Publications:

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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: 370T>A; C124S

PubMed Link: 36879825

Variant Present in the following documents:

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

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ESR1 gene amplification and MAP3K mutations are selected during adjuvant endocrine therapies in relapsing Hormone Receptor-positive, HER2-negative breast cancer (HR+ HER2- BC).

Plos Genetics

Ferrando, Lorenzo L; Vingiani, Andrea A; Garuti, Anna A; Vernieri, Claudio C; Belfiore, Antonino A; Agnelli, Luca L; Dagrada, Gianpaolo G; Ivanoiu, Diana D; Bonizzi, Giuseppina G; Munzone, Elisabetta E; Lippolis, Luana L; Dameri, Martina M; Ravera, Francesco F; Colleoni, Marco M; Viale, Giuseppe G; Magnani, Luca L; Ballestrero, Alberto A; Zoppoli, Gabriele G; Pruneri, Giancarlo G

Publication Date: 2023-01-03

Variant appearance in text: rs730881997

PubMed Link: 36595552

Variant Present in the following documents:

• pgen.1010563.s004.xlsx, sheet 1

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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: rs730881997

PubMed Link: 36561320

Variant Present in the following documents:

• Table2.xlsx, sheet 7

View BVdb publication page

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A small molecule reacts with the p53 somatic mutant Y220C to rescue wild-type thermal stability.

Cancer Discovery

Guiley, Keelan Z KZ; Shokat, Kevan M KM

Publication Date: 2022-10-05

Variant appearance in text: p53: C124S

PubMed Link: 36197521

Variant Present in the following documents:

• Main text
• 56.pdf

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Client binding shifts the populations of dynamic Hsp90 conformations through an allosteric network.

Science Advances

Lopez, Abraham A; Dahiya, Vinay V; Delhommel, Florent F; Freiburger, Lee L; Stehle, Ralf R; Asami, Sam S; Rutz, Daniel D; Blair, Laura L; Buchner, Johannes J; Sattler, Michael M

Publication Date: 2021-12-17

Variant appearance in text: p53: C124S

PubMed Link: 34919431

Variant Present in the following documents:

• Main text
• sciadv.abl7295.pdf

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Client binding shifts the populations of dynamic Hsp90 conformations through an allosteric network.

Science Advances

Lopez, Abraham A; Dahiya, Vinay V; Delhommel, Florent F; Freiburger, Lee L; Stehle, Ralf R; Asami, Sam S; Rutz, Daniel D; Blair, Laura L; Buchner, Johannes J; Sattler, Michael M

Publication Date: 2021-12-17

Variant appearance in text: p53: C124S

PubMed Link: 34919431

Variant Present in the following documents:

• Main text
• sciadv.abl7295.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: TP53: 370T>A; Cys124Ser; rs730881997

PubMed Link: 34253785

Variant Present in the following documents:

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

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Comparison of two targeted ultra-deep sequencing technologies for analysis of plasma circulating tumour DNA in endocrine-therapy-resistant breast cancer patients.

Breast Cancer Research And Treatment

Nteliopoulos, Georgios G; Page, Karen K; Hills, Allison A; Howarth, Karen K; Emmett, Warren W; Green, Emma E; Martinson, Luke J LJ; Fernadez-Garcia, Daniel D; Hastings, Robert R; Guttery, David S DS; Kenny, Laura L; Stebbing, Justin J; Cleator, Susan S; Rehman, Farah F; Gleason, Kelly L T KLT; Sanela, Andrijac A; Ion, Charlotte C; Rushton, Amelia J AJ; Rosenfeld, Nitzan N; Coombes, R Charles RC; Shaw, Jacqueline A JA

Publication Date: 2021-07

Variant appearance in text: TP53: C124S

PubMed Link: 34097174

Variant Present in the following documents:

• 10549_2021_6220_MOESM2_ESM.xlsx, sheet 4

View BVdb publication page

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A phosphorylation-dependent switch in the disordered p53 transactivation domain regulates DNA binding.

Proceedings Of The National Academy Of Sciences Of The United States Of America

Sun, Xun X; Dyson, H Jane HJ; Wright, Peter E PE

Publication Date: 2021-01-05

Variant appearance in text: p53: C124S

PubMed Link: 33443163

Variant Present in the following documents:

• Main text

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: rs730881997

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: rs730881997

PubMed Link: 33257846

Variant Present in the following documents:

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

View BVdb publication page

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Characterization of the genomic landscape and actionable mutations in Chinese breast cancers by clinical sequencing.

Nature Communications

Lang, Guan-Tian GT; Jiang, Yi-Zhou YZ; Shi, Jin-Xiu JX; Yang, Fan F; Li, Xiao-Guang XG; Pei, Yu-Chen YC; Zhang, Chen-Hui CH; Ma, Ding D; Xiao, Yi Y; Hu, Peng-Chen PC; Wang, Hai H; Yang, Yun-Song YS; Guo, Lin-Wei LW; Lu, Xun-Xi XX; Xue, Meng-Zhu MZ; Wang, Peng P; Cao, A-Yong AY; Ling, Hong H; Wang, Zhong-Hua ZH; Yu, Ke-Da KD; Di, Gen-Hong GH; Li, Da-Qiang DQ; Wang, Yun-Jin YJ; Yu, Ying Y; Shi, Le-Ming LM; Hu, Xin X; Huang, Wei W; Shao, Zhi-Ming ZM

Publication Date: 2020-11-10

Variant appearance in text: TP53: C124S

PubMed Link: 33173047

Variant Present in the following documents:

• 41467_2020_19342_MOESM7_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: C124S

PubMed Link: 32958805

Variant Present in the following documents:

• 41598_2020_72404_MOESM2_ESM.xlsx, sheet 3

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: C124S

PubMed Link: 31034466

Variant Present in the following documents:

• pcbi.1006981.s010.xlsx, sheet 1

View BVdb publication page

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The NRF2 transcriptional target NQO1 has low mRNA levels in TP53-mutated endometrial carcinomas.

Plos One

Beinse, Guillaume G; Just, Pierre-Alexandre PA; Rance, Bastien B; Izac, Brigitte B; Letourneur, Franck F; Saidu, Nathaniel Edward Bennett NEB; Chouzenoux, Sandrine S; Nicco, Carole C; Goldwasser, François F; Pasmant, Eric E; Batteux, Frederic F; Borghese, Bruno B; Alexandre, Jérôme J; Leroy, Karen K

Publication Date: 2019

Variant appearance in text: N/A

PubMed Link: 30908539

Variant Present in the following documents:

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: 370T>A; Cys124Ser

PubMed Link: 30886117

Variant Present in the following documents:

• supp_mcs.a003921_Supplemental_Table_1a.xlsx, sheet 1

View BVdb publication page

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Long-range regulation of p53 DNA binding by its intrinsically disordered N-terminal transactivation domain.

Proceedings Of The National Academy Of Sciences Of The United States Of America

Krois, Alexander S AS; Dyson, H Jane HJ; Wright, Peter E PE

Publication Date: 2018-11-27

Variant appearance in text: p53: C124S

PubMed Link: 30420502

Variant Present in the following documents:

• Main text

View BVdb publication page

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appreci8: a pipeline for precise variant calling integrating 8 tools.

Bioinformatics (Oxford, England)

Sandmann, Sarah S; Karimi, Mohsen M; de Graaf, Aniek O AO; Rohde, Christian C; Göllner, Stefanie S; Varghese, Julian J; Ernsting, Jan J; Walldin, Gunilla G; van der Reijden, Bert A BA; Müller-Tidow, Carsten C; Malcovati, Luca L; Hellström-Lindberg, Eva E; Jansen, Joop H JH; Dugas, Martin M

Publication Date: 2018-12-15

Variant appearance in text: TP53: 370T>A; Cys124Ser

PubMed Link: 29945233

Variant Present in the following documents:

• bty518_supplementary_data_s2.xlsx, sheet 8

View BVdb publication page

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The curcumin analog HO-3867 selectively kills cancer cells by converting mutant p53 protein to transcriptionally active wildtype p53.

The Journal Of Biological Chemistry

Madan, Esha E; Parker, Taylor M TM; Bauer, Matthias R MR; Dhiman, Alisha A; Pelham, Christopher J CJ; Nagane, Masaki M; Kuppusamy, M Lakshmi ML; Holmes, Matti M; Holmes, Thomas R TR; Shaik, Kranti K; Shee, Kevin K; Kiparoidze, Salome S; Smith, Sean D SD; Park, Yu-Soon A YA; Gomm, Jennifer J JJ; Jones, Louise J LJ; Tomás, Ana R AR; Cunha, Ana C AC; Selvendiran, Karuppaiyah K; Hansen, Laura A LA; Fersht, Alan R AR; Hideg, Kálmán K; Gogna, Rajan R; Kuppusamy, Periannan P

Publication Date: 2018-03-23

Variant appearance in text: p53: C124S

PubMed Link: 29382728

Variant Present in the following documents:

• Main text

View BVdb publication page

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Altered S-nitrosylation of p53 is responsible for impaired antioxidant response in skeletal muscle during aging.

Aging

Baldelli, Sara S; Ciriolo, Maria Rosa MR

Publication Date: 2016-12-20

Variant appearance in text: p53: C124S

PubMed Link: 28025407

Variant Present in the following documents:

• Main text
• aging-08-3450.pdf
• aging-08-3450-s001.pdf

View BVdb publication page

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2-Sulfonylpyrimidines: Mild alkylating agents with anticancer activity toward p53-compromised cells.

Proceedings Of The National Academy Of Sciences Of The United States Of America

Bauer, Matthias R MR; Joerger, Andreas C AC; Fersht, Alan R AR

Publication Date: 2016-09-06

Variant appearance in text: p53: C124S

PubMed Link: 27551077

Variant Present in the following documents:

• Main text

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: C124S

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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Oxidation of p53 through DNA charge transport involves a network of disulfides within the DNA-binding domain.

Biochemistry

Schaefer, Kathryn N KN; Geil, Wendy M WM; Sweredoski, Michael J MJ; Moradian, Annie A; Hess, Sonja S; Barton, Jacqueline K JK

Publication Date: 2015-01-27

Variant appearance in text: p53: C124S

PubMed Link: 25584637

Variant Present in the following documents:

• Main text
• bi501424v.pdf

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: C124S

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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Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine.

Nature Medicine

Van Allen, Eliezer M EM; Wagle, Nikhil N; Stojanov, Petar P; Perrin, Danielle L DL; Cibulskis, Kristian K; Marlow, Sara S; Jane-Valbuena, Judit J; Friedrich, Dennis C DC; Kryukov, Gregory G; Carter, Scott L SL; McKenna, Aaron A; Sivachenko, Andrey A; Rosenberg, Mara M; Kiezun, Adam A; Voet, Douglas D; Lawrence, Michael M; Lichtenstein, Lee T LT; Gentry, Jeff G JG; Huang, Franklin W FW; Fostel, Jennifer J; Farlow, Deborah D; Barbie, David D; Gandhi, Leena L; Lander, Eric S ES; Gray, Stacy W SW; Joffe, Steven S; Janne, Pasi P; Garber, Judy J; MacConaill, Laura L; Lindeman, Neal N; Rollins, Barrett B; Kantoff, Philip P; Fisher, Sheila A SA; Gabriel, Stacey S; Getz, Gad G; Garraway, Levi A LA

Publication Date: 2014-06

Variant appearance in text: p53: C124S

PubMed Link: 24836576

Variant Present in the following documents:

• NIHMS531666-supplement-10.xlsx, sheet 1

View BVdb publication page

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Modulation of allostery by protein intrinsic disorder.

Nature

Ferreon, Allan Chris M AC; Ferreon, Josephine C JC; Wright, Peter E PE; Deniz, Ashok A AA

Publication Date: 2013-06-20

Variant appearance in text: p53: C124S

PubMed Link: 23783631

Variant Present in the following documents:

• Main text
• nihms-482139.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: C124S

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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Effect of thioredoxin deletion and p53 cysteine replacement on human p53 activity in wild-type and thioredoxin reductase null yeast.

Biochemistry

Stoner, Christopher S CS; Pearson, George D GD; Koç, Ahmet A; Merwin, Jason R JR; Lopez, Nathan I NI; Merrill, Gary F GF

Publication Date: 2009-09-29

Variant appearance in text: p53: C124S

PubMed Link: 19681600

Variant Present in the following documents:

• Main text

View BVdb publication page

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Human p53 is inhibited by glutathionylation of cysteines present in the proximal DNA-binding domain during oxidative stress.

Biochemistry

Velu, Chinavenmeni S CS; Niture, Suryakant K SK; Doneanu, Catalin E CE; Pattabiraman, Nagarajan N; Srivenugopal, Kalkunte S KS

Publication Date: 2007-07-03

Variant appearance in text: p53: Cys124Ser

PubMed Link: 17555331

Variant Present in the following documents:

• Main text

View BVdb publication page

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Adenovirus E4 34k and E1b 55k oncoproteins target host DNA ligase IV for proteasomal degradation.

Journal Of Virology

Baker, Amy A; Rohleder, Kent J KJ; Hanakahi, Les A LA; Ketner, Gary G

Publication Date: 2007-07

Variant appearance in text: p53: C124S

PubMed Link: 17459921

Variant Present in the following documents:

• Main text

View BVdb publication page

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Redox state of tumor suppressor p53 regulates its sequence-specific DNA binding in DNA-damaged cells by cysteine 277.

Nucleic Acids Research

Buzek, Jiri J; Latonen, Leena L; Kurki, Sari S; Peltonen, Karita K; Laiho, Marikki M

Publication Date: 2002-06-01

Variant appearance in text: p53: C124S

PubMed Link: 12034820

Variant Present in the following documents:

• Main text

View BVdb publication page

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