Publications:

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Evaluation of AlphaFold structure-based protein stability prediction on missense variations in cancer.

Frontiers In Genetics

Keskin Karakoyun, Hilal H; Yüksel, Şirin K ŞK; Amanoglu, Ilayda I; Naserikhojasteh, Lara L; Yeşilyurt, Ahmet A; Yakıcıer, Cengiz C; Timuçin, Emel E; Akyerli, Cemaliye B CB

Publication Date: 2023

Variant appearance in text: TP53: I251L

PubMed Link: 36896237

Variant Present in the following documents:

• Table1.xlsx, sheet 1

View BVdb publication page

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Integration of deep learning with Ramachandran plot molecular dynamics simulation for genetic variant classification.

Iscience

Tam, Benjamin B; Qin, Zixin Z; Zhao, Bojin B; Wang, San Ming SM; Lei, Chon Lok CL

Publication Date: 2023-03-17

Variant appearance in text: TP53: 751A>C; I251L

PubMed Link: 36879825

Variant Present in the following documents:

• mmc2.xlsx, sheet 1
• mmc3.xlsx, sheet 1
• mmc4.xlsx, sheet 1

View BVdb publication page

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Integrative pan-cancer genomic and transcriptomic analyses of refractory metastatic cancer.

Cancer Discovery

Pradat, Yoann Y; Viot, Julien J; Yurchenko, Andrey A AA; Gunbin, Konstantin K; Cerbone, Luigi L; Deloger, Marc M; Grisay, Guillaume G; Verlingue, Loic L; Scott, Veronique V; Padioleau, Ismael I; Panunzi, Leonardo L; Michiels, Stefan S; Hollebecque, Antoine A; Jules-Clement, Gerome G; Mezquita, Laura L; Laine, Antoine A; Loriot, Yohann Y; Besse, Benjamin B; Friboulet, Luc L; Andre, Fabrice F; Cournede, Paul-Henry PH; Gautheret, Daniel D; Nikolaev, Sergey I SI

Publication Date: 2023-03-02

Variant appearance in text: TP53: 751A>C; Ile251Leu; rs730882007

PubMed Link: 36862804

Variant Present in the following documents:

• cd-22-0966_supplementary_tables_s1-s11_suppst1.xlsx, sheet 6

View BVdb publication page

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Network expansion of genetic associations defines a pleiotropy map of human cell biology.

Nature Genetics

Barrio-Hernandez, Inigo I; Schwartzentruber, Jeremy J; Shrivastava, Anjali A; Del-Toro, Noemi N; Gonzalez, Asier A; Zhang, Qian Q; Mountjoy, Edward E; Suveges, Daniel D; Ochoa, David D; Ghoussaini, Maya M; Bradley, Glyn G; Hermjakob, Henning H; Orchard, Sandra S; Dunham, Ian I; Anderson, Carl A CA; Porras, Pablo P; Beltrao, Pedro P

Publication Date: 2023-02-23

Variant appearance in text: TP53: 751A>C; Ile251Leu

PubMed Link: 36823319

Variant Present in the following documents:

• 41588_2023_1327_MOESM4_ESM.xlsx, sheet 6

View BVdb publication page

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Analysis of single-nucleotide polymorphisms in genes associated with triple-negative breast cancer.

Frontiers In Genetics

G, Vigneshwaran V; Hasan, Qurratulain Annie QA; Kumar, Rahul R; Eranki, Avinash A

Publication Date: 2022

Variant appearance in text: TP53: I251L

PubMed Link: 36561320

Variant Present in the following documents:

• Table3.xlsx, sheet 1
• Table2.xlsx, sheet 7

View BVdb publication page

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A sex-informed approach to improve the personalised decision making process in myelodysplastic syndromes: a multicentre, observational cohort study.

The Lancet. Haematology

,

Publication Date: 2022-11-24

Variant appearance in text: TP53: 751A>C

PubMed Link: 36436542

Variant Present in the following documents:

• mmc2.xlsx, sheet 1

View BVdb publication page

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NF1 loss of function as an alternative initiating event in pancreatic ductal adenocarcinoma.

Cell Reports

Ramakrishnan, Gopalakrishnan G; Parajuli, Parash P; Singh, Pura P; Friend, Creighton C; Hurwitz, Eric E; Prunier, Celine C; Razzaque, Mohammed S MS; Xu, Keli K; Atfi, Azeddine A

Publication Date: 2022-11-08

Variant appearance in text: TP53: I251L

PubMed Link: 36351408

Variant Present in the following documents:

• NIHMS1848910-supplement-2.xlsx, sheet 3
• NIHMS1848910-supplement-2.xlsx, sheet 2

View BVdb publication page

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Genomic characterization reveals distinct mutation landscapes and therapeutic implications in neuroendocrine carcinomas of the gastrointestinal tract.

Cancer Communications (London, England)

Wu, Huanwen H; Yu, Zicheng Z; Liu, Yueping Y; Guo, Lei L; Teng, Lianghong L; Guo, Lingchuan L; Liang, Li L; Wang, Jing J; Gao, Jie J; Li, Ruiyu R; Yang, Ling L; Nie, Xiu X; Su, Dan D; Liang, Zhiyong Z

Publication Date: 2022-10-20

Variant appearance in text: TP53: 751A>C; I251L; rs730882007

PubMed Link: 36264285

Variant Present in the following documents:

• CAC2-42-1367-s002.xlsx, sheet 3

View BVdb publication page

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CTCF DNA-binding domain undergoes dynamic and selective protein-protein interactions.

Iscience

Zhou, Rong R; Tian, Kai K; Huang, Jie J; Duan, Wenjia W; Fu, Hongye H; Feng, Ying Y; Wang, Hui H; Jiang, Yongpeng Y; Li, Yuanjun Y; Wang, Rui R; Hu, Jiazhi J; Ma, Hanhui H; Qi, Zhi Z; Ji, Xiong X

Publication Date: 2022-09-16

Variant appearance in text: p53: 751A>C

PubMed Link: 36117989

Variant Present in the following documents:

• mmc4.xlsx, sheet 1

View BVdb publication page

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The spectrum of subclonal TP53 mutations in chronic lymphocytic leukemia: A next generation sequencing retrospective study.

Hematological Oncology

De Luca, Giuseppa G; Cerruti, Giannamaria G; Lastraioli, Sonia S; Conte, Romana R; Ibatici, Adalberto A; Di Felice, Nikki N; Morabito, Fortunato F; Monti, Paola P; Fronza, Gilberto G; Matis, Serena S; Colombo, Monica M; Fabris, Sonia S; Ciarrocchi, Alessia A; Neri, Antonino A; Menichini, Paola P; Ferrarini, Manlio M; Nozza, Paolo P; Fais, Franco F; Cutrona, Giovanna G; Dono, Mariella M

Publication Date: 2022-08-12

Variant appearance in text: TP53: 751A>C

PubMed Link: 35961859

Variant Present in the following documents:

• Main text
• HON-40-962.pdf

View BVdb publication page

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A computational and structural analysis of germline and somatic variants affecting the DDR mechanism, and their impact on human diseases.

Scientific Reports

Magraner-Pardo, Lorena L; Laskowski, Roman A RA; Pons, Tirso T; Thornton, Janet M JM

Publication Date: 2021-07-12

Variant appearance in text: rs730882007

PubMed Link: 34253785

Variant Present in the following documents:

• 41598_2021_93715_MOESM3_ESM.xlsx, sheet 4
• 41598_2021_93715_MOESM3_ESM.xlsx, sheet 6
• 41598_2021_93715_MOESM3_ESM.xlsx, sheet 2
• 41598_2021_93715_MOESM3_ESM.xlsx, sheet 5

View BVdb publication page

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Mutation profile and immunoscore signature in thymic carcinomas: An exploratory study and review of the literature.

Thoracic Cancer

Asselta, Rosanna R; Di Tommaso, Luca L; Perrino, Matteo M; Destro, Annarita A; Giordano, Laura L; Cardamone, Giulia G; Rubino, Luca L; Santoro, Armando A; Duga, Stefano S; Zucali, Paolo Andrea PA

Publication Date: 2021-05

Variant appearance in text: TP53: 751A>C; I251L

PubMed Link: 33704917

Variant Present in the following documents:

• TCA-12-1271-s003.xls, sheet 1

View BVdb publication page

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Pan-cancer circulating tumor DNA detection in over 10,000 Chinese patients.

Nature Communications

Zhang, Yongliang Y; Yao, Yu Y; Xu, Yaping Y; Li, Lifeng L; Gong, Yan Y; Zhang, Kai K; Zhang, Meng M; Guan, Yanfang Y; Chang, Lianpeng L; Xia, Xuefeng X; Li, Lin L; Jia, Shuqin S; Zeng, Qiang Q

Publication Date: 2021-01-04

Variant appearance in text: TP53: 751A>C; I251L

PubMed Link: 33397889

Variant Present in the following documents:

• 41467_2020_20162_MOESM6_ESM.xlsx, sheet 1

View BVdb publication page

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Identification of pathogenic missense mutations using protein stability predictors.

Scientific Reports

Gerasimavicius, Lukas L; Liu, Xin X; Marsh, Joseph A JA

Publication Date: 2020-09-21

Variant appearance in text: TP53: I251L

PubMed Link: 32958805

Variant Present in the following documents:

• 41598_2020_72404_MOESM2_ESM.xlsx, sheet 2

View BVdb publication page

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Defining relative mutational difficulty to understand cancer formation.

Cell Discovery

Shan, Lin L; Yu, Jiao J; He, Zhengjin Z; Chen, Shishuang S; Liu, Mingxian M; Ding, Hongyu H; Xu, Liang L; Zhao, Jie J; Yang, Ailing A; Jiang, Hai H

Publication Date: 2020

Variant appearance in text: p53: I251L

PubMed Link: 32704382

Variant Present in the following documents:

• 41421_2020_177_MOESM5_ESM.xlsx, sheet 1
• 41421_2020_177_MOESM6_ESM.xlsx, sheet 1

View BVdb publication page

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Criteria of the German Consortium for Hereditary Breast and Ovarian Cancer for the Classification of Germline Sequence Variants in Risk Genes for Hereditary Breast and Ovarian Cancer.

Geburtshilfe Und Frauenheilkunde

Wappenschmidt, Barbara B; Hauke, Jan J; Faust, Ulrike U; Niederacher, Dieter D; Wiesmüller, Lisa L; Schmidt, Gunnar G; Groß, Evi E; Gehrig, Andrea A; Sutter, Christian C; Ramser, Juliane J; Rump, Andreas A; Arnold, Norbert N; Meindl, Alfons A

Publication Date: 2020-04

Variant appearance in text: p53: Ile251Leu

PubMed Link: 32322110

Variant Present in the following documents:

• Main text

View BVdb publication page

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Recurrent PTPRT/JAK2 mutations in lung adenocarcinoma among African Americans.

Nature Communications

Mitchell, Khadijah A KA; Nichols, Noah N; Tang, Wei W; Walling, Jennifer J; Stevenson, Holly H; Pineda, Marbin M; Stefanescu, Roxana R; Edelman, Daniel C DC; Girvin, Andrew T AT; Zingone, Adriana A; Sinha, Sanju S; Bowman, Elise E; Rossi, Emily L EL; Arauz, Rony F RF; Jack Zhu, Yuelin Y; Lack, Justin J; Weingartner, Elizabeth E; Waterfall, Joshua J JJ; Pine, Sharon R SR; Simmons, John J; Meltzer, Paul P; Ryan, Bríd M BM

Publication Date: 2019-12-16

Variant appearance in text: TP53: 751A>C; I251L

PubMed Link: 31844068

Variant Present in the following documents:

• 41467_2019_13732_MOESM12_ESM.xlsx, sheet 1

View BVdb publication page

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Optimizing clinical exome design and parallel gene-testing for recessive genetic conditions in preconception carrier screening: Translational research genomic data from 14,125 exomes.

Plos Genetics

Capalbo, Antonio A; Valero, Roberto Alonso RA; Jimenez-Almazan, Jorge J; Pardo, Pere Mir PM; Fabiani, Marco M; Jiménez, David D; Simon, Carlos C; Rodriguez, Julio Martin JM

Publication Date: 2019-10

Variant appearance in text: TP53: 751A>C; rs730882007

PubMed Link: 31589614

Variant Present in the following documents:

• pgen.1008409.s003.xlsx, sheet 1
• pgen.1008409.s001.xlsx, sheet 1

View BVdb publication page

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REVEL and BayesDel outperform other in silico meta-predictors for clinical variant classification.

Scientific Reports

Tian, Yuan Y; Pesaran, Tina T; Chamberlin, Adam A; Fenwick, R Bryn RB; Li, Shuwei S; Gau, Chia-Ling CL; Chao, Elizabeth C EC; Lu, Hsiao-Mei HM; Black, Mary Helen MH; Qian, Dajun D

Publication Date: 2019-09-04

Variant appearance in text: TP53: 751A>C; I251L

PubMed Link: 31484976

Variant Present in the following documents:

• 41598_2019_49224_MOESM2_ESM.xlsx, sheet 1

View BVdb publication page

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Finding driver mutations in cancer: Elucidating the role of background mutational processes.

Plos Computational Biology

Brown, Anna-Leigh AL; Li, Minghui M; Goncearenco, Alexander A; Panchenko, Anna R AR

Publication Date: 2019-04

Variant appearance in text: TP53: I251L

PubMed Link: 31034466

Variant Present in the following documents:

• pcbi.1006981.s010.xlsx, sheet 1

View BVdb publication page

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An enhanced workflow for variant interpretation in UniProtKB/Swiss-Prot improves consistency and reuse in ClinVar.

Database : The Journal Of Biological Databases And Curation

Famiglietti, M L ML; Estreicher, A A; Breuza, L L; Poux, S S; Redaschi, N N; Xenarios, I I; Bridge, A A; ,

Publication Date: 2019-01-01

Variant appearance in text: TP53: 751A>C; Ile251Leu

PubMed Link: 30937429

Variant Present in the following documents:

• famiglietti_supplementarytables1_rev_baz040.xlsx, sheet 1

View BVdb publication page

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From uncertainty to pathogenicity: clinical and functional interrogation of a rare TP53 in-frame deletion.

Cold Spring Harbor Molecular Case Studies

Quinn, Emily A EA; Maciaszek, Jamie L JL; Pinto, Emilia M EM; Phillips, Aaron H AH; Berdy, David D; Khandwala, Mohammad M; Upadhyaya, Santhosh A SA; Zambetti, Gerard P GP; Kriwacki, Richard W RW; Ellison, David W DW; Nichols, Kim E KE; Kesserwan, Chimene C

Publication Date: 2019-08

Variant appearance in text: TP53: 751A>C; Ile251Leu

PubMed Link: 30886117

Variant Present in the following documents:

• supp_mcs.a003921_Supplemental_Table_2.xlsx, sheet 1
• supp_mcs.a003921_Supplemental_Table_1a.xlsx, sheet 1

View BVdb publication page

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Mutation of TP53, translocation analysis and immunohistochemical expression of MYC, BCL-2 and BCL-6 in patients with DLBCL treated with R-CHOP.

Scientific Reports

Peroja, Pekka P; Pedersen, Mette M; Mantere, Tuomo T; Nørgaard, Peter P; Peltonen, Jenni J; Haapasaari, Kirsi-Maria KM; Böhm, Jan J; Jantunen, Esa E; Turpeenniemi-Hujanen, Taina T; Rapakko, Katrin K; Karihtala, Peeter P; Soini, Ylermi Y; Vasala, Kaija K; Kuittinen, Outi O

Publication Date: 2018-10-04

Variant appearance in text: TP53: 751A>C

PubMed Link: 30287880

Variant Present in the following documents:

• Main text
• 41598_2018_Article_33230.pdf

View BVdb publication page

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A Bayesian framework for efficient and accurate variant prediction.

Plos One

Qian, Dajun D; Li, Shuwei S; Tian, Yuan Y; Clifford, Jacob W JW; Sarver, Brice A J BAJ; Pesaran, Tina T; Gau, Chia-Ling CL; Elliott, Aaron M AM; Lu, Hsiao-Mei HM; Black, Mary Helen MH

Publication Date: 2018

Variant appearance in text: TP53: 751A>C; I251L

PubMed Link: 30212499

Variant Present in the following documents:

• pone.0203553.s008.xlsx, sheet 2

View BVdb publication page

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Centrosome amplification arises before neoplasia and increases upon p53 loss in tumorigenesis.

The Journal Of Cell Biology

Lopes, Carla A M CAM; Mesquita, Marta M; Cunha, Ana Isabel AI; Cardoso, Joana J; Carapeta, Sara S; Laranjeira, Cátia C; Pinto, António E AE; Pereira-Leal, José B JB; Dias-Pereira, António A; Bettencourt-Dias, Mónica M; Chaves, Paula P

Publication Date: 2018-07-02

Variant appearance in text: TP53: I251L

PubMed Link: 29739803

Variant Present in the following documents:

• JCB_201711191_sm.pdf

View BVdb publication page

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BRD4 regulates cellular senescence in gastric cancer cells via E2F/miR-106b/p21 axis.

Cell Death & Disease

Dong, Xingchen X; Hu, Xiangming X; Chen, Jinjing J; Hu, Dan D; Chen, Lin-Feng LF

Publication Date: 2018-02-12

Variant appearance in text: TP53: I251L

PubMed Link: 29434197

Variant Present in the following documents:

• Main text
• 41419_2017_Article_181.pdf

View BVdb publication page

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Pan-urologic cancer genomic subtypes that transcend tissue of origin.

Nature Communications

Chen, Fengju F; Zhang, Yiqun Y; Bossé, Dominick D; Lalani, Aly-Khan A AA; Hakimi, A Ari AA; Hsieh, James J JJ; Choueiri, Toni K TK; Gibbons, Don L DL; Ittmann, Michael M; Creighton, Chad J CJ

Publication Date: 2017-08-04

Variant appearance in text: TP53: 751A>C; I251L

PubMed Link: 28775315

Variant Present in the following documents:

• 41467_2017_289_MOESM7_ESM.xlsx, sheet 1

View BVdb publication page

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Inhibiting the system xC-/glutathione axis selectively targets cancers with mutant-p53 accumulation.

Nature Communications

Liu, David S DS; Duong, Cuong P CP; Haupt, Sue S; Montgomery, Karen G KG; House, Colin M CM; Azar, Walid J WJ; Pearson, Helen B HB; Fisher, Oliver M OM; Read, Matthew M; Guerra, Glen R GR; Haupt, Ygal Y; Cullinane, Carleen C; Wiman, Klas G KG; Abrahmsen, Lars L; Phillips, Wayne A WA; Clemons, Nicholas J NJ

Publication Date: 2017-03-28

Variant appearance in text: p53: 751A>C

PubMed Link: 28348409

Variant Present in the following documents:

• ncomms14844-s1.pdf

View BVdb publication page

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Dies1/VISTA expression loss is a recurrent event in gastric cancer due to epigenetic regulation.

Scientific Reports

Oliveira, Patrícia P; Carvalho, Joana J; Rocha, Sara S; Azevedo, Mafalda M; Reis, Inês I; Camilo, Vânia V; Sousa, Bárbara B; Valente, Sofia S; Paredes, Joana J; Almeida, Raquel R; Huntsman, David D; Oliveira, Carla C

Publication Date: 2016-10-10

Variant appearance in text: TP53: I251L

PubMed Link: 27721458

Variant Present in the following documents:

• Main text

View BVdb publication page

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A Landscape of Pharmacogenomic Interactions in Cancer.

Cell

Iorio, Francesco F; Knijnenburg, Theo A TA; Vis, Daniel J DJ; Bignell, Graham R GR; Menden, Michael P MP; Schubert, Michael M; Aben, Nanne N; Gonçalves, Emanuel E; Barthorpe, Syd S; Lightfoot, Howard H; Cokelaer, Thomas T; Greninger, Patricia P; van Dyk, Ewald E; Chang, Han H; de Silva, Heshani H; Heyn, Holger H; Deng, Xianming X; Egan, Regina K RK; Liu, Qingsong Q; Mironenko, Tatiana T; Mitropoulos, Xeni X; Richardson, Laura L; Wang, Jinhua J; Zhang, Tinghu T; Moran, Sebastian S; Sayols, Sergi S; Soleimani, Maryam M; Tamborero, David D; Lopez-Bigas, Nuria N; Ross-Macdonald, Petra P; Esteller, Manel M; Gray, Nathanael S NS; Haber, Daniel A DA; Stratton, Michael R MR; Benes, Cyril H CH; Wessels, Lodewyk F A LFA; Saez-Rodriguez, Julio J; McDermott, Ultan U; Garnett, Mathew J MJ

Publication Date: 2016-07-28

Variant appearance in text: TP53: 751A>C; I251L

PubMed Link: 27397505

Variant Present in the following documents:

• mmc3.xlsx, sheet 3

View BVdb publication page

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Targeting the WEE1 kinase as a molecular targeted therapy for gastric cancer.

Oncotarget

Kim, Hye-Young HY; Cho, Yunhee Y; Kang, HyeokGu H; Yim, Ye-Seal YS; Kim, Seok-Jun SJ; Song, Jaewhan J; Chun, Kyung-Hee KH

Publication Date: 2016-08-02

Variant appearance in text: p53: I251L

PubMed Link: 27363019

Variant Present in the following documents:

• Main text
• oncotarget-07-49902.pdf

View BVdb publication page

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REGene: a literature-based knowledgebase of animal regeneration that bridge tissue regeneration and cancer.

Scientific Reports

Zhao, Min M; Rotgans, Bronwyn B; Wang, Tianfang T; Cummins, S F SF

Publication Date: 2016-03-15

Variant appearance in text: TP53: I251L

PubMed Link: 26975833

Variant Present in the following documents:

• srep23167-s9.xls, sheet 1

View BVdb publication page

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GESPA: classifying nsSNPs to predict disease association.

Bmc Bioinformatics

Khurana, Jay K JK; Reeder, Jay E JE; Shrimpton, Antony E AE; Thakar, Juilee J

Publication Date: 2015-07-25

Variant appearance in text: TP53: I251L

PubMed Link: 26206375

Variant Present in the following documents:

• 12859_2015_673_MOESM1_ESM.xls, sheet 1

View BVdb publication page

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Benchmarking mutation effect prediction algorithms using functionally validated cancer-related missense mutations.

Genome Biology

Martelotto, Luciano G LG; Ng, Charlotte Ky CK; De Filippo, Maria R MR; Zhang, Yan Y; Piscuoglio, Salvatore S; Lim, Raymond S RS; Shen, Ronglai R; Norton, Larry L; Reis-Filho, Jorge S JS; Weigelt, Britta B

Publication Date: 2014-10-28

Variant appearance in text: TP53: I251L

PubMed Link: 25348012

Variant Present in the following documents:

• 13059_2014_484_MOESM2_ESM.xlsx, sheet 1

View BVdb publication page

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Integrated exome and transcriptome sequencing reveals ZAK isoform usage in gastric cancer.

Nature Communications

Liu, Jinfeng J; McCleland, Mark M; Stawiski, Eric W EW; Gnad, Florian F; Mayba, Oleg O; Haverty, Peter M PM; Durinck, Steffen S; Chen, Ying-Jiun YJ; Klijn, Christiaan C; Jhunjhunwala, Suchit S; Lawrence, Michael M; Liu, Hanbin H; Wan, Yinan Y; Chopra, Vivek V; Yaylaoglu, Murat B MB; Yuan, Wenlin W; Ha, Connie C; Gilbert, Houston N HN; Reeder, Jens J; Pau, Gregoire G; Stinson, Jeremy J; Stern, Howard M HM; Manning, Gerard G; Wu, Thomas D TD; Neve, Richard M RM; de Sauvage, Frederic J FJ; Modrusan, Zora Z; Seshagiri, Somasekar S; Firestein, Ron R; Zhang, Zemin Z

Publication Date: 2014-05-08

Variant appearance in text: TP53: I251L

PubMed Link: 24807215

Variant Present in the following documents:

• ncomms4830-s10.xls, sheet 1

View BVdb publication page

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Assessment of computational methods for predicting the effects of missense mutations in human cancers.

Bmc Genomics

Gnad, Florian F; Baucom, Albion A; Mukhyala, Kiran K; Manning, Gerard G; Zhang, Zemin Z

Publication Date: 2013

Variant appearance in text: TP53: I251L

PubMed Link: 23819521

Variant Present in the following documents:

• 1471-2164-14-S3-S7-S1.xlsx, sheet 1

View BVdb publication page

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Predicting the functional impact of protein mutations: application to cancer genomics.

Nucleic Acids Research

Reva, Boris B; Antipin, Yevgeniy Y; Sander, Chris C

Publication Date: 2011-09-01

Variant appearance in text: TP53: I251L

PubMed Link: 21727090

Variant Present in the following documents:

• supp_gkr407_Supplement2_Table_SM1_COSMIC_mutations.xls, sheet 1

View BVdb publication page

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