Breast Cancer Research and Treatment

, Volume 173, Issue 1, pp 79–86 | Cite as

A synonymous germline variant PALB2 c.18G>T (p.Gly6=) disrupts normal splicing in a family with pancreatic and breast cancers

  • Ciyu Yang
  • Ozge Ceyhan-Birsoy
  • Diana Mandelker
  • Sowmya Jairam
  • Amanda Catchings
  • Eileen M. O’Reilly
  • Michael F. Walsh
  • Liying ZhangEmail author
Preclinical study



Mutations in PALB2 have been associated with a predisposition to breast and pancreatic cancers. This study aims to characterize a novel PALB2 synonymous variant c.18G>T (p.Gly6=) identified in a family with pancreatic and breast cancers.


The PALB2 c.18G>T (p.Gly6=) variant in this family was identified using Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT™). RT-PCR and subsequent cloning were performed to investigate whether this variant affects normal splicing.


This variant completely disrupts normal splicing and leads to several abnormal transcripts, which presumably leads to premature protein truncation. The major abnormal transcript resulted in a deletion of 32 base pairs in exon 1 and frameshift.


Our results indicate that the PALB2 c.18G>T (p.Gly6=) variant is likely pathogenic. This study provided important laboratory evidence for classification of this variant and guided improved patient management.


Synonymous germline variant PALB2 Splicing 



This study was funded by Department of Pathology, Memorial Sloan Kettering Cancer Center.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.

Informed consent

Informed consent was obtained from all individual participants included in the study.


  1. 1.
    Xia B, Sheng Q, Nakanishi K, Ohashi A, Wu J, Christ N, Liu X, Jasin M, Couch FJ, Livingston DM (2006) Control of BRCA2 cellular and clinical functions by a nuclear partner, PALB2. Mol Cell 22(6):719–729CrossRefGoogle Scholar
  2. 2.
    Sy SM, Huen MS, Chen J (2009) PALB2 is an integral component of the BRCA complex required for homologous recombination repair. Proc Natl Acad Sci USA 106(17):7155–7160CrossRefGoogle Scholar
  3. 3.
    Zhang F, Ma J, Wu J, Ye L, Cai H, Xia B, Yu X (2009) PALB2 links BRCA1 and BRCA2 in the DNA-damage response. Curr Biol 19(6):524–529CrossRefGoogle Scholar
  4. 4.
    Southey MC, Teo ZL, Winship I (2013) PALB2 and breast cancer: ready for clinical translation! Appl Clin Genet 6:43–52CrossRefGoogle Scholar
  5. 5.
    Tischkowitz M, Xia B, Sabbaghian N, Reis-Filho JS, Hamel N, Li G, van Beers EH, Li L, Khalil T, Quenneville LA et al (2007) Analysis of PALB2/FANCN-associated breast cancer families. Proc Natl Acad Sci USA 104(16):6788–6793CrossRefGoogle Scholar
  6. 6.
    Xia B, Dorsman JC, Ameziane N, de Vries Y, Rooimans MA, Sheng Q, Pals G, Errami A, Gluckman E, Llera J et al (2007) Fanconi anemia is associated with a defect in the BRCA2 partner PALB2. Nat Genet 39(2):159–161CrossRefGoogle Scholar
  7. 7.
    Bleuyard JY, Buisson R, Masson JY, Esashi F (2012) ChAM, a novel motif that mediates PALB2 intrinsic chromatin binding and facilitates DNA repair. EMBO Rep 13(2):135–141CrossRefGoogle Scholar
  8. 8.
    Buisson R, Masson JY (2012) PALB2 self-interaction controls homologous recombination. Nucleic Acids Res 40(20):10312–10323CrossRefGoogle Scholar
  9. 9.
    Sy SM, Huen MS, Zhu Y, Chen J (2009) PALB2 regulates recombinational repair through chromatin association and oligomerization. J Biol Chem 284(27):18302–18310CrossRefGoogle Scholar
  10. 10.
    Oliver AW, Swift S, Lord CJ, Ashworth A, Pearl LH (2009) Structural basis for recruitment of BRCA2 by PALB2. EMBO Rep 10(9):990–996CrossRefGoogle Scholar
  11. 11.
    Reid S, Schindler D, Hanenberg H, Barker K, Hanks S, Kalb R, Neveling K, Kelly P, Seal S, Freund M et al (2007) Biallelic mutations in PALB2 cause Fanconi anemia subtype FA-N and predispose to childhood cancer. Nat Genet 39(2):162–164CrossRefGoogle Scholar
  12. 12.
    Tischkowitz M, Xia B (2010) PALB2/FANCN: recombining cancer and Fanconi anemia. Can Res 70(19):7353–7359CrossRefGoogle Scholar
  13. 13.
    Jones S, Hruban RH, Kamiyama M, Borges M, Zhang X, Parsons DW, Lin JC, Palmisano E, Brune K, Jaffee EM et al (2009) Exomic sequencing identifies PALB2 as a pancreatic cancer susceptibility gene. Science 324(5924):217CrossRefGoogle Scholar
  14. 14.
    Southey MC, Teo ZL, Dowty JG, Odefrey FA, Park DJ, Tischkowitz M, Sabbaghian N, Apicella C, Byrnes GB, Winship I et al (2010) A PALB2 mutation associated with high risk of breast cancer. Breast Cancer Res 12(6):R109CrossRefGoogle Scholar
  15. 15.
    Rahman N, Seal S, Thompson D, Kelly P, Renwick A, Elliott A, Reid S, Spanova K, Barfoot R, Chagtai T et al (2007) PALB2, which encodes a BRCA2-interacting protein, is a breast cancer susceptibility gene. Nature genetics 39(2):165–167CrossRefGoogle Scholar
  16. 16.
    Blanco A, de la Hoya M, Balmana J, Ramon y Cajal T, Teule A, Miramar MD, Esteban E, Infante M, Benitez J, Torres A et al (2012) Detection of a large rearrangement in PALB2 in Spanish breast cancer families with male breast cancer. Breast Cancer Res Treat 132(1):307–315CrossRefGoogle Scholar
  17. 17.
    Antoniou AC, Casadei S, Heikkinen T, Barrowdale D, Pylkas K, Roberts J, Lee A, Subramanian D, De Leeneer K, Fostira F et al (2014) Breast-cancer risk in families with mutations in PALB2. N Engl J Med 371(6):497–506CrossRefGoogle Scholar
  18. 18.
    Norquist BM, Harrell MI, Brady MF, Walsh T, Lee MK, Gulsuner S, Bernards SS, Casadei S, Yi Q, Burger RA et al (2016) Inherited mutations in women with ovarian carcinoma. JAMA Oncol 2(4):482–490CrossRefGoogle Scholar
  19. 19.
    Pritchard CC, Mateo J, Walsh MF, De Sarkar N, Abida W, Beltran H, Garofalo A, Gulati R, Carreira S, Eeles R et al (2016) Inherited DNA-repair gene mutations in men with metastatic prostate cancer. N Engl J Med 375(5):443–453CrossRefGoogle Scholar
  20. 20.
    Kim MS, Lee SH, Yoo NJ, Lee SH (2013) Frameshift mutation of a tumor suppressor gene PALB2 in gastric and colorectal cancers with microsatellite instability. APMIS 121(10):1015–1016CrossRefGoogle Scholar
  21. 21.
    Aoude LG, Xu M, Zhao ZZ, Kovacs M, Palmer JM, Johansson P, Symmons J, Trent JM, Martin NG, Montgomery GW et al (2014) Assessment of PALB2 as a candidate melanoma susceptibility gene. PloS ONE 9(6):e100683CrossRefGoogle Scholar
  22. 22.
    Hofstatter EW, Domchek SM, Miron A, Garber J, Wang M, Componeschi K, Boghossian L, Miron PL, Nathanson KL, Tung N (2011) PALB2 mutations in familial breast and pancreatic cancer. Fam Cancer 10(2):225–231CrossRefGoogle Scholar
  23. 23.
    Slater EP, Langer P, Niemczyk E, Strauch K, Butler J, Habbe N, Neoptolemos JP, Greenhalf W, Bartsch DK (2010) PALB2 mutations in European familial pancreatic cancer families. Clin Genet 78(5):490–494CrossRefGoogle Scholar
  24. 24.
    Lowery MA, Wong W, Jordan EJ, Lee JW, Kemel Y, Vijai J, Mandelker D, Zehir A, Capanu M, Salo-Mullen E et al: Prospective evaluation of germline alterations in patients with exocrine pancreatic neoplasms. J Natl Cancer Inst 2018Google Scholar
  25. 25.
    Hollestelle A, Wasielewski M, Martens JW, Schutte M (2010) Discovering moderate-risk breast cancer susceptibility genes. Curr Opin Genet Dev 20(3):268–276CrossRefGoogle Scholar
  26. 26.
    Erkko H, Dowty JG, Nikkila J, Syrjakoski K, Mannermaa A, Pylkas K, Southey MC, Holli K, Kallioniemi A, Jukkola-Vuorinen A et al (2015) Penetrance analysis of the PALB2 c.1592delT founder mutation. Clin Cancer Res 17(5):405–424Google Scholar
  27. 27.
    Liu HX, Cartegni L, Zhang MQ, Krainer AR (2001) A mechanism for exon skipping caused by nonsense or missense mutations in BRCA1 and other genes. Nat Genet 27(1):55–58CrossRefGoogle Scholar
  28. 28.
    Cartegni L, Chew SL, Krainer AR (2002) Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat Rev Genet 3(4):285–298CrossRefGoogle Scholar
  29. 29.
    Wang GS, Cooper TA (2007) Splicing in disease: disruption of the splicing code and the decoding machinery. Nat Rev Genet 8(10):749–761CrossRefGoogle Scholar
  30. 30.
    Jensen CJ, Oldfield BJ, Rubio JP (2009) Splicing, cis genetic variation and disease. Biochem Soc T 37:1311–1315CrossRefGoogle Scholar
  31. 31.
    Jian X, Boerwinkle E, Liu X (2014) In silico tools for splicing defect prediction: a survey from the viewpoint of end users. Genet Med 16(7):497–503CrossRefGoogle Scholar
  32. 32.
    Houdayer C, Caux-Moncoutier V, Krieger S, Barrois M, Bonnet F, Bourdon V, Bronner M, Buisson M, Coulet F, Gaildrat P et al (2012) Guidelines for splicing analysis in molecular diagnosis derived from a set of 327 combined in silico/in vitro studies on BRCA1 and BRCA2 variants. Hum Mutat 33(8):1228–1238CrossRefGoogle Scholar
  33. 33.
    Vreeswijk MP, Kraan JN, van der Klift HM, Vink GR, Cornelisse CJ, Wijnen JT, Bakker E, van Asperen CJ, Devilee P (2009) Intronic variants in BRCA1 and BRCA2 that affect RNA splicing can be reliably selected by splice-site prediction programs. Hum Mutat 30(1):107–114CrossRefGoogle Scholar
  34. 34.
    Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E et al (2015) Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med 17(5):405–424CrossRefGoogle Scholar
  35. 35.
    Catucci I, Peterlongo P, Ciceri S, Colombo M, Pasquini G, Barile M, Bonanni B, Verderio P, Pizzamiglio S, Foglia C et al (2014) PALB2 sequencing in Italian familial breast cancer cases reveals a high-risk mutation recurrent in the province of Bergamo. Genet Med 16(9):688–694CrossRefGoogle Scholar
  36. 36.
    Casadei S, Norquist BM, Walsh T, Stray S, Mandell JB, Lee MK, Stamatoyannopoulos JA, King MC (2011) Contribution of inherited mutations in the BRCA2-interacting protein PALB2 to familial breast cancer. Can Res 71(6):2222–2229CrossRefGoogle Scholar
  37. 37.
    Foulkes WD, Ghadirian P, Akbari MR, Hamel N, Giroux S, Sabbaghian N, Darnel A, Royer R, Poll A, Fafard E et al (2007) Identification of a novel truncating PALB2 mutation and analysis of its contribution to early-onset breast cancer in French-Canadian women. Breast Cancer Res 9(6):R83CrossRefGoogle Scholar
  38. 38.
    Easton DF, Pharoah PD, Antoniou AC, Tischkowitz M, Tavtigian SV, Nathanson KL, Devilee P, Meindl A, Couch FJ, Southey M et al (2015) Gene-panel sequencing and the prediction of breast-cancer risk. N Engl J Med 372(23):2243–2257CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Departments of PathologyMemorial Sloan Kettering Cancer CenterNew YorkUSA
  2. 2.Departments of PediatricsMemorial Sloan Kettering Cancer CenterNew YorkUSA

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