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. 1998 Feb;62(2):286–294. doi: 10.1086/301705

Germ-line mutational analysis of the TSC2 gene in 90 tuberous-sclerosis patients.

K S Au 1, J A Rodriguez 1, J L Finch 1, K A Volcik 1, E S Roach 1, M R Delgado 1, E Rodriguez Jr 1, H Northrup 1
PMCID: PMC1376882  PMID: 9463313

Abstract

Ninety patients with tuberous-sclerosis complex (TSC) were tested for subtle mutations in the TSC2 gene, by means of single-strand conformational analysis (SSCA) of genomic DNA. Patients included 56 sporadic cases and 34 familial probands. For all patients, SSCA was performed for each of the 41 exons of the TSC2 gene. We identified 32 SSCA changes, 22 disease-causing mutations, and 10 polymorphic variants. Interestingly, we detected mutations at a much higher frequency in the sporadic cases (32%) than in the multiplex families (9%). Among the eight families for which linkage to the TSC2 region had been determined, only one mutation was found. Mutations were distributed equally across the gene; they included 5 deletions, 3 insertions, 10 missense mutations, 2 nonsense mutations, and 2 tandem duplications. We did not detect an increase in mutations either in the GTPase-activating protein (GAP)-related domains of TSC2 or in the activating domains that have been identified in rat tuberin. We did not detect any mutations in the exons (25 and 31) that are spliced out in the isoforms. There was no evidence for correspondence between variability of phenotype and type of mutation (missense versus early termination). Diagnostic testing will be difficult because of the genetic heterogeneity of TSC (which has at least two causative genes: TSC1 and TSC2), the large size of the TSC2 gene, and the variety of mutations. More than half of the mutations that we identified (missense, small in-frame deletion, and tandem duplication) are not amenable to the mutation-detection methods, such as protein-truncation testing, that are commonly employed for genes that encode proteins with tumor-suppressor function.

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Selected References

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  1. Au K. S., Rodriguez J. A., Rodriguez E., Jr, Dobyns W. B., Delgado M. R., Northrup H. Mutations and polymorphisms in the tuberous sclerosis complex gene on chromosome 16. Hum Mutat. 1997;9(1):23–29. doi: 10.1002/(SICI)1098-1004(1997)9:1<23::AID-HUMU4>3.0.CO;2-Q. [DOI] [PubMed] [Google Scholar]
  2. Baker S. J., Preisinger A. C., Jessup J. M., Paraskeva C., Markowitz S., Willson J. K., Hamilton S., Vogelstein B. p53 gene mutations occur in combination with 17p allelic deletions as late events in colorectal tumorigenesis. Cancer Res. 1990 Dec 1;50(23):7717–7722. [PubMed] [Google Scholar]
  3. Brook-Carter P. T., Peral B., Ward C. J., Thompson P., Hughes J., Maheshwar M. M., Nellist M., Gamble V., Harris P. C., Sampson J. R. Deletion of the TSC2 and PKD1 genes associated with severe infantile polycystic kidney disease--a contiguous gene syndrome. Nat Genet. 1994 Dec;8(4):328–332. doi: 10.1038/ng1294-328. [DOI] [PubMed] [Google Scholar]
  4. Calvert R. J., Weghorst C. M., Buzard G. S. PCR amplification of silver-stained SSCP bands from cold SSCP gels. Biotechniques. 1995 May;18(5):782-4, 786. [PubMed] [Google Scholar]
  5. Chiba I., Takahashi T., Nau M. M., D'Amico D., Curiel D. T., Mitsudomi T., Buchhagen D. L., Carbone D., Piantadosi S., Koga H. Mutations in the p53 gene are frequent in primary, resected non-small cell lung cancer. Lung Cancer Study Group. Oncogene. 1990 Oct;5(10):1603–1610. [PubMed] [Google Scholar]
  6. Curatolo P., Cusmai R., Cortesi F., Chiron C., Jambaque I., Dulac O. Neuropsychiatric aspects of tuberous sclerosis. Ann N Y Acad Sci. 1991;615:8–16. doi: 10.1111/j.1749-6632.1991.tb37743.x. [DOI] [PubMed] [Google Scholar]
  7. Fryer A. E., Chalmers A., Connor J. M., Fraser I., Povey S., Yates A. D., Yates J. R., Osborne J. P. Evidence that the gene for tuberous sclerosis is on chromosome 9. Lancet. 1987 Mar 21;1(8534):659–661. doi: 10.1016/s0140-6736(87)90416-8. [DOI] [PubMed] [Google Scholar]
  8. Green A. J., Smith M., Yates J. R. Loss of heterozygosity on chromosome 16p13.3 in hamartomas from tuberous sclerosis patients. Nat Genet. 1994 Feb;6(2):193–196. doi: 10.1038/ng0294-193. [DOI] [PubMed] [Google Scholar]
  9. Haines J. L., Short M. P., Kwiatkowski D. J., Jewell A., Andermann E., Bejjani B., Yang C. H., Gusella J. F., Amos J. A. Localization of one gene for tuberous sclerosis within 9q32-9q34, and further evidence for heterogeneity. Am J Hum Genet. 1991 Oct;49(4):764–772. [PMC free article] [PubMed] [Google Scholar]
  10. Henske E. P., Scheithauer B. W., Short M. P., Wollmann R., Nahmias J., Hornigold N., van Slegtenhorst M., Welsh C. T., Kwiatkowski D. J. Allelic loss is frequent in tuberous sclerosis kidney lesions but rare in brain lesions. Am J Hum Genet. 1996 Aug;59(2):400–406. [PMC free article] [PubMed] [Google Scholar]
  11. Hughes J., Ward C. J., Peral B., Aspinwall R., Clark K., San Millán J. L., Gamble V., Harris P. C. The polycystic kidney disease 1 (PKD1) gene encodes a novel protein with multiple cell recognition domains. Nat Genet. 1995 Jun;10(2):151–160. doi: 10.1038/ng0695-151. [DOI] [PubMed] [Google Scholar]
  12. Hunt A., Dennis J. Psychiatric disorder among children with tuberous sclerosis. Dev Med Child Neurol. 1987 Apr;29(2):190–198. doi: 10.1111/j.1469-8749.1987.tb02135.x. [DOI] [PubMed] [Google Scholar]
  13. Janssen L. A., Sandkuyl L. A., Merkens E. C., Maat-Kievit J. A., Sampson J. R., Fleury P., Hennekam R. C., Grosveld G. C., Lindhout D., Halley D. J. Genetic heterogeneity in tuberous sclerosis. Genomics. 1990 Oct;8(2):237–242. doi: 10.1016/0888-7543(90)90277-2. [DOI] [PubMed] [Google Scholar]
  14. Jin F., Wienecke R., Xiao G. H., Maize J. C., Jr, DeClue J. E., Yeung R. S. Suppression of tumorigenicity by the wild-type tuberous sclerosis 2 (Tsc2) gene and its C-terminal region. Proc Natl Acad Sci U S A. 1996 Aug 20;93(17):9154–9159. doi: 10.1073/pnas.93.17.9154. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Kandt R. S., Haines J. L., Smith M., Northrup H., Gardner R. J., Short M. P., Dumars K., Roach E. S., Steingold S., Wall S. Linkage of an important gene locus for tuberous sclerosis to a chromosome 16 marker for polycystic kidney disease. Nat Genet. 1992 Sep;2(1):37–41. doi: 10.1038/ng0992-37. [DOI] [PubMed] [Google Scholar]
  16. Keen J., Lester D., Inglehearn C., Curtis A., Bhattacharya S. Rapid detection of single base mismatches as heteroduplexes on Hydrolink gels. Trends Genet. 1991 Jan;7(1):5–5. doi: 10.1016/0168-9525(91)90004-a. [DOI] [PubMed] [Google Scholar]
  17. Kumar A., Kandt R. S., Wolpert C., Roses A. D., Pericak-Vance M. A., Gilbert J. R. Mutation analysis of the TSC2 gene in an African-American family. Hum Mol Genet. 1995 Dec;4(12):2295–2298. doi: 10.1093/hmg/4.12.2295. [DOI] [PubMed] [Google Scholar]
  18. Kumar A., Wolpert C., Kandt R. S., Segal J., Pufky J., Roses A. D., Pericak-Vance M. A., Gilbert J. R. A de novo frame-shift mutation in the tuberin gene. Hum Mol Genet. 1995 Aug;4(8):1471–1472. doi: 10.1093/hmg/4.8.1471. [DOI] [PubMed] [Google Scholar]
  19. Kwiatkowski D. J., Dib C., Slaugenhaupt S. A., Povey S., Gusella J. F., Haines J. L. An index marker map of chromosome 9 provides strong evidence for positive interference. Am J Hum Genet. 1993 Dec;53(6):1279–1288. [PMC free article] [PubMed] [Google Scholar]
  20. Latif F., Tory K., Gnarra J., Yao M., Duh F. M., Orcutt M. L., Stackhouse T., Kuzmin I., Modi W., Geil L. Identification of the von Hippel-Lindau disease tumor suppressor gene. Science. 1993 May 28;260(5112):1317–1320. doi: 10.1126/science.8493574. [DOI] [PubMed] [Google Scholar]
  21. Legius E., Marchuk D. A., Collins F. S., Glover T. W. Somatic deletion of the neurofibromatosis type 1 gene in a neurofibrosarcoma supports a tumour suppressor gene hypothesis. Nat Genet. 1993 Feb;3(2):122–126. doi: 10.1038/ng0293-122. [DOI] [PubMed] [Google Scholar]
  22. Liu Q., Sommer S. S. Parameters affecting the sensitivities of dideoxy fingerprinting and SSCP. PCR Methods Appl. 1994 Oct;4(2):97–108. doi: 10.1101/gr.4.2.97. [DOI] [PubMed] [Google Scholar]
  23. Maheshwar M. M., Cheadle J. P., Jones A. C., Myring J., Fryer A. E., Harris P. C., Sampson J. R. The GAP-related domain of tuberin, the product of the TSC2 gene, is a target for missense mutations in tuberous sclerosis. Hum Mol Genet. 1997 Oct;6(11):1991–1996. doi: 10.1093/hmg/6.11.1991. [DOI] [PubMed] [Google Scholar]
  24. Northrup H., Kwiatkowski D. J., Roach E. S., Dobyns W. B., Lewis R. A., Herman G. E., Rodriguez E., Jr, Daiger S. P., Blanton S. H. Evidence for genetic heterogeneity in tuberous sclerosis: one locus on chromosome 9 and at least one locus elsewhere. Am J Hum Genet. 1992 Oct;51(4):709–720. [PMC free article] [PubMed] [Google Scholar]
  25. Osborne J. P., Fryer A., Webb D. Epidemiology of tuberous sclerosis. Ann N Y Acad Sci. 1991;615:125–127. doi: 10.1111/j.1749-6632.1991.tb37754.x. [DOI] [PubMed] [Google Scholar]
  26. Roach E. S., Smith M., Huttenlocher P., Bhat M., Alcorn D., Hawley L. Diagnostic criteria: tuberous sclerosis complex. Report of the Diagnostic Criteria Committee of the National Tuberous Sclerosis Association. J Child Neurol. 1992 Apr;7(2):221–224. doi: 10.1177/088307389200700219. [DOI] [PubMed] [Google Scholar]
  27. Roth D. B., Porter T. N., Wilson J. H. Mechanisms of nonhomologous recombination in mammalian cells. Mol Cell Biol. 1985 Oct;5(10):2599–2607. doi: 10.1128/mcb.5.10.2599. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Rouleau G. A., Merel P., Lutchman M., Sanson M., Zucman J., Marineau C., Hoang-Xuan K., Demczuk S., Desmaze C., Plougastel B. Alteration in a new gene encoding a putative membrane-organizing protein causes neuro-fibromatosis type 2. Nature. 1993 Jun 10;363(6429):515–521. doi: 10.1038/363515a0. [DOI] [PubMed] [Google Scholar]
  29. Sampson J. R., Yates J. R., Pirrit L. A., Fleury P., Winship I., Beighton P., Connor J. M. Evidence for genetic heterogeneity in tuberous sclerosis. J Med Genet. 1989 Aug;26(8):511–516. doi: 10.1136/jmg.26.8.511. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Sheffield V. C., Beck J. S., Kwitek A. E., Sandstrom D. W., Stone E. M. The sensitivity of single-strand conformation polymorphism analysis for the detection of single base substitutions. Genomics. 1993 May;16(2):325–332. doi: 10.1006/geno.1993.1193. [DOI] [PubMed] [Google Scholar]
  31. Shepherd C. W., Gomez M. R., Lie J. T., Crowson C. S. Causes of death in patients with tuberous sclerosis. Mayo Clin Proc. 1991 Aug;66(8):792–796. doi: 10.1016/s0025-6196(12)61196-3. [DOI] [PubMed] [Google Scholar]
  32. Tassabehji M., Strachan T., Sharland M., Colley A., Donnai D., Harris R., Thakker N. Tandem duplication within a neurofibromatosis type 1 (NF1) gene exon in a family with features of Watson syndrome and Noonan syndrome. Am J Hum Genet. 1993 Jul;53(1):90–95. [PMC free article] [PubMed] [Google Scholar]
  33. Tiller G. E., Rimoin D. L., Murray L. W., Cohn D. H. Tandem duplication within a type II collagen gene (COL2A1) exon in an individual with spondyloepiphyseal dysplasia. Proc Natl Acad Sci U S A. 1990 May;87(10):3889–3893. doi: 10.1073/pnas.87.10.3889. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Toguchida J., Yamaguchi T., Ritchie B., Beauchamp R. L., Dayton S. H., Herrera G. E., Yamamuro T., Kotoura Y., Sasaki M. S., Little J. B. Mutation spectrum of the p53 gene in bone and soft tissue sarcomas. Cancer Res. 1992 Nov 15;52(22):6194–6199. [PubMed] [Google Scholar]
  35. Trofatter J. A., MacCollin M. M., Rutter J. L., Murrell J. R., Duyao M. P., Parry D. M., Eldridge R., Kley N., Menon A. G., Pulaski K. A novel moesin-, ezrin-, radixin-like gene is a candidate for the neurofibromatosis 2 tumor suppressor. Cell. 1993 Mar 12;72(5):791–800. doi: 10.1016/0092-8674(93)90406-g. [DOI] [PubMed] [Google Scholar]
  36. Tsuchiya H., Orimoto K., Kobayashi K., Hino O. Presence of potent transcriptional activation domains in the predisposing tuberous sclerosis (Tsc2) gene product of the Eker rat model. Cancer Res. 1996 Feb 1;56(3):429–433. [PubMed] [Google Scholar]
  37. Vrtel R., Verhoef S., Bouman K., Maheshwar M. M., Nellist M., van Essen A. J., Bakker P. L., Hermans C. J., Bink-Boelkens M. T., van Elburg R. M. Identification of a nonsense mutation at the 5' end of the TSC2 gene in a family with a presumptive diagnosis of tuberous sclerosis complex. J Med Genet. 1996 Jan;33(1):47–51. doi: 10.1136/jmg.33.1.47. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Webb D. W., Clarke A., Fryer A., Osborne J. P. The cutaneous features of tuberous sclerosis: a population study. Br J Dermatol. 1996 Jul;135(1):1–5. [PubMed] [Google Scholar]
  39. Wiederholt W. C., Gomez M. R., Kurland L. T. Incidence and prevalence of tuberous sclerosis in Rochester, Minnesota, 1950 through 1982. Neurology. 1985 Apr;35(4):600–603. doi: 10.1212/wnl.35.4.600. [DOI] [PubMed] [Google Scholar]
  40. Wienecke R., König A., DeClue J. E. Identification of tuberin, the tuberous sclerosis-2 product. Tuberin possesses specific Rap1GAP activity. J Biol Chem. 1995 Jul 7;270(27):16409–16414. doi: 10.1074/jbc.270.27.16409. [DOI] [PubMed] [Google Scholar]
  41. Wilson P. J., Ramesh V., Kristiansen A., Bove C., Jozwiak S., Kwiatkowski D. J., Short M. P., Haines J. L. Novel mutations detected in the TSC2 gene from both sporadic and familial TSC patients. Hum Mol Genet. 1996 Feb;5(2):249–256. doi: 10.1093/hmg/5.2.249. [DOI] [PubMed] [Google Scholar]
  42. Xiao G. H., Shoarinejad F., Jin F., Golemis E. A., Yeung R. S. The tuberous sclerosis 2 gene product, tuberin, functions as a Rab5 GTPase activating protein (GAP) in modulating endocytosis. J Biol Chem. 1997 Mar 7;272(10):6097–6100. doi: 10.1074/jbc.272.10.6097. [DOI] [PubMed] [Google Scholar]
  43. Xu L., Sterner C., Maheshwar M. M., Wilson P. J., Nellist M., Short P. M., Haines J. L., Sampson J. R., Ramesh V. Alternative splicing of the tuberous sclerosis 2 (TSC2) gene in human and mouse tissues. Genomics. 1995 Jun 10;27(3):475–480. doi: 10.1006/geno.1995.1079. [DOI] [PubMed] [Google Scholar]
  44. van Bakel I., Sepp T., Ward S., Yates J. R., Green A. J. Mutations in the TSC2 gene: analysis of the complete coding sequence using the protein truncation test (PTT). Hum Mol Genet. 1997 Sep;6(9):1409–1414. doi: 10.1093/hmg/6.9.1409. [DOI] [PubMed] [Google Scholar]
  45. van Slegtenhorst M., de Hoogt R., Hermans C., Nellist M., Janssen B., Verhoef S., Lindhout D., van den Ouweland A., Halley D., Young J. Identification of the tuberous sclerosis gene TSC1 on chromosome 9q34. Science. 1997 Aug 8;277(5327):805–808. doi: 10.1126/science.277.5327.805. [DOI] [PubMed] [Google Scholar]

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