Arg156Arg, C/A) were significantly different between BC and control groups (P < 0.0001, odds ratio = 2.14; 95% confidence interval 1.44-3.17).", "ASSOC", "113 subjects, 114 patients", "1", "1", "156", "156", "R", "R" ], [ "P18074-1", "18415712", "2068", "XPD", "1612, 3459", "breast cancer, breast carcinoma", "BC", "Amino acid", "Conclusion", "5", "The data indicate a possible role for XPD (Arg156Arg, C/A) polymorphisms in BC susceptibility.", "ASSOC", "113 subjects, 114 patients", "1", "1", "156", "156", "R", "R" ], [ "P15056-1", "27655717", "673", "BRAF", "1909", "melanoma", "BRAF-V600E melanoma", "Amino acid", "Title", "0", "Targeting Notch enhances the efficacy of ERK inhibitors in BRAF-V600E melanoma.", "", "", "1", "1", "600", "600", "V", "E" ], [ "P09211-1", "28176509", "2950", "GSTP1", "9952", "acute lymphocytic leukemia", "acute lymphoblastic leukemia", "Amino acid", "Title", "0", "Role of polymorphisms of GSTM1, GSTT1 and GSTP1 Ile105Val in childhood acute lymphoblastic leukemia risk: an updated meta-analysis.", "ASSOC", "", "1", "1", "105", "105", "I", "V" ], [ "P09211-1", "28176509", "2950", "GSTP1", "9952", "acute lymphocytic leukemia", "acute lymphoblastic leukemia", "Amino acid", "Introduction", "1", "INTRODUCTION: The association between glutathione-S-transferase polymorphisms (GSTM1, GSTT1 and GSTP1 Ile105Val) and risk of childhood acute lymphoblastic leukemia (ALL) remains controversial.", "ASSOC", "", "1", "1", "105", "105", "I", "V" ], [ "P00533-1", "23518631", "1956", "epidermal growth factor receptor", "4552", "large cell carcinoma", "LCNEC", "Amino acid", "Conclusion", "5", "Tumor cells were separately collected from components of both the LCNEC and adenocarcinoma, and a mutational analysis of the epidermal growth factor receptor (EGFR) gene demonstrated that both components had the same L861Q mutation at exon 21.", "", "1 female", "1", "1", "861", "861", "L", "Q" ], [ "P00533-1", "23518631", "1956", "epidermal growth factor receptor", "299", "adenocarcinoma", "adenocarcinoma", "Amino acid", "Conclusion", "5", "Tumor cells were separately collected from components of both the LCNEC and adenocarcinoma, and a mutational analysis of the epidermal growth factor receptor (EGFR) gene demonstrated that both components had the same L861Q mutation at exon 21.", "", "1 female", "1", "1", "861", "861", "L", "Q" ], [ "P09211-1", "22502660", "2950", "GSTP1", "3070, 5076", "malignant glioma, mixed glioma", "adult gliomas", "Amino acid", "Result", "8", "RESULTS: The quantitative synthesis showed no significant evidence to indicate an association exists between the presence of a GSTM1, GSTT1 or GSTP1 Ile105Val haplotype polymorphism and the risk of adult gliomas (OR, 1.008, 1.246, 1.061 respectively; 95% CI, 0.901-1.129, 0.963-1.611, 0.653-1.724 respectively).", "", "", "1", "1", "105", "105", "I", "V" ], [ "Q6P1J9-1", "17130827", "79577", "parafibromin", "2154", "nephroblastoma", "Wilms tumors", "Amino acid", "Result", "5", "In addition, two novel HRPT2 point mutations, causing K34Q and R292K changes in parafibromin, were detected in one clear cell carcinoma and one Wilms tumor, respectively.", "MutFound", "4 tumors, 1 carcinoma, 1 tumor", "1", "1", "34", "34", "K", "Q" ], [ "Q6P1J9-1", "17130827", "79577", "parafibromin", "4464, 4473, 4450, 4467, 4465, 4471", "collecting duct carcinoma, sarcomatoid renal cell carcinoma, renal cell carcinoma, clear cell renal cell carcinoma, papillary renal cell carcinoma, chromophobe renal cell carcinoma", "clear cell carcinoma", "Amino acid", "Result", "5", "In addition, two novel HRPT2 point mutations, causing K34Q and R292K changes in parafibromin, were detected in one clear cell carcinoma and one Wilms tumor, respectively.", "MutFound", "4 tumors, 1 carcinoma, 1 tumor", "1", "1", "292", "292", "R", "K" ], [ "Q6P1J9-1", "17130827", "79577", "parafibromin", "4464, 4473, 4450, 4467, 4465, 4471", "collecting duct carcinoma, sarcomatoid renal cell carcinoma, renal cell carcinoma, clear cell renal cell carcinoma, papillary renal cell carcinoma, chromophobe renal cell carcinoma", "renal cell carcinomas", "Amino acid", "Result", "5", "In addition, two novel HRPT2 point mutations, causing K34Q and R292K changes in parafibromin, were detected in one clear cell carcinoma and one Wilms tumor, respectively.", "MutFound", "4 tumors, 1 carcinoma, 1 tumor", "1", "1", "292", "292", "R", "K" ], [ "Q6P1J9-1", "17130827", "79577", "parafibromin", "4464, 4473, 4450, 4467, 4465, 4471", "collecting duct carcinoma, sarcomatoid renal cell carcinoma, renal cell carcinoma, clear cell renal cell carcinoma, papillary renal cell carcinoma, chromophobe renal cell carcinoma", "clear cell carcinoma", "Amino acid", "Result", "5", "In addition, two novel HRPT2 point mutations, causing K34Q and R292K changes in parafibromin, were detected in one clear cell carcinoma and one Wilms tumor, respectively.", "MutFound", "4 tumors, 1 carcinoma, 1 tumor", "1", "1", "34", "34", "K", "Q" ], [ "Q6P1J9-1", "17130827", "79577", "parafibromin", "2154", "nephroblastoma", "Wilms tumor", "Amino acid", "Result", "5", "In addition, two novel HRPT2 point mutations, causing K34Q and R292K changes in parafibromin, were detected in one clear cell carcinoma and one Wilms tumor, respectively.", "MutFound", "4 tumors, 1 carcinoma, 1 tumor", "1", "1", "292", "292", "R", "K" ], [ "Q6P1J9-1", "17130827", "79577", "parafibromin", "2154", "nephroblastoma", "Wilms tumors", "Amino acid", "Result", "5", "In addition, two novel HRPT2 point mutations, causing K34Q and R292K changes in parafibromin, were detected in one clear cell carcinoma and one Wilms tumor, respectively.", "MutFound", "4 tumors, 1 carcinoma, 1 tumor", "1", "1", "292", "292", "R", "K" ], [ "Q6P1J9-1", "17130827", "79577", "parafibromin", "263", "kidney cancer", "sporadic renal tumors", "Amino acid", "Result", "5", "In addition, two novel HRPT2 point mutations, causing K34Q and R292K changes in parafibromin, were detected in one clear cell carcinoma and one Wilms tumor, respectively.", "MutFound", "4 tumors, 1 carcinoma, 1 tumor", "1", "1", "34", "34", "K", "Q" ], [ "Q6P1J9-1", "17130827", "79577", "parafibromin", "2154", "nephroblastoma", "Wilms tumor", "Amino acid", "Result", "5", "In addition, two novel HRPT2 point mutations, causing K34Q and R292K changes in parafibromin, were detected in one clear cell carcinoma and one Wilms tumor, respectively.", "MutFound", "4 tumors, 1 carcinoma, 1 tumor", "1", "1", "34", "34", "K", "Q" ], [ "Q6P1J9-1", "17130827", "79577", "parafibromin", "4464, 4473, 4450, 4467, 4465, 4471", "collecting duct carcinoma, sarcomatoid renal cell carcinoma, renal cell carcinoma, clear cell renal cell carcinoma, papillary renal cell carcinoma, chromophobe renal cell carcinoma", "renal cell carcinomas", "Amino acid", "Result", "5", "In addition, two novel HRPT2 point mutations, causing K34Q and R292K changes in parafibromin, were detected in one clear cell carcinoma and one Wilms tumor, respectively.", "MutFound", "4 tumors, 1 carcinoma, 1 tumor", "1", "1", "34", "34", "K", "Q" ], [ "Q6P1J9-1", "17130827", "79577", "parafibromin", "263", "kidney cancer", "sporadic renal tumors", "Amino acid", "Result", "5", "In addition, two novel HRPT2 point mutations, causing K34Q and R292K changes in parafibromin, were detected in one clear cell carcinoma and one Wilms tumor, respectively.", "MutFound", "4 tumors, 1 carcinoma, 1 tumor", "1", "1", "292", "292", "R", "K" ], [ "O75874-1", "23527265", "3417", "IDH1", "3070, 5076", "malignant glioma, mixed glioma", "glioma", "Amino acid", "Conclusion", "7", "This glioma xenograft is the first to display a pure oligodendroglioma histology and expression of R132H.", "", "1 tumors, 1 tumor", "1", "1", "132", "132", "R", "H" ], [ "O75874-1", "23527265", "3417", "IDH1", "3181", "oligodendroglioma", "oligodendroglioma", "Amino acid", "Conclusion", "7", "This glioma xenograft is the first to display a pure oligodendroglioma histology and expression of R132H.", "", "1 tumors, 1 tumor", "1", "1", "132", "132", "R", "H" ], [ "Q9UM73-1", "27655666", "238", "ALK", "769", "neuroblastoma", "neuroblastoma", "Amino acid", "Title", "0", "Smac mimetic LCL161 supports neuroblastoma chemotherapy in a drug class-dependent manner and synergistically interacts with ALK inhibitor TAE684 in cells with ALK mutation F1174L.", "", "", "1", "1", "1174", "1174", "F", "L" ], [ "Q9UM73-1", "27655666", "238", "ALK", "60058", "lymphoma", "anaplastic lymphoma", "Amino acid", "Result", "3", "In contrast, combination of anthracyclines or topoisomerase inhibitors with LCL161 showed a synergism for single drugs and/or cell lines only.Furthermore, we could show that insensibility to LCL161-mediated sensitization for chemotherapeutics is associated with aberrant activation of anaplastic lymphoma kinase (ALK) by common mutation F1174L.", "ASSOC", "", "1", "1", "1174", "1174", "F", "L" ], [ "O60674-1", "19135773", "3717", "JAK2", "4960", "bone marrow cancer", "MPDs", "Amino acid", "Introduction", "1", "Myeloproliferative disorders (MPDs) are often associated with the presence of the JAK2-V617F mutation in hematopoietic cells.", "ASSOC", "", "1", "1", "617", "617", "V", "F" ], [ "O60674-1", "19135773", "3717", "JAK2", "4960", "bone marrow cancer", "Myeloproliferative disorders", "Amino acid", "Introduction", "1", "Myeloproliferative disorders (MPDs) are often associated with the presence of the JAK2-V617F mutation in hematopoietic cells.", "ASSOC", "", "1", "1", "617", "617", "V", "F" ], [ "O60674-1", "19135773", "3717", "JAK2", "4960", "bone marrow cancer", "myeloproliferative disorders", "Amino acid", "Title", "0", "Bone marrow mesenchymal stromal cells of patients with myeloproliferative disorders do not carry the JAK2-V617F mutation.", "", "", "1", "1", "617", "617", "V", "F" ], [ "O60674-1", "20955399", "3717", "JAK2", "4972", "myelodysplastic/myeloproliferative neoplasm", "myelodysplastic and/or myeloproliferative syndromes", "Amino acid", "Method", "3", "Mutations in TET2, RUNX1 and JAK2(V617F) are involved in myelodysplastic and/or myeloproliferative syndromes, and more specifically in CMML but were not found in JMML.", "ASSOC", "68 patients", "1", "1", "617", "617", "V", "F" ], [ "O60674-1", "20955399", "3717", "JAK2", "50458", "juvenile myelomonocytic leukemia", "CMML", "Amino acid", "Method", "3", "Mutations in TET2, RUNX1 and JAK2(V617F) are involved in myelodysplastic and/or myeloproliferative syndromes, and more specifically in CMML but were not found in JMML.", "ASSOC", "68 patients", "1", "1", "617", "617", "V", "F" ], [ "P31213-1", "11355945", "6716", "SRD5A2", "10283", "prostate cancer", "PC", "Amino acid", "Result", "5", "Here, we report that the prevalence of the A49T variant in 449 Finnish PC patients was 6.0%, not significantly different from 6.3% observed in 223 patients with benign prostatic hyperplasia or 5.8% in 588 population-based controls (odds ratio for PC 1.04, 95% C.I. 0.62-1.76, P = 0.89).", "", "449 patients", "1", "1", "49", "49", "A", "T" ], [ "P31213-1", "11355945", "6716", "SRD5A2", "10283", "prostate cancer", "prostate cancer", "Amino acid", "Title", "0", "A missense substitution A49T in the steroid 5-alpha-reductase gene (SRD5A2) is not associated with prostate cancer in Finland.", "ASSOC", "449 patients", "1", "1", "49", "49", "A", "T" ], [ "P31213-1", "11355945", "6716", "SRD5A2", "10283", "prostate cancer", "prostate cancer", "Amino acid", "Conclusion", "7", "Our results argue against a prominent role of the A49T variant as a genetic risk factor for prostate cancer development and progression in the Finnish population.", "", "449 patients", "1", "1", "49", "49", "A", "T" ], [ "P31213-1", "11355945", "6716", "SRD5A2", "10283", "prostate cancer", "prostate cancer", "Amino acid", "Result", "3", "The A49T variant was recently associated with 2.5 to 3.28-fold increased risk of prostate cancer (PC) in African-American and Hispanic men (Makridakis et al, 1999).", "ASSOC", "449 patients", "1", "1", "49", "49", "A", "T" ], [ "Q16678-1", "22504876", "1545", "CYP1B1", "10283", "prostate cancer", "Prostate cancer", "Amino acid", "Title", "0", "Prostate cancer risk and aggressiveness associated with the CYP1B1 4326C/G (Leu432Val) polymorphism: a meta-analysis of 2788 cases and 2968 controls.", "ASSOC", "2968 controls, 2788 cases", "1", "1", "432", "432", "L", "V" ], [ "P01111-1", "14695143", "4893", "N-RAS", "1909", "melanoma", "melanoma", "Amino acid", "Method", "4", "EXPERIMENTAL DESIGN: We screened 85 melanoma samples for the most common B-RAF and N-RAS mutations found in melanoma using a site-directed mutagenesis-based detection technique.", "MutFound", "6 metastases, 15 metastases, 5 metastases", "1", "1", "61", "61", "Q", "K" ], [ "P01111-1", "14695143", "4893", "N-RAS", "1909", "melanoma", "melanoma", "Amino acid", "Method", "4", "EXPERIMENTAL DESIGN: We screened 85 melanoma samples for the most common B-RAF and N-RAS mutations found in melanoma using a site-directed mutagenesis-based detection technique.", "MutFound", "6 metastases, 15 metastases, 5 metastases", "1", "1", "61", "61", "Q", "R" ], [ "P00533-1", "27508108", "1956", "EGFR", "3908", "lung non-small cell carcinoma", "non-small cell lung cancer", "Amino acid", "Title", "0", "Non-invasive urine testing of EGFR activating mutation and T790M resistance mutation in non-small cell lung cancer.", "", "", "1", "1", "790", "790", "T", "M" ], [ "P15056-1", "23528169", "673", "BRAF", "9256", "colorectal cancer", "colorectal cancer", "Amino acid", "Result", "13", "BRAF mutation in both tissues was detected in the 4 patients.", "MutFound", "33 patients, 4 patients, 3 cases, 132 patients, 17 specimen, 1 case, 9 patients", "1", "1", "600", "600", "V", "E" ], [ "P21964-1", "18424824", "1312", "COMT", "1612", "breast cancer", "breast cancer", "Amino acid", "Introduction", "2", "In humans there is a single nucleotide polymorphism in COMT gene (COMT val158met) that has been associated with an increased risk for developing breast cancer.", "ASSOC", "90 tumors", "1", "1", "158", "158", "V", "M" ], [ "Q92889-1", "23619551", "2072", "XPF", "1612", "breast cancer", "breast cancer", "Amino acid", "Title", "0", "Methodological remarks concerning a recent meta-analysis on XPG Asp1104His and XPF Arg415Gln polymorphisms and breast cancer risk.", "", "", "1", "1", "415", "415", "R", "Q" ], [ "P00519-1", "20963643", "25", "ABL", "8552", "chronic myeloid leukemia", "CML", "Amino acid", "Introduction", "2", "We report a chronic-phase CML patient undergoing IM treatment, who showed the overt existence of the T315I mutation after 15 months.", "", "1 patient", "1", "1", "315", "315", "T", "I" ], [ "P15056-1", "27666765", "673", "BRAF", "1909", "melanoma", "melanoma", "Amino acid", "Conclusion", "12", "These findings suggest that BRAF V600E mutation in CN of SLN may be useful as an adverse predictive biomarker in patients with melanoma.", "", "12 cases, 19 cases, 30 cases, 20 specimens", "1", "1", "600", "600", "V", "E" ], [ "P15056-1", "27666765", "673", "BRAF", "1909", "melanoma", "primary cutaneous melanoma", "Amino acid", "Title", "0", "Clinical significance of BRAF V600E mutational status in capsular nevi of sentinel lymph nodes in patients with primary cutaneous melanoma.", "", "12 cases, 19 cases, 30 cases, 20 specimens", "1", "1", "600", "600", "V", "E" ], [ "Q13315-1", "19147782", "472", "ATM", "1793", "pancreatic cancer", "pancreatic cancer", "Amino acid", "Result", "4", "RESULTS: The homozygous mutant genotype of LIG3 G-39A [odds ratio (OR), 0.23; 95% confidence interval (CI), 0.06-0.82; P = 0.027] and ATM D1853N (OR, 2.55; 95% CI, 1.08-6.00; P = 0.032) was significantly associated with altered risk for pancreatic cancer.", "ASSOC", "1 cancer, 780 controls", "1", "1", "1853", "1853", "D", "N" ], [ "P00533-1", "23527257", "1956", "EGFR", "3908", "lung non-small cell carcinoma", "NSCLC", "Amino acid", "Conclusion", "12", "In a conclusion, our findings offer preclinical proof of principle for combined inhibition as a promising treatment strategy for NSCLC, especially for patients in whom current EGFR-targeted treatments fail due to the presence of the T790M-EGFR-mutation or high c-MET expression.", "", "", "1", "1", "790", "790", "T", "M" ], [ "Q08334-1", "23519428", "3588", "IL-10RB", "684", "hepatocellular carcinoma", "hepatoma", "Amino acid", "Result", "7", "RESULTS: IL-10RB K47E was associated with chronic HBV infection but not with hepatoma in the Korean population.", "ASSOC", "1,000 patients", "1", "1", "47", "47", "K", "E" ], [ "P04637-1", "27517620", "7157", "p53", "219", "colon cancer", "colon cancer", "Amino acid", "Title", "0", "Inhibition of glucosylceramide synthase eliminates the oncogenic function of p53 R273H mutant in the epithelial-mesenchymal transition and induced pluripotency of colon cancer cells.", "", "", "1", "1", "273", "273", "R", "H" ], [ "P01111-1", "25252692", "4893", "NRAS", "1909", "melanoma", "melanoma", "Amino acid", "Introduction", "3", "With concomitant p16INK4a inactivation, KrasG12D or NrasQ61R expression efficiently promoted melanoma in vivo, whereas NrasG12D did not.", "ASSOC", "", "1", "1", "61", "61", "Q", "R" ], [ "O75874-1", "20077503", "3417", "IDH1", "3070, 5076", "malignant glioma, mixed glioma", "glioma", "Amino acid", "Conclusion", "13", "R132H mutated IDH1 may explain the segregation in distinct glioma subtypes.", "", "", "1", "1", "132", "132", "R", "H" ], [ "O60674-1", "17133423", "3717", "JAK2", "4971", "myelofibrosis", "myelofibrosis", "Amino acid", "Title", "0", "Clearance of the Janus kinase 2 (JAK2) V617F mutation after allogeneic stem cell transplantation in a patient with myelofibrosis with myeloid metaplasia.", "", "", "1", "1", "617", "617", "V", "F" ], [ "O60674-1", "17133423", "3717", "JAK2", "4971", "myelofibrosis", "myeloid metaplasia", "Amino acid", "Title", "0", "Clearance of the Janus kinase 2 (JAK2) V617F mutation after allogeneic stem cell transplantation in a patient with myelofibrosis with myeloid metaplasia.", "", "", "1", "1", "617", "617", "V", "F" ], [ "P41597-1", "22612293", "729230", "CCR2", "10283", "prostate cancer", "prostate cancer", "Amino acid", "Method", "3", "Individuals with AA genotype or at least one A allele of CCR2 V64I gene polymorphism had a higher risk for prostate cancer as compared with those with GG genotype (p=0.010 and p=0.028, respectively).", "ASSOC", "156 patients, 1 cancer, 152 subjects", "1", "1", "64", "64", "V", "I" ], [ "P41597-1", "22612293", "729230", "CCR2", "10283", "prostate cancer", "prostate cancer", "Amino acid", "Conclusion", "8", "Our data indicate that gene polymorphism of CCR2 V64I may influence the susceptibility and clinicopathological characteristics of prostate cancer and CCR5 \u039432 allele may also be an important risk factor for prostate cancer in Turkish men population.", "ASSOC", "156 patients, 1 cancer, 152 subjects", "1", "1", "64", "64", "V", "I" ], [ "P00519-1", "17130834", "25", "E255K BCR/ABL", "8552", "chronic myeloid leukemia", "CML blast crisis", "Amino acid", "Conclusion", "7", "Rottlerin also enhanced the cytotoxic effect of imatinib in leukemic cells from patients with CML blast crisis and Ph-positive ALL or a cell line expressing the imatinib-resistant E255K BCR/ABL mutant.", "", "", "1", "1", "255", "255", "E", "K" ] ] }, "readme": "Name\n - Human Literature Mutations\n\nVersion\n - 1.5.23\n\nCreated on\n - 2020-04-03T17:37:22.702254\n\nModified on\n - 2020-04-03T17:43:08.293957\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Xavier Holmes [xavierh@email.gwu.edu]\n\nAuthors\n - Maria Martin [martin@ebi.ac.uk], Preethi Vasudev [pvasudev@ebi.ac.uk]\n\nChecksum\n - \n\nUsability Domain\n - The Human Literature Mutation dataset contains human [taxid:9606] mutation data extracted from literature using the DIMEX tool. The dataset contains only the mutations that have amino acid information and position in the mutation mention column.. If you use this dataset provide proper attribution to GlyGen and OncoMX.\n\nDescription Domain\n Keywords\n - single-nucleotide variations (nsSNVs)\n - literature mutations\n - dbSNP\n - disease\n - ClinVar\n\n Pipeline Steps\n - Step-1: The script extracts the mutation data only for the mutations that have amino acid information and position from the input file and maps the UniProtKB accession 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: human_cancer_mutation_literature.csv\n URI: https://data.glygen.org/ln2wwwdata/source/human_cancer_mutation_literature.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_mutation_literature.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/human_protein_mutation_literature.csv\n Name: human_protein_mutation_literature.stat.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/human_protein_mutation_literature.stat.csv\n\nFields\n Name: \"doid\"\n Description: \"Disease ID from Disease ontology database\"\n Unique Values: \"255\"\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: \"459\"\n Name: \"entrez_id\"\n Description: \"Unique\n Unique Values: \"463\"\n Name: \"do_name\"\n Description: \"Disease Ontology term or name for the disease assigned to the Disease Ontology identifier\"\n Unique Values: \"255\"\n Name: \"abstract_extraction\"\n Description: \"Portion of the abstract from which sentence was extracted\"\n Unique Values: \"5\"\n Name: \"sentence_text\"\n Description: \"Text of sentence extracted\"\n Unique Values: \"7159\"\n Name: \"patient_control_counts\"\n Description: \"Counts of patients and controls reported in the publication\n Unique Values: \"2295\"\n Name: \"alt_aa\"\n Description: \"Altered amino acid residue\"\n Unique Values: \"20\"\n Name: \"ref_aa\"\n Description: \"Reference amino acid residue\"\n Unique Values: \"20\"\n Name: \"gene_mention\"\n Description: \"Specific form/spelling of gene or transcript mentioned in the retrieved publication\"\n Unique Values: \"780\"\n Name: \"sentence_number\"\n Description: \"Number of sentence in abstract\"\n Unique Values: \"24\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"697\"\n Name: \"is_review\"\n Description: \"Denotes whether the publication is a review\"\n Unique Values: \"1\"\n Name: \"pmid\"\n Description: \"NCBI PubMed database Identifier\"\n Unique Values: \"4666\"\n Name: \"extraction_method\"\n Description: \"Denotes confidence in the reported association of the mutation and disease\"\n Unique Values: \"3\"\n Name: \"mutation_type\"\n Description: \"Types of nonsynonymous substitution mutations\"\n Unique Values: \"2\"\n Name: \"disease_mention\"\n Description: \"Specific form/spelling of disease mentioned in the retrieved publication\"\n Unique Values: \"1176\"\n Name: \"is_meta\"\n Description: \"Denotes whether the publication is a meta-analysis\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.5.23/reviewed/human_protein_mutation_literature.csv" }