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: BRCA1: P1238L

PubMed Link: 36896237

Variant Present in the following documents:

• Table1.xlsx, sheet 1

View BVdb publication page

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APPLICATION OF THE ACMG/AMP FRAMEWORK TO CAPTURE EVIDENCE RELEVANT TO PREDICTED AND OBSERVED IMPACT ON SPLICING: RECOMMENDATIONS FROM THE CLINGEN SVI SPLICING SUBGROUP.

Medrxiv : The Preprint Server For Health Sciences

Walker, Logan C LC; de la Hoya, Miguel M; Wiggins, George Ar GA; Lindy, Amanda A; Vincent, Lisa M LM; Parsons, Michael M; Canson, Daffodil M DM; Bis-Brewer, Dana D; Cass, Ashley A; Tchourbanov, Alexander A; Zimmermann, Heather H; Byrne, Alicia B AB; Pesaran, Tina T; Karam, Rachid R; Harrison, Steven M SM; , ; Spurdle, Amanda B AB

Publication Date: 2023-02-26

Variant appearance in text: BRCA1: 3713C>T

PubMed Link: 36865205

Variant Present in the following documents:

• media-10.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: rs28897688

PubMed Link: 36561320

Variant Present in the following documents:

• Table2.xlsx, sheet 2

View BVdb publication page

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Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria.

American Journal Of Human Genetics

Pejaver, Vikas V; Byrne, Alicia B AB; Feng, Bing-Jian BJ; Pagel, Kymberleigh A KA; Mooney, Sean D SD; Karchin, Rachel R; O'Donnell-Luria, Anne A; Harrison, Steven M SM; Tavtigian, Sean V SV; Greenblatt, Marc S MS; Biesecker, Leslie G LG; Radivojac, Predrag P; Brenner, Steven E SE; ,

Publication Date: 2022-12-01

Variant appearance in text: BRCA1: P1238L; rs28897688

PubMed Link: 36413997

Variant Present in the following documents:

• mmc2.xlsx, sheet 1

View BVdb publication page

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SNP allele calling of Illumina Infinium Omni5-4 data using the butterfly method.

Scientific Reports

Andersen, Mikkel Meyer MM; Christiansen, Steffan Noe SN; Andersen, Jeppe Dyrberg JD; Eriksen, Poul Svante PS; Morling, Niels N

Publication Date: 2022-10-12

Variant appearance in text: rs28897688

PubMed Link: 36224332

Variant Present in the following documents:

• Main text
• 41598_2022_Article_22162.pdf

View BVdb publication page

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Distinct non-clock-like signatures of the basal cell carcinomas from three sisters with a lethal Gorlin-Goltz syndrome.

Bmc Medical Genomics

Ye, Lihua L; Wang, Li L; Peng, Kexin K; Fang, Ou O; Tian, Zhen Z; Li, Caihua C; Fu, Xiaopeng X; Chen, Qingdong Q; Chen, Jia J; Luan, Jing J; Zhang, Zhenghua Z; Zhang, Qiaoan Q

Publication Date: 2022-08-05

Variant appearance in text: BRCA1: 3713C>T; Pro1238Leu

PubMed Link: 35932013

Variant Present in the following documents:

• 12920_2022_1324_MOESM1_ESM.xlsx, sheet 1

View BVdb publication page

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Understanding and predicting the functional consequences of missense mutations in BRCA1 and BRCA2.

Scientific Reports

Aljarf, Raghad R; Shen, Mengyuan M; Pires, Douglas E V DEV; Ascher, David B DB

Publication Date: 2022-06-21

Variant appearance in text: BRCA1: P1238L

PubMed Link: 35729312

Variant Present in the following documents:

• 41598_2022_13508_MOESM2_ESM.xlsx, sheet 1

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: BRCA1: 3713C>T; Pro1238Leu; rs28897688

PubMed Link: 34253785

Variant Present in the following documents:

• 41598_2021_93715_MOESM2_ESM.xlsx, sheet 6

View BVdb publication page

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Identification of pathogenic variants in cancer genes using base editing screens with editing efficiency correction.

Genome Biology

Huang, Changcai C; Li, Guangyu G; Wu, Jiayu J; Liang, Junbo J; Wang, Xiaoyue X

Publication Date: 2021-03-10

Variant appearance in text: BRCA1: P1238L

PubMed Link: 33691754

Variant Present in the following documents:

• 13059_2021_2305_MOESM7_ESM.xlsx, sheet 1

View BVdb publication page

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Integrative molecular characterization of sarcomatoid and rhabdoid renal cell carcinoma.

Nature Communications

Bakouny, Ziad Z; Braun, David A DA; Shukla, Sachet A SA; Pan, Wenting W; Gao, Xin X; Hou, Yue Y; Flaifel, Abdallah A; Tang, Stephen S; Bosma-Moody, Alice A; He, Meng Xiao MX; Vokes, Natalie N; Nyman, Jackson J; Xie, Wanling W; Nassar, Amin H AH; Abou Alaiwi, Sarah S; Flippot, Ronan R; Bouchard, Gabrielle G; Steinharter, John A JA; Nuzzo, Pier Vitale PV; Ficial, Miriam M; Sant'Angelo, Miriam M; Forman, Juliet J; Berchuck, Jacob E JE; Dudani, Shaan S; Bi, Kevin K; Park, Jihye J; Camp, Sabrina S; Sticco-Ivins, Maura M; Hirsch, Laure L; Baca, Sylvan C SC; Wind-Rotolo, Megan M; Ross-Macdonald, Petra P; Sun, Maxine M; Lee, Gwo-Shu Mary GM; Chang, Steven L SL; Wei, Xiao X XX; McGregor, Bradley A BA; Harshman, Lauren C LC; Genovese, Giannicola G; Ellis, Leigh L; Pomerantz, Mark M; Hirsch, Michelle S MS; Freedman, Matthew L ML; Atkins, Michael B MB; Wu, Catherine J CJ; Ho, Thai H TH; Linehan, W Marston WM; McDermott, David F DF; Heng, Daniel Y C DYC; Viswanathan, Srinivas R SR; Signoretti, Sabina S; Van Allen, Eliezer M EM; Choueiri, Toni K TK

Publication Date: 2021-02-05

Variant appearance in text: BRCA1: 3713C>T; P1238L

PubMed Link: 33547292

Variant Present in the following documents:

• 41467_2021_21068_MOESM4_ESM.xlsx, sheet 6

View BVdb publication page

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Prediction of the functional impact of missense variants in BRCA1 and BRCA2 with BRCA-ML.

Npj Breast Cancer

Hart, Steven N SN; Polley, Eric C EC; Shimelis, Hermella H; Yadav, Siddhartha S; Couch, Fergus J FJ

Publication Date: 2020

Variant appearance in text: BRCA1: 3713C>T; Pro1238Leu

PubMed Link: 32377563

Variant Present in the following documents:

• 41523_2020_159_MOESM3_ESM.xlsx, sheet 1

View BVdb publication page

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A phase I dose-escalation study of enzalutamide in combination with the AKT inhibitor AZD5363 (capivasertib) in patients with metastatic castration-resistant prostate cancer.

Annals Of Oncology : Official Journal Of The European Society For Medical Oncology

Kolinsky, M P MP; Rescigno, P P; Bianchini, D D; Zafeiriou, Z Z; Mehra, N N; Mateo, J J; Michalarea, V V; Riisnaes, R R; Crespo, M M; Figueiredo, I I; Miranda, S S; Nava Rodrigues, D D; Flohr, P P; Tunariu, N N; Banerji, U U; Ruddle, R R; Sharp, A A; Welti, J J; Lambros, M M; Carreira, S S; Raynaud, F I FI; Swales, K E KE; Plymate, S S; Luo, J J; Tovey, H H; Porta, N N; Slade, R R; Leonard, L L; Hall, E E; de Bono, J S JS

Publication Date: 2020-05

Variant appearance in text: BRCA1: P1238L

PubMed Link: 32205016

Variant Present in the following documents:

• mmc9.xlsx, sheet 1

View BVdb publication page

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Systematic misclassification of missense variants in BRCA1 and BRCA2 "coldspots".

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

Dines, Jennifer N JN; Shirts, Brian H BH; Slavin, Thomas P TP; Walsh, Tom T; King, Mary-Claire MC; Fowler, Douglas M DM; Pritchard, Colin C CC

Publication Date: 2020-05

Variant appearance in text: BRCA1: 3713C>T; Pro1238Leu; rs28897688

PubMed Link: 31911673

Variant Present in the following documents:

• 41436_2019_740_MOESM2_ESM.xlsx, sheet 2
• 41436_2019_740_MOESM2_ESM.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: BRCA1: 3713C>T; P1238L

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: BRCA1: P1238L

PubMed Link: 31034466

Variant Present in the following documents:

• pcbi.1006981.s010.xlsx, sheet 1

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: BRCA1: 3713C>T; P1238L

PubMed Link: 30212499

Variant Present in the following documents:

• pone.0203553.s008.xlsx, sheet 2

View BVdb publication page

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Comprehensive annotation of BRCA1 and BRCA2 missense variants by functionally validated sequence-based computational prediction models.

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

Hart, Steven N SN; Hoskin, Tanya T; Shimelis, Hermela H; Moore, Raymond M RM; Feng, Bingjian B; Thomas, Abigail A; Lindor, Noralane M NM; Polley, Eric C EC; Goldgar, David E DE; Iversen, Edwin E; Monteiro, Alvaro N A ANA; Suman, Vera J VJ; Couch, Fergus J FJ

Publication Date: 2019-01

Variant appearance in text: BRCA1: P1238L

PubMed Link: 29884841

Variant Present in the following documents:

• NIHMS953431-supplement-Table_S2.xls, sheet 1

View BVdb publication page

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Performance of in silico prediction tools for the classification of rare BRCA1/2 missense variants in clinical diagnostics.

Bmc Medical Genomics

Ernst, Corinna C; Hahnen, Eric E; Engel, Christoph C; Nothnagel, Michael M; Weber, Jonas J; Schmutzler, Rita K RK; Hauke, Jan J

Publication Date: 2018-03-27

Variant appearance in text: BRCA1: P1238L

PubMed Link: 29580235

Variant Present in the following documents:

• 12920_2018_353_MOESM1_ESM.xlsx, sheet 1

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: BRCA1: 3713C>T; Pro1238Leu

PubMed Link: 28569743

Variant Present in the following documents:

• gim201760x7.xlsx, sheet 2

View BVdb publication page

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Whole-genome sequencing in multiplex families with psychoses reveals mutations in the SHANK2 and SMARCA1 genes segregating with illness.

Molecular Psychiatry

Homann, O R OR; Misura, K K; Lamas, E E; Sandrock, R W RW; Nelson, P P; McDonough, S I SI; DeLisi, L E LE

Publication Date: 2016-12

Variant appearance in text: BRCA1: P1238L; rs28897688

PubMed Link: 27001614

Variant Present in the following documents:

• NIHMS753666-supplement-2.xlsx, sheet 10

View BVdb publication page

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Adding In Silico Assessment of Potential Splice Aberration to the Integrated Evaluation of BRCA Gene Unclassified Variants.

Human Mutation

Vallée, Maxime P MP; Di Sera, Tonya L TL; Nix, David A DA; Paquette, Andrew M AM; Parsons, Michael T MT; Bell, Russel R; Hoffman, Andrea A; Hogervorst, Frans B L FB; Goldgar, David E DE; Spurdle, Amanda B AB; Tavtigian, Sean V SV

Publication Date: 2016-07

Variant appearance in text: BRCA1: 3713C>T; P1238L

PubMed Link: 26913838

Variant Present in the following documents:

• HUMU-37-627-s001.xlsx, sheet 1

View BVdb publication page

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Patterns and functional implications of rare germline variants across 12 cancer types.

Nature Communications

Lu, Charles C; Xie, Mingchao M; Wendl, Michael C MC; Wang, Jiayin J; McLellan, Michael D MD; Leiserson, Mark D M MD; Huang, Kuan-Lin KL; Wyczalkowski, Matthew A MA; Jayasinghe, Reyka R; Banerjee, Tapahsama T; Ning, Jie J; Tripathi, Piyush P; Zhang, Qunyuan Q; Niu, Beifang B; Ye, Kai K; Schmidt, Heather K HK; Fulton, Robert S RS; McMichael, Joshua F JF; Batra, Prag P; Kandoth, Cyriac C; Bharadwaj, Maheetha M; Koboldt, Daniel C DC; Miller, Christopher A CA; Kanchi, Krishna L KL; Eldred, James M JM; Larson, David E DE; Welch, John S JS; You, Ming M; Ozenberger, Bradley A BA; Govindan, Ramaswamy R; Walter, Matthew J MJ; Ellis, Matthew J MJ; Mardis, Elaine R ER; Graubert, Timothy A TA; Dipersio, John F JF; Ley, Timothy J TJ; Wilson, Richard K RK; Goodfellow, Paul J PJ; Raphael, Benjamin J BJ; Chen, Feng F; Johnson, Kimberly J KJ; Parvin, Jeffrey D JD; Ding, Li L

Publication Date: 2015-12-22

Variant appearance in text: BRCA1: P1238L

PubMed Link: 26689913

Variant Present in the following documents:

• ncomms10086-s24.xlsx, sheet 1
• ncomms10086-s13.xlsx, sheet 1
• ncomms10086-s22.xlsx, sheet 1
• ncomms10086-s1.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: BRCA1: P1238L

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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Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins.

Nature Communications

Carmi, Shai S; Hui, Ken Y KY; Kochav, Ethan E; Liu, Xinmin X; Xue, James J; Grady, Fillan F; Guha, Saurav S; Upadhyay, Kinnari K; Ben-Avraham, Dan D; Mukherjee, Semanti S; Bowen, B Monica BM; Thomas, Tinu T; Vijai, Joseph J; Cruts, Marc M; Froyen, Guy G; Lambrechts, Diether D; Plaisance, Stéphane S; Van Broeckhoven, Christine C; Van Damme, Philip P; Van Marck, Herwig H; Barzilai, Nir N; Darvasi, Ariel A; Offit, Kenneth K; Bressman, Susan S; Ozelius, Laurie J LJ; Peter, Inga I; Cho, Judy H JH; Ostrer, Harry H; Atzmon, Gil G; Clark, Lorraine N LN; Lencz, Todd T; Pe'er, Itsik I

Publication Date: 2014-09-09

Variant appearance in text: BRCA1: P1238L

PubMed Link: 25203624

Variant Present in the following documents:

• ncomms5835-s5.xlsx, sheet 4

View BVdb publication page

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Estimation of the RNU2 macrosatellite mutation rate by BRCA1 mutation tracing.

Nucleic Acids Research

Tessereau, Chloé C; Lesecque, Yann Y; Monnet, Nastasia N; Buisson, Monique M; Barjhoux, Laure L; Léoné, Mélanie M; Feng, Bingjian B; Goldgar, David E DE; Sinilnikova, Olga M OM; Mousset, Sylvain S; Duret, Laurent L; Mazoyer, Sylvie S

Publication Date: 2014-08

Variant appearance in text: rs28897688

PubMed Link: 25034697

Variant Present in the following documents:

• supp_gku639_nar-00908-d-2014-File008.xlsx, sheet 1

View BVdb publication page

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Clinical characteristics of ovarian cancer classified by BRCA1, BRCA2, and RAD51C status.

Scientific Reports

Cunningham, J M JM; Cicek, M S MS; Larson, N B NB; Davila, J J; Wang, C C; Larson, M C MC; Song, H H; Dicks, E M EM; Harrington, P P; Wick, M M; Winterhoff, B J BJ; Hamidi, H H; Konecny, G E GE; Chien, J J; Bibikova, M M; Fan, J-B JB; Kalli, K R KR; Lindor, N M NM; Fridley, B L BL; Pharoah, P P D PP; Goode, E L EL

Publication Date: 2014-02-07

Variant appearance in text: BRCA1: P1238L; rs28897688

PubMed Link: 24504028

Variant Present in the following documents:

• srep04026-s1.pdf

View BVdb publication page

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Analysis of single nucleotide polymorphisms and radiation sensitivity of the lung assessed with an objective radiologic endpoin.

Clinical Lung Cancer

Kelsey, Chris R CR; Jackson, Isabel L IL; Langdon, Scott S; Owzar, Kouros K; Hubbs, Jessica J; Vujaskovic, Zeljko Z; Das, Shiva S; Marks, Lawrence B LB

Publication Date: 2013-05

Variant appearance in text: rs28897688

PubMed Link: 23313170

Variant Present in the following documents:

• Main text

View BVdb publication page

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BRCA1, TP53, and CHEK2 germline mutations in uterine serous carcinoma.

Cancer

Pennington, Kathryn P KP; Walsh, Tom T; Lee, Ming M; Pennil, Christopher C; Novetsky, Akiva P AP; Agnew, Kathy J KJ; Thornton, Anne A; Garcia, Rochelle R; Mutch, David D; King, Mary-Claire MC; Goodfellow, Paul P; Swisher, Elizabeth M EM

Publication Date: 2013-01-15

Variant appearance in text: BRCA1: P1238L

PubMed Link: 22811390

Variant Present in the following documents:

• Main text

View BVdb publication page

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A guide for functional analysis of BRCA1 variants of uncertain significance.

Human Mutation

Millot, Gaël A GA; Carvalho, Marcelo A MA; Caputo, Sandrine M SM; Vreeswijk, Maaike P G MP; Brown, Melissa A MA; Webb, Michelle M; Rouleau, Etienne E; Neuhausen, Susan L SL; Hansen, Thomas v O Tv; Galli, Alvaro A; Brandão, Rita D RD; Blok, Marinus J MJ; Velkova, Aneliya A; Couch, Fergus J FJ; Monteiro, Alvaro N A AN; ,

Publication Date: 2012-11

Variant appearance in text: BRCA1: Pro1238Leu

PubMed Link: 22753008

Variant Present in the following documents:

• Main text

View BVdb publication page

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A review of a multifactorial probability-based model for classification of BRCA1 and BRCA2 variants of uncertain significance (VUS).

Human Mutation

Lindor, Noralane M NM; Guidugli, Lucia L; Wang, Xianshu X; Vallée, Maxime P MP; Monteiro, Alvaro N A AN; Tavtigian, Sean S; Goldgar, David E DE; Couch, Fergus J FJ

Publication Date: 2012-01

Variant appearance in text: BRCA1: 3713C>T; P1238L

PubMed Link: 21990134

Variant Present in the following documents:

• Main text

View BVdb publication page

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Evaluation of unclassified variants in the breast cancer susceptibility genes BRCA1 and BRCA2 using five methods: results from a population-based study of young breast cancer patients.

Breast Cancer Research : Bcr

Lee, Eunjung E; McKean-Cowdin, Roberta R; Ma, Huiyan H; Chen, Zhengjia Z; Van Den Berg, David D; Henderson, Brian E BE; Bernstein, Leslie L; Ursin, Giske G

Publication Date: 2008

Variant appearance in text: BRCA1: P1238L

PubMed Link: 18284688

Variant Present in the following documents:

View BVdb publication page

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A systematic genetic assessment of 1,433 sequence variants of unknown clinical significance in the BRCA1 and BRCA2 breast cancer-predisposition genes.

American Journal Of Human Genetics

Easton, Douglas F DF; Deffenbaugh, Amie M AM; Pruss, Dmitry D; Frye, Cynthia C; Wenstrup, Richard J RJ; Allen-Brady, Kristina K; Tavtigian, Sean V SV; Monteiro, Alvaro N A AN; Iversen, Edwin S ES; Couch, Fergus J FJ; Goldgar, David E DE

Publication Date: 2007-11

Variant appearance in text: BRCA1: P1238L

PubMed Link: 17924331

Variant Present in the following documents:

• Main text

View BVdb publication page

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