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: G293W

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: 877G>T; G293W

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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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: rs587780076

PubMed Link: 36561320

Variant Present in the following documents:

• Table2.xlsx, sheet 7

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: 877G>T

PubMed Link: 36117989

Variant Present in the following documents:

• mmc4.xlsx, sheet 1

View BVdb publication page

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Reversal of viral and epigenetic HLA class I repression in Merkel cell carcinoma.

The Journal Of Clinical Investigation

Lee, Patrick C PC; Klaeger, Susan S; Le, Phuong M PM; Korthauer, Keegan K; Cheng, Jingwei J; Ananthapadmanabhan, Varsha V; Frost, Thomas C TC; Stevens, Jonathan D JD; Wong, Alan Yl AY; Iorgulescu, J Bryan JB; Tarren, Anna Y AY; Chea, Vipheaviny A VA; Carulli, Isabel P IP; Lemvigh, Camilla K CK; Pedersen, Christina B CB; Gartin, Ashley K AK; Sarkizova, Siranush S; Wright, Kyle T KT; Li, Letitia W LW; Nomburg, Jason J; Li, Shuqiang S; Huang, Teddy T; Liu, Xiaoxi X; Pomerance, Lucas L; Doherty, Laura M LM; Apffel, Annie M AM; Wallace, Luke J LJ; Rachimi, Suzanna S; Felt, Kristen D KD; Wolff, Jacquelyn O JO; Witten, Elizabeth E; Zhang, Wandi W; Neuberg, Donna D; Lane, William J WJ; Zhang, Guanglan G; Olsen, Lars R LR; Thakuria, Manisha M; Rodig, Scott J SJ; Clauser, Karl R KR; Starrett, Gabriel J GJ; Doench, John G JG; Buhrlage, Sara J SJ; Carr, Steven A SA; DeCaprio, James A JA; Wu, Catherine J CJ; Keskin, Derin B DB

Publication Date: 2022-07-01

Variant appearance in text: TP53: 877G>T; G293W

PubMed Link: 35775490

Variant Present in the following documents:

• jci-132-151666-s195.xlsx, sheet 2

View BVdb publication page

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Clinical genomic profiling in the management of patients with soft tissue and bone sarcoma.

Nature Communications

Gounder, Mrinal M MM; Agaram, Narasimhan P NP; Trabucco, Sally E SE; Robinson, Victoria V; Ferraro, Richard A RA; Millis, Sherri Z SZ; Krishnan, Anita A; Lee, Jessica J; Attia, Steven S; Abida, Wassim W; Drilon, Alexander A; Chi, Ping P; Angelo, Sandra P D' SP; Dickson, Mark A MA; Keohan, Mary Lou ML; Kelly, Ciara M CM; Agulnik, Mark M; Chawla, Sant P SP; Choy, Edwin E; Chugh, Rashmi R; Meyer, Christian F CF; Myer, Parvathi A PA; Moore, Jessica L JL; Okimoto, Ross A RA; Pollock, Raphael E RE; Ravi, Vinod V; Singh, Arun S AS; Somaiah, Neeta N; Wagner, Andrew J AJ; Healey, John H JH; Frampton, Garrett M GM; Venstrom, Jeffrey M JM; Ross, Jeffrey S JS; Ladanyi, Marc M; Singer, Samuel S; Brennan, Murray F MF; Schwartz, Gary K GK; Lazar, Alexander J AJ; Thomas, David M DM; Maki, Robert G RG; Tap, William D WD; Ali, Siraj M SM; Jin, Dexter X DX

Publication Date: 2022-06-15

Variant appearance in text: TP53: G293W

PubMed Link: 35705558

Variant Present in the following documents:

• 41467_2022_30496_MOESM2_ESM.xls, sheet 1

View BVdb publication page

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TP53_PROF: a machine learning model to predict impact of missense mutations in TP53.

Briefings In Bioinformatics

Ben-Cohen, Gil G; Doffe, Flora F; Devir, Michal M; Leroy, Bernard B; Soussi, Thierry T; Rosenberg, Shai S

Publication Date: 2022-03-10

Variant appearance in text: TP53: 877G>T; G293W; rs587780076

PubMed Link: 35043155

Variant Present in the following documents:

• Main text
• bbab524.pdf
• supplementary_table_s7_bbab524.xlsx, sheet 2
• supplementary_figure_s4a_and_b_bbab524.pdf

View BVdb publication page

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LYRUS: a machine learning model for predicting the pathogenicity of missense variants.

Bioinformatics Advances

Lai, Jiaying J; Yang, Jordan J; Gamsiz Uzun, Ece D ED; Rubenstein, Brenda M BM; Sarkar, Indra Neil IN

Publication Date: 2022

Variant appearance in text: TP53: G293W

PubMed Link: 35036922

Variant Present in the following documents:

• Main text

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: TP53: 877G>T; Gly293Trp; rs587780076

PubMed Link: 34253785

Variant Present in the following documents:

• 41598_2021_93715_MOESM3_ESM.xlsx, sheet 2
• 41598_2021_93715_MOESM3_ESM.xlsx, sheet 3
• 41598_2021_93715_MOESM3_ESM.xlsx, sheet 5
• 41598_2021_93715_MOESM3_ESM.xlsx, sheet 4
• 41598_2021_93715_MOESM2_ESM.xlsx, sheet 8
• 41598_2021_93715_MOESM3_ESM.xlsx, sheet 6

View BVdb publication page

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Combined assay of Circulating Tumor DNA and Protein Biomarkers for early noninvasive detection and prognosis of Non-Small Cell Lung Cancer.

Journal Of Cancer

Yin, Jian-Xin JX; Hu, Wen-Wei WW; Gu, Hua H; Fang, Jian-Min JM

Publication Date: 2021

Variant appearance in text: TP53: 877G>T; G293W

PubMed Link: 33442424

Variant Present in the following documents:

• jcav12p1258s2.xlsx, sheet 7

View BVdb publication page

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Combining Ramachandran plot and molecular dynamics simulation for structural-based variant classification: Using TP53 variants as model.

Computational And Structural Biotechnology Journal

Tam, Benjamin B; Sinha, Siddharth S; Wang, San Ming SM

Publication Date: 2020

Variant appearance in text: TP53: G293W

PubMed Link: 33363700

Variant Present in the following documents:

• Main text
• mmc1.xlsx, sheet 1
• main.pdf

View BVdb publication page

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Identification and functional characterization of new missense SNPs in the coding region of the TP53 gene.

Cell Death And Differentiation

Doffe, Flora F; Carbonnier, Vincent V; Tissier, Manon M; Leroy, Bernard B; Martins, Isabelle I; Mattsson, Johanna S M JSM; Micke, Patrick P; Pavlova, Sarka S; Pospisilova, Sarka S; Smardova, Jana J; Joerger, Andreas C AC; Wiman, Klas G KG; Kroemer, Guido G; Soussi, Thierry T

Publication Date: 2021-05

Variant appearance in text: rs587780076

PubMed Link: 33257846

Variant Present in the following documents:

• 41418_2020_672_MOESM3_ESM.xlsx, sheet 2
• 41418_2020_672_MOESM3_ESM.xlsx, sheet 4

View BVdb publication page

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Identification and functional characterization of new missense SNPs in the coding region of the TP53 gene.

Cell Death And Differentiation

Doffe, Flora F; Carbonnier, Vincent V; Tissier, Manon M; Leroy, Bernard B; Martins, Isabelle I; Mattsson, Johanna S M JSM; Micke, Patrick P; Pavlova, Sarka S; Pospisilova, Sarka S; Smardova, Jana J; Joerger, Andreas C AC; Wiman, Klas G KG; Kroemer, Guido G; Soussi, Thierry T

Publication Date: 2021-05

Variant appearance in text: rs587780076

PubMed Link: 33257846

Variant Present in the following documents:

• 41418_2020_672_MOESM3_ESM.xlsx, sheet 2
• 41418_2020_672_MOESM3_ESM.xlsx, sheet 4

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: G293W

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: 877G>T; Gly293Trp

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: 877G>T; G293W

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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Analysis on GENIE reveals novel recurrent variants that affect molecular diagnosis of sizable number of cancer patients.

Bmc Cancer

Koyama, Takahiko T; Rhrissorrakrai, Kahn K; Parida, Laxmi L

Publication Date: 2019-02-01

Variant appearance in text: TP53: 877G>T; G293W

PubMed Link: 30709382

Variant Present in the following documents:

• 12885_2019_5313_MOESM3_ESM.xlsx, sheet 1

View BVdb publication page

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Variable population prevalence estimates of germline TP53 variants: A gnomAD-based analysis.

Human Mutation

de Andrade, Kelvin C KC; Frone, Megan N MN; Wegman-Ostrosky, Talia T; Khincha, Payal P PP; Kim, Jung J; Amadou, Amina A; Santiago, Karina M KM; Fortes, Fernanda P FP; Lemonnier, Nathanaël N; Mirabello, Lisa L; Stewart, Douglas R DR; Hainaut, Pierre P; Kowalski, Luiz P LP; Savage, Sharon A SA; Achatz, Maria I MI

Publication Date: 2019-01

Variant appearance in text: TP53: 877G>T; G293W

PubMed Link: 30352134

Variant Present in the following documents:

• Main text

View BVdb publication page

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Germline mutations in candidate predisposition genes in individuals with cutaneous melanoma and at least two independent additional primary cancers.

Plos One

Pritchard, Antonia L AL; Johansson, Peter A PA; Nathan, Vaishnavi V; Howlie, Madeleine M; Symmons, Judith J; Palmer, Jane M JM; Hayward, Nicholas K NK

Publication Date: 2018

Variant appearance in text: rs587780076

PubMed Link: 29641532

Variant Present in the following documents:

• pone.0194098.s003.xlsx, sheet 2

View BVdb publication page

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Sources of discordance among germ-line variant classifications in ClinVar.

Genetics In Medicine : Official Journal Of The American College Of Medical Genetics

Yang, Shan S; Lincoln, Stephen E SE; Kobayashi, Yuya Y; Nykamp, Keith K; Nussbaum, Robert L RL; Topper, Scott S

Publication Date: 2017-10

Variant appearance in text: TP53: 877G>T; Gly293Trp

PubMed Link: 28569743

Variant Present in the following documents:

• gim201760x7.xlsx, sheet 2

View BVdb publication page

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Frequency of Germline Mutations in 25 Cancer Susceptibility Genes in a Sequential Series of Patients With Breast Cancer.

Journal Of Clinical Oncology : Official Journal Of The American Society Of Clinical Oncology

Tung, Nadine N; Lin, Nancy U NU; Kidd, John J; Allen, Brian A BA; Singh, Nanda N; Wenstrup, Richard J RJ; Hartman, Anne-Renee AR; Winer, Eric P EP; Garber, Judy E JE

Publication Date: 2016-05-01

Variant appearance in text: TP53: 877G>T; Gly293Trp

PubMed Link: 26976419

Variant Present in the following documents:

• Main text

View BVdb publication page

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The UK10K project identifies rare variants in health and disease.

Nature

, ; Walter, Klaudia K; Min, Josine L JL; Huang, Jie J; Crooks, Lucy L; Memari, Yasin Y; McCarthy, Shane S; Perry, John R B JR; Xu, ChangJiang C; Futema, Marta M; Lawson, Daniel D; Iotchkova, Valentina V; Schiffels, Stephan S; Hendricks, Audrey E AE; Danecek, Petr P; Li, Rui R; Floyd, James J; Wain, Louise V LV; Barroso, Inês I; Humphries, Steve E SE; Hurles, Matthew E ME; Zeggini, Eleftheria E; Barrett, Jeffrey C JC; Plagnol, Vincent V; Richards, J Brent JB; Greenwood, Celia M T CM; Timpson, Nicholas J NJ; Durbin, Richard R; Soranzo, Nicole N

Publication Date: 2015-10-01

Variant appearance in text: TP53: G293W

PubMed Link: 26367797

Variant Present in the following documents:

• 41586_2015_BFnature14962_MOESM15_ESM.xlsx, sheet 16

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: G293W

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: G293W

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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High frequency of germline TP53 mutations in a prospective adult-onset sarcoma cohort.

Plos One

Mitchell, Gillian G; Ballinger, Mandy L ML; Wong, Stephen S; Hewitt, Chelsee C; James, Paul P; Young, Mary-Anne MA; Cipponi, Arcadi A; Pang, Tiffany T; Goode, David L DL; Dobrovic, Alex A; Thomas, David M DM; ,

Publication Date: 2013

Variant appearance in text: TP53: Gly293Trp

PubMed Link: 23894400

Variant Present in the following documents:

• Main text
• pone.0069026.pdf

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: G293W

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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