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. 2005 Feb;42(2):138–146. doi: 10.1136/jmg.2004.024711

Classification of BRCA1 missense variants of unknown clinical significance

C Phelan 1, V Dapic 1, B Tice 1, R Favis 1, E Kwan 1, F Barany 1, S Manoukian 1, P Radice 1, R B van der Luijt 1, B P M van Nesselrooij 1, G Chenevix-Trench 1, kConFab 1, T Caldes 1, M de La Hoya 1, S Lindquist 1, S Tavtigian 1, D Goldgar 1, A Borg 1, S Narod 1, A Monteiro 1
PMCID: PMC1735988  PMID: 15689452

Abstract

Background: BRCA1 is a tumour suppressor with pleiotropic actions. Germline mutations in BRCA1 are responsible for a large proportion of breast–ovarian cancer families. Several missense variants have been identified throughout the gene but because of lack of information about their impact on the function of BRCA1, predictive testing is not always informative. Classification of missense variants into deleterious/high risk or neutral/low clinical significance is essential to identify individuals at risk.

Objective: To investigate a panel of missense variants.

Methods and results: The panel was investigated in a comprehensive framework that included (1) a functional assay based on transcription activation; (2) segregation analysis and a method of using incomplete pedigree data to calculate the odds of causality; (3) a method based on interspecific sequence variation. It was shown that the transcriptional activation assay could be used as a test to characterise mutations in the carboxy-terminus region of BRCA1 encompassing residues 1396–1863. Thirteen missense variants (H1402Y, L1407P, H1421Y, S1512I, M1628T, M1628V, T1685I, G1706A, T1720A, A1752P, G1788V, V1809F, and W1837R) were specifically investigated.

Conclusions: While individual classification schemes for BRCA1 alleles still present limitations, a combination of several methods provides a more powerful way of identifying variants that are causally linked to a high risk of breast and ovarian cancer. The framework presented here brings these variants nearer to clinical applicability.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Abkevich V., Zharkikh A., Deffenbaugh A. M., Frank D., Chen Y., Shattuck D., Skolnick M. H., Gutin A., Tavtigian S. V. Analysis of missense variation in human BRCA1 in the context of interspecific sequence variation. J Med Genet. 2004 Jul;41(7):492–507. doi: 10.1136/jmg.2003.015867. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Anderson S. F., Schlegel B. P., Nakajima T., Wolpin E. S., Parvin J. D. BRCA1 protein is linked to the RNA polymerase II holoenzyme complex via RNA helicase A. Nat Genet. 1998 Jul;19(3):254–256. doi: 10.1038/930. [DOI] [PubMed] [Google Scholar]
  3. Antoniou Antonis C., Easton Douglas F. Polygenic inheritance of breast cancer: Implications for design of association studies. Genet Epidemiol. 2003 Nov;25(3):190–202. doi: 10.1002/gepi.10261. [DOI] [PubMed] [Google Scholar]
  4. Baer Richard, Ludwig Thomas. The BRCA1/BARD1 heterodimer, a tumor suppressor complex with ubiquitin E3 ligase activity. Curr Opin Genet Dev. 2002 Feb;12(1):86–91. doi: 10.1016/s0959-437x(01)00269-6. [DOI] [PubMed] [Google Scholar]
  5. Berchuck A., Heron K. A., Carney M. E., Lancaster J. M., Fraser E. G., Vinson V. L., Deffenbaugh A. M., Miron A., Marks J. R., Futreal P. A. Frequency of germline and somatic BRCA1 mutations in ovarian cancer. Clin Cancer Res. 1998 Oct;4(10):2433–2437. [PubMed] [Google Scholar]
  6. Berger B., Wilson D. B., Wolf E., Tonchev T., Milla M., Kim P. S. Predicting coiled coils by use of pairwise residue correlations. Proc Natl Acad Sci U S A. 1995 Aug 29;92(18):8259–8263. doi: 10.1073/pnas.92.18.8259. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Bonnen Penelope E., Wang Peggy J., Kimmel Marek, Chakraborty Ranajit, Nelson David L. Haplotype and linkage disequilibrium architecture for human cancer-associated genes. Genome Res. 2002 Dec;12(12):1846–1853. doi: 10.1101/gr.483802. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Bork P., Hofmann K., Bucher P., Neuwald A. F., Altschul S. F., Koonin E. V. A superfamily of conserved domains in DNA damage-responsive cell cycle checkpoint proteins. FASEB J. 1997 Jan;11(1):68–76. [PubMed] [Google Scholar]
  9. Brent R., Ptashne M. A eukaryotic transcriptional activator bearing the DNA specificity of a prokaryotic repressor. Cell. 1985 Dec;43(3 Pt 2):729–736. doi: 10.1016/0092-8674(85)90246-6. [DOI] [PubMed] [Google Scholar]
  10. Brodie S. G., Deng C. X. BRCA1-associated tumorigenesis: what have we learned from knockout mice? Trends Genet. 2001 Oct;17(10):S18–S22. doi: 10.1016/s0168-9525(01)02451-9. [DOI] [PubMed] [Google Scholar]
  11. Brzovic P. S., Meza J. E., King M. C., Klevit R. E. BRCA1 RING domain cancer-predisposing mutations. Structural consequences and effects on protein-protein interactions. J Biol Chem. 2001 Aug 28;276(44):41399–41406. doi: 10.1074/jbc.M106551200. [DOI] [PubMed] [Google Scholar]
  12. Brzovic P. S., Meza J., King M. C., Klevit R. E. The cancer-predisposing mutation C61G disrupts homodimer formation in the NH2-terminal BRCA1 RING finger domain. J Biol Chem. 1998 Apr 3;273(14):7795–7799. doi: 10.1074/jbc.273.14.7795. [DOI] [PubMed] [Google Scholar]
  13. Callebaut I., Mornon J. P. From BRCA1 to RAP1: a widespread BRCT module closely associated with DNA repair. FEBS Lett. 1997 Jan 2;400(1):25–30. doi: 10.1016/s0014-5793(96)01312-9. [DOI] [PubMed] [Google Scholar]
  14. Chapman M. S., Verma I. M. Transcriptional activation by BRCA1. Nature. 1996 Aug 22;382(6593):678–679. doi: 10.1038/382678a0. [DOI] [PubMed] [Google Scholar]
  15. Couch F. J., Weber B. L. Mutations and polymorphisms in the familial early-onset breast cancer (BRCA1) gene. Breast Cancer Information Core. Hum Mutat. 1996;8(1):8–18. doi: 10.1002/humu.1380080102. [DOI] [PubMed] [Google Scholar]
  16. Deffenbaugh Amie M., Frank Thomas S., Hoffman Michael, Cannon-Albright Lisa, Neuhausen Susan L. Characterization of common BRCA1 and BRCA2 variants. Genet Test. 2002 Summer;6(2):119–121. doi: 10.1089/10906570260199375. [DOI] [PubMed] [Google Scholar]
  17. Dunning A. M., Chiano M., Smith N. R., Dearden J., Gore M., Oakes S., Wilson C., Stratton M., Peto J., Easton D. Common BRCA1 variants and susceptibility to breast and ovarian cancer in the general population. Hum Mol Genet. 1997 Feb;6(2):285–289. doi: 10.1093/hmg/6.2.285. [DOI] [PubMed] [Google Scholar]
  18. Durocher F., Shattuck-Eidens D., McClure M., Labrie F., Skolnick M. H., Goldgar D. E., Simard J. Comparison of BRCA1 polymorphisms, rare sequence variants and/or missense mutations in unaffected and breast/ovarian cancer populations. Hum Mol Genet. 1996 Jun;5(6):835–842. doi: 10.1093/hmg/5.6.835. [DOI] [PubMed] [Google Scholar]
  19. Estojak J., Brent R., Golemis E. A. Correlation of two-hybrid affinity data with in vitro measurements. Mol Cell Biol. 1995 Oct;15(10):5820–5829. doi: 10.1128/mcb.15.10.5820. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Favis R., Day J. P., Gerry N. P., Phelan C., Narod S., Barany F. Universal DNA array detection of small insertions and deletions in BRCA1 and BRCA2. Nat Biotechnol. 2000 May;18(5):561–564. doi: 10.1038/75452. [DOI] [PubMed] [Google Scholar]
  21. Fleming Melissa A., Potter John D., Ramirez Christina J., Ostrander Gary K., Ostrander Elaine A. Understanding missense mutations in the BRCA1 gene: an evolutionary approach. Proc Natl Acad Sci U S A. 2003 Jan 16;100(3):1151–1156. doi: 10.1073/pnas.0237285100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Frank Thomas S., Deffenbaugh Amie M., Reid Julia E., Hulick Mark, Ward Brian E., Lingenfelter Beth, Gumpper Kathi L., Scholl Thomas, Tavtigian Sean V., Pruss Dmitry R. Clinical characteristics of individuals with germline mutations in BRCA1 and BRCA2: analysis of 10,000 individuals. J Clin Oncol. 2002 Mar 15;20(6):1480–1490. doi: 10.1200/JCO.2002.20.6.1480. [DOI] [PubMed] [Google Scholar]
  23. Friedman L. S., Ostermeyer E. A., Szabo C. I., Dowd P., Lynch E. D., Rowell S. E., King M. C. Confirmation of BRCA1 by analysis of germline mutations linked to breast and ovarian cancer in ten families. Nat Genet. 1994 Dec;8(4):399–404. doi: 10.1038/ng1294-399. [DOI] [PubMed] [Google Scholar]
  24. Futreal P. A., Liu Q., Shattuck-Eidens D., Cochran C., Harshman K., Tavtigian S., Bennett L. M., Haugen-Strano A., Swensen J., Miki Y. BRCA1 mutations in primary breast and ovarian carcinomas. Science. 1994 Oct 7;266(5182):120–122. doi: 10.1126/science.7939630. [DOI] [PubMed] [Google Scholar]
  25. Goldgar David E., Easton Douglas F., Deffenbaugh Amie M., Monteiro Alvaro N. A., Tavtigian Sean V., Couch Fergus J., Breast Cancer Information Core (BIC) Steering Committee Integrated evaluation of DNA sequence variants of unknown clinical significance: application to BRCA1 and BRCA2. Am J Hum Genet. 2004 Aug 2;75(4):535–544. doi: 10.1086/424388. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Greenman J., Mohammed S., Ellis D., Watts S., Scott G., Izatt L., Barnes D., Solomon E., Hodgson S., Mathew C. Identification of missense and truncating mutations in the BRCA1 gene in sporadic and familial breast and ovarian cancer. Genes Chromosomes Cancer. 1998 Mar;21(3):244–249. [PubMed] [Google Scholar]
  27. Hayes F., Cayanan C., Barillà D., Monteiro A. N. Functional assay for BRCA1: mutagenesis of the COOH-terminal region reveals critical residues for transcription activation. Cancer Res. 2000 May 1;60(9):2411–2418. [PMC free article] [PubMed] [Google Scholar]
  28. Hu Y. F., Miyake T., Ye Q., Li R. Characterization of a novel trans-activation domain of BRCA1 that functions in concert with the BRCA1 C-terminal (BRCT) domain. J Biol Chem. 2000 Dec 29;275(52):40910–40915. doi: 10.1074/jbc.C000607200. [DOI] [PubMed] [Google Scholar]
  29. Hu Yan-Fen, Li Rong. JunB potentiates function of BRCA1 activation domain 1 (AD1) through a coiled-coil-mediated interaction. Genes Dev. 2002 Jun 15;16(12):1509–1517. doi: 10.1101/gad.995502. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Humphrey J. S., Salim A., Erdos M. R., Collins F. S., Brody L. C., Klausner R. D. Human BRCA1 inhibits growth in yeast: potential use in diagnostic testing. Proc Natl Acad Sci U S A. 1997 May 27;94(11):5820–5825. doi: 10.1073/pnas.94.11.5820. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Inoue R., Fukutomi T., Ushijima T., Matsumoto Y., Sugimura T., Nagao M. Germline mutation of BRCA1 in Japanese breast cancer families. Cancer Res. 1995 Aug 15;55(16):3521–3524. [PubMed] [Google Scholar]
  32. Krum Susan A., Miranda Gustavo A., Lin Chenwei, Lane Timothy F. BRCA1 associates with processive RNA polymerase II. J Biol Chem. 2003 Sep 23;278(52):52012–52020. doi: 10.1074/jbc.M308418200. [DOI] [PubMed] [Google Scholar]
  33. Miki Y., Swensen J., Shattuck-Eidens D., Futreal P. A., Harshman K., Tavtigian S., Liu Q., Cochran C., Bennett L. M., Ding W. A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science. 1994 Oct 7;266(5182):66–71. doi: 10.1126/science.7545954. [DOI] [PubMed] [Google Scholar]
  34. Mirkovic Nebojsa, Marti-Renom Marc A., Weber Barbara L., Sali Andrej, Monteiro Alvaro N. A. Structure-based assessment of missense mutations in human BRCA1: implications for breast and ovarian cancer predisposition. Cancer Res. 2004 Jun 1;64(11):3790–3797. doi: 10.1158/0008-5472.CAN-03-3009. [DOI] [PubMed] [Google Scholar]
  35. Montagna M., Santacatterina M., Corneo B., Menin C., Serova O., Lenoir G. M., Chieco-Bianchi L., D'Andrea E. Identification of seven new BRCA1 germline mutations in Italian breast and breast/ovarian cancer families. Cancer Res. 1996 Dec 1;56(23):5466–5469. [PubMed] [Google Scholar]
  36. Monteiro A. N., August A., Hanafusa H. Common BRCA1 variants and transcriptional activation. Am J Hum Genet. 1997 Sep;61(3):761–762. doi: 10.1086/515515. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Monteiro A. N., August A., Hanafusa H. Evidence for a transcriptional activation function of BRCA1 C-terminal region. Proc Natl Acad Sci U S A. 1996 Nov 26;93(24):13595–13599. doi: 10.1073/pnas.93.24.13595. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Monteiro A. N. BRCA1: exploring the links to transcription. Trends Biochem Sci. 2000 Oct;25(10):469–474. doi: 10.1016/s0968-0004(00)01632-7. [DOI] [PubMed] [Google Scholar]
  39. Monteiro A. N., Humphrey J. S. Yeast-based assays for detection and characterization of mutations in BRCA1. Breast Dis. 1998 Apr;10(1-2):61–70. doi: 10.3233/bd-1998-101-208. [DOI] [PubMed] [Google Scholar]
  40. Ouchi T., Lee S. W., Ouchi M., Aaronson S. A., Horvath C. M. Collaboration of signal transducer and activator of transcription 1 (STAT1) and BRCA1 in differential regulation of IFN-gamma target genes. Proc Natl Acad Sci U S A. 2000 May 9;97(10):5208–5213. doi: 10.1073/pnas.080469697. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Ouchi T., Monteiro A. N., August A., Aaronson S. A., Hanafusa H. BRCA1 regulates p53-dependent gene expression. Proc Natl Acad Sci U S A. 1998 Mar 3;95(5):2302–2306. doi: 10.1073/pnas.95.5.2302. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Ruffner H., Joazeiro C. A., Hemmati D., Hunter T., Verma I. M. Cancer-predisposing mutations within the RING domain of BRCA1: loss of ubiquitin protein ligase activity and protection from radiation hypersensitivity. Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):5134–5139. doi: 10.1073/pnas.081068398. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Scully R., Anderson S. F., Chao D. M., Wei W., Ye L., Young R. A., Livingston D. M., Parvin J. D. BRCA1 is a component of the RNA polymerase II holoenzyme. Proc Natl Acad Sci U S A. 1997 May 27;94(11):5605–5610. doi: 10.1073/pnas.94.11.5605. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Scully R., Ganesan S., Vlasakova K., Chen J., Socolovsky M., Livingston D. M. Genetic analysis of BRCA1 function in a defined tumor cell line. Mol Cell. 1999 Dec;4(6):1093–1099. doi: 10.1016/s1097-2765(00)80238-5. [DOI] [PubMed] [Google Scholar]
  45. Sharan S. K., Wims M., Bradley A. Murine Brca1: sequence and significance for human missense mutations. Hum Mol Genet. 1995 Dec;4(12):2275–2278. doi: 10.1093/hmg/4.12.2275. [DOI] [PubMed] [Google Scholar]
  46. Smith S. A., Easton D. F., Evans D. G., Ponder B. A. Allele losses in the region 17q12-21 in familial breast and ovarian cancer involve the wild-type chromosome. Nat Genet. 1992 Oct;2(2):128–131. doi: 10.1038/ng1092-128. [DOI] [PubMed] [Google Scholar]
  47. Somasundaram K., Zhang H., Zeng Y. X., Houvras Y., Peng Y., Zhang H., Wu G. S., Licht J. D., Weber B. L., El-Deiry W. S. Arrest of the cell cycle by the tumour-suppressor BRCA1 requires the CDK-inhibitor p21WAF1/CiP1. Nature. 1997 Sep 11;389(6647):187–190. doi: 10.1038/38291. [DOI] [PubMed] [Google Scholar]
  48. Struewing J. P., Abeliovich D., Peretz T., Avishai N., Kaback M. M., Collins F. S., Brody L. C. The carrier frequency of the BRCA1 185delAG mutation is approximately 1 percent in Ashkenazi Jewish individuals. Nat Genet. 1995 Oct;11(2):198–200. doi: 10.1038/ng1095-198. [DOI] [PubMed] [Google Scholar]
  49. Szabo C. I., Wagner L. A., Francisco L. V., Roach J. C., Argonza R., King M. C., Ostrander E. A. Human, canine and murine BRCA1 genes: sequence comparison among species. Hum Mol Genet. 1996 Sep;5(9):1289–1298. doi: 10.1093/hmg/5.9.1289. [DOI] [PubMed] [Google Scholar]
  50. Takimoto Rishu, MacLachlan Timothy K., Dicker David T., Niitsu Yoshiro, Mori Toshio, el-Deiry Wafik S. BRCA1 transcriptionally regulates damaged DNA binding protein (DDB2) in the DNA repair response following UV-irradiation. Cancer Biol Ther. 2002 Mar-Apr;1(2):177–186. doi: 10.4161/cbt.65. [DOI] [PubMed] [Google Scholar]
  51. Thangaraju M., Kaufmann S. H., Couch F. J. BRCA1 facilitates stress-induced apoptosis in breast and ovarian cancer cell lines. J Biol Chem. 2000 Oct 27;275(43):33487–33496. doi: 10.1074/jbc.M005824200. [DOI] [PubMed] [Google Scholar]
  52. Thompson Deborah, Easton Douglas F., Goldgar David E. A full-likelihood method for the evaluation of causality of sequence variants from family data. Am J Hum Genet. 2003 Jul 29;73(3):652–655. doi: 10.1086/378100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Vallon-Christersson J., Cayanan C., Haraldsson K., Loman N., Bergthorsson J. T., Brøndum-Nielsen K., Gerdes A. M., Møller P., Kristoffersson U., Olsson H. Functional analysis of BRCA1 C-terminal missense mutations identified in breast and ovarian cancer families. Hum Mol Genet. 2001 Feb 15;10(4):353–360. doi: 10.1093/hmg/10.4.353. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Venkitaraman Ashok R. Cancer susceptibility and the functions of BRCA1 and BRCA2. Cell. 2002 Jan 25;108(2):171–182. doi: 10.1016/s0092-8674(02)00615-3. [DOI] [PubMed] [Google Scholar]
  55. Williams R. S., Green R., Glover J. N. Crystal structure of the BRCT repeat region from the breast cancer-associated protein BRCA1. Nat Struct Biol. 2001 Oct;8(10):838–842. doi: 10.1038/nsb1001-838. [DOI] [PubMed] [Google Scholar]
  56. Williams R. Scott, Chasman Daniel I., Hau D. Duong, Hui Benjamin, Lau Albert Y., Glover J. N. Mark. Detection of protein folding defects caused by BRCA1-BRCT truncation and missense mutations. J Biol Chem. 2003 Oct 8;278(52):53007–53016. doi: 10.1074/jbc.M310182200. [DOI] [PubMed] [Google Scholar]

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