Skip to main content
American Journal of Human Genetics logoLink to American Journal of Human Genetics
. 1999 May;64(5):1305–1315. doi: 10.1086/302381

Comprehensive mutation analysis of TSC1 and TSC2-and phenotypic correlations in 150 families with tuberous sclerosis.

A C Jones 1, M M Shyamsundar 1, M W Thomas 1, J Maynard 1, S Idziaszczyk 1, S Tomkins 1, J R Sampson 1, J P Cheadle 1
PMCID: PMC1377866  PMID: 10205261

Abstract

Tuberous sclerosis (TSC [MIM 191090 and MIM 191100]) is an autosomal dominant disorder characterized by hamartomas in many organs. Two thirds of cases are sporadic and are thought to represent new mutations. TSC is caused by mutations affecting either of the presumed tumor-suppressor genes, TSC1 and TSC2. Both appear to function as tumor suppressors, because somatic loss or intragenic mutation of the corresponding wild-type allele is seen in the associated hamartomas. Here we report the first comprehensive mutation analysis of TSC1 and TSC2 in a cohort of 150 unrelated TSC patients and their families, using heteroduplex and SSCP analysis of all coding exons and using pulsed-field gel electrophoresis and conventional Southern blot analysis and long PCR to screen for large rearrangements. Mutations were characterized in 120 (80%) of the 150 cases, affecting TSC1 in 22 cases and TSC2 in 98 cases. TSC1 mutations were significantly underrepresented in sporadic cases (P=. 000185). Twenty-two patients had TSC2 missense mutations that were found predominantly in the GAP-related domain (eight cases) and in a small region encoded in exons 16 and 17, between nucleotides 1849 and 1859 (eight cases), consistent with the presence of residues performing key functions at these sites. In contrast, all TSC1 mutations were predicted to be truncating, consistent with a structural or adapter role for the encoded protein. Intellectual disability was significantly more frequent in TSC2 sporadic cases than in TSC1 sporadic cases (P=.0145). These data provide the first representative picture of the distribution and spectrum of mutations across the TSC1 and TSC2 loci in clinically ascertained TSC and support a difference in severity of TSC1- and TSC2-associated disease.

Full Text

The Full Text of this article is available as a PDF (282.3 KB).

Selected References

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

  1. Ali J. B., Sepp T., Ward S., Green A. J., Yates J. R. Mutations in the TSC1 gene account for a minority of patients with tuberous sclerosis. J Med Genet. 1998 Dec;35(12):969–972. doi: 10.1136/jmg.35.12.969. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Altschuler D. L., Ribeiro-Neto F. Mitogenic and oncogenic properties of the small G protein Rap1b. Proc Natl Acad Sci U S A. 1998 Jun 23;95(13):7475–7479. doi: 10.1073/pnas.95.13.7475. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Au K. S., Rodriguez J. A., Finch J. L., Volcik K. A., Roach E. S., Delgado M. R., Rodriguez E., Jr, Northrup H. Germ-line mutational analysis of the TSC2 gene in 90 tuberous-sclerosis patients. Am J Hum Genet. 1998 Feb;62(2):286–294. doi: 10.1086/301705. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Beauchamp R. L., Banwell A., McNamara P., Jacobsen M., Higgins E., Northrup H., Short P., Sims K., Ozelius L., Ramesh V. Exon scanning of the entire TSC2 gene for germline mutations in 40 unrelated patients with tuberous sclerosis. Hum Mutat. 1998;12(6):408–416. doi: 10.1002/(SICI)1098-1004(1998)12:6<408::AID-HUMU7>3.0.CO;2-P. [DOI] [PubMed] [Google Scholar]
  5. 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]
  6. European Chromosome 16 Tuberous Sclerosis Consortium Identification and characterization of the tuberous sclerosis gene on chromosome 16. Cell. 1993 Dec 31;75(7):1305–1315. doi: 10.1016/0092-8674(93)90618-z. [DOI] [PubMed] [Google Scholar]
  7. Fleury P., de Groot W. P., Delleman J. W., Verbeeten B., Jr, Frankenmolen-Witkiezwicz I. M. Tuberous sclerosis: the incidence of sporadic cases versus familial cases. Brain Dev. 1980;2(2):107–117. doi: 10.1016/s0387-7604(80)80031-3. [DOI] [PubMed] [Google Scholar]
  8. Gorvel J. P., Chavrier P., Zerial M., Gruenberg J. rab5 controls early endosome fusion in vitro. Cell. 1991 Mar 8;64(5):915–925. doi: 10.1016/0092-8674(91)90316-q. [DOI] [PubMed] [Google Scholar]
  9. 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]
  10. Jobert S., Bragado-Nilsson E., Samolyk D., Pedespan J. M., Marchal C., Reichert S., Mallet J., Pitiot G. Deletion of 11 amino acids in tuberin associated with severe tuberous sclerosis phenotypes: evidence for a new essential domain in the first third of the protein. Eur J Hum Genet. 1997 Sep-Oct;5(5):280–287. [PubMed] [Google Scholar]
  11. Jones A. C., Daniells C. E., Snell R. G., Tachataki M., Idziaszczyk S. A., Krawczak M., Sampson J. R., Cheadle J. P. Molecular genetic and phenotypic analysis reveals differences between TSC1 and TSC2 associated familial and sporadic tuberous sclerosis. Hum Mol Genet. 1997 Nov;6(12):2155–2161. doi: 10.1093/hmg/6.12.2155. [DOI] [PubMed] [Google Scholar]
  12. Knudson A. G., Jr Mutation and cancer: statistical study of retinoblastoma. Proc Natl Acad Sci U S A. 1971 Apr;68(4):820–823. doi: 10.1073/pnas.68.4.820. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Kobayashi T., Mitani H., Takahashi R., Hirabayashi M., Ueda M., Tamura H., Hino O. Transgenic rescue from embryonic lethality and renal carcinogenesis in the Eker rat model by introduction of a wild-type Tsc2 gene. Proc Natl Acad Sci U S A. 1997 Apr 15;94(8):3990–3993. doi: 10.1073/pnas.94.8.3990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Kumar A., Kandt R. S., Wolpert C., Roses A. D., Pericak-Vance M. A., Gilbert J. R. A novel splice site mutation (156 + 1G-->A) in the TSC2 gene. Hum Mutat. 1997;9(1):64–65. doi: 10.1002/(SICI)1098-1004(1997)9:1<64::AID-HUMU12>3.0.CO;2-N. [DOI] [PubMed] [Google Scholar]
  15. 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]
  16. 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]
  17. Kwiatkowska J., Jozwiak S., Hall F., Henske E. P., Haines J. L., McNamara P., Braiser J., Wigowska-Sowinska J., Kasprzyk-Obara J., Short M. P. Comprehensive mutational analysis of the TSC1 gene: observations on frequency of mutation, associated features, and nonpenetrance. Ann Hum Genet. 1998 Jul;62(Pt 4):277–285. doi: 10.1046/j.1469-1809.1998.6240277.x. [DOI] [PubMed] [Google Scholar]
  18. Longa L., Scolari F., Brusco A., Carbonara C., Polidoro S., Valzorio B., Riegler P., Migone N., Maiorca R. A large TSC2 and PKD1 gene deletion is associated with renal and extrarenal signs of autosomal dominant polycystic kidney disease. Nephrol Dial Transplant. 1997 Sep;12(9):1900–1907. doi: 10.1093/ndt/12.9.1900. [DOI] [PubMed] [Google Scholar]
  19. 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]
  20. Maheshwar M. M., Sandford R., Nellist M., Cheadle J. P., Sgotto B., Vaudin M., Sampson J. R. Comparative analysis and genomic structure of the tuberous sclerosis 2 (TSC2) gene in human and pufferfish. Hum Mol Genet. 1996 Jan;5(1):131–137. doi: 10.1093/hmg/5.1.131. [DOI] [PubMed] [Google Scholar]
  21. 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]
  22. Plank T. L., Yeung R. S., Henske E. P. Hamartin, the product of the tuberous sclerosis 1 (TSC1) gene, interacts with tuberin and appears to be localized to cytoplasmic vesicles. Cancer Res. 1998 Nov 1;58(21):4766–4770. [PubMed] [Google Scholar]
  23. Povey S., Burley M. W., Attwood J., Benham F., Hunt D., Jeremiah S. J., Franklin D., Gillett G., Malas S., Robson E. B. Two loci for tuberous sclerosis: one on 9q34 and one on 16p13. Ann Hum Genet. 1994 May;58(Pt 2):107–127. doi: 10.1111/j.1469-1809.1994.tb01881.x. [DOI] [PubMed] [Google Scholar]
  24. Roach E. S., Gomez M. R., Northrup H. Tuberous sclerosis complex consensus conference: revised clinical diagnostic criteria. J Child Neurol. 1998 Dec;13(12):624–628. doi: 10.1177/088307389801301206. [DOI] [PubMed] [Google Scholar]
  25. Sampson J. R., Janssen L. A., Sandkuijl L. A. Linkage investigation of three putative tuberous sclerosis determining loci on chromosomes 9q, 11q, and 12q. The Tuberous Sclerosis Collaborative Group. J Med Genet. 1992 Dec;29(12):861–866. doi: 10.1136/jmg.29.12.861. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Sampson J. R., Maheshwar M. M., Aspinwall R., Thompson P., Cheadle J. P., Ravine D., Roy S., Haan E., Bernstein J., Harris P. C. Renal cystic disease in tuberous sclerosis: role of the polycystic kidney disease 1 gene. Am J Hum Genet. 1997 Oct;61(4):843–851. doi: 10.1086/514888. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Sampson J. R., Scahill S. J., Stephenson J. B., Mann L., Connor J. M. Genetic aspects of tuberous sclerosis in the west of Scotland. J Med Genet. 1989 Jan;26(1):28–31. doi: 10.1136/jmg.26.1.28. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Sepp T., Yates J. R., Green A. J. Loss of heterozygosity in tuberous sclerosis hamartomas. J Med Genet. 1996 Nov;33(11):962–964. doi: 10.1136/jmg.33.11.962. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Smolarek T. A., Wessner L. L., McCormack F. X., Mylet J. C., Menon A. G., Henske E. P. Evidence that lymphangiomyomatosis is caused by TSC2 mutations: chromosome 16p13 loss of heterozygosity in angiomyolipomas and lymph nodes from women with lymphangiomyomatosis. Am J Hum Genet. 1998 Apr;62(4):810–815. doi: 10.1086/301804. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Soucek T., Hölzl G., Bernaschek G., Hengstschläger M. A role of the tuberous sclerosis gene-2 product during neuronal differentiation. Oncogene. 1998 Apr 30;16(17):2197–2204. doi: 10.1038/sj.onc.1201743. [DOI] [PubMed] [Google Scholar]
  31. Soucek T., Pusch O., Wienecke R., DeClue J. E., Hengstschläger M. Role of the tuberous sclerosis gene-2 product in cell cycle control. Loss of the tuberous sclerosis gene-2 induces quiescent cells to enter S phase. J Biol Chem. 1997 Nov 14;272(46):29301–29308. doi: 10.1074/jbc.272.46.29301. [DOI] [PubMed] [Google Scholar]
  32. Verhoef S., Vrtel R., Bakker L., Stolte-Dijkstra I., Nellist M., Begeer J. H., Zaremba J., Jozwiak S., Tempelaars A. M., Lindhout D. Recurrent mutation 4882delTT in the GAP-related domain of the tuberous sclerosis TSC2 gene. Hum Mutat. 1998;Suppl 1:S85–S87. doi: 10.1002/humu.1380110129. [DOI] [PubMed] [Google Scholar]
  33. 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]
  34. Wang Q., Verhoef S., Tempelaars A. M., Bakker P. L., Vrtel R., Hesseling-Janssen A. L., Nellist M., Oranje A. P., Stroink H., Lindhout D. Identification of a large insertion and two novel point mutations (3671del8 and S1221X) in tuberous sclerosis complex (TSC) patients. Mutations in brief no. 119. Online. Hum Mutat. 1998;11(4):331–332. doi: 10.1002/(SICI)1098-1004(1998)11:4<331::AID-HUMU12>3.0.CO;2-3. [DOI] [PubMed] [Google Scholar]
  35. 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]
  36. 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]
  37. 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]
  38. York R. D., Yao H., Dillon T., Ellig C. L., Eckert S. P., McCleskey E. W., Stork P. J. Rap1 mediates sustained MAP kinase activation induced by nerve growth factor. Nature. 1998 Apr 9;392(6676):622–626. doi: 10.1038/33451. [DOI] [PubMed] [Google Scholar]
  39. Young J. M., Burley M. W., Jeremiah S. J., Jeganathan D., Ekong R., Osborne J. P., Povey S. A mutation screen of the TSC1 gene reveals 26 protein truncating mutations and 1 splice site mutation in a panel of 79 tuberous sclerosis patients. Ann Hum Genet. 1998 May;62(Pt 3):203–213. doi: 10.1046/j.1469-1809.1998.6230203.x. [DOI] [PubMed] [Google Scholar]
  40. 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]
  41. van Slegtenhorst M., Nellist M., Nagelkerken B., Cheadle J., Snell R., van den Ouweland A., Reuser A., Sampson J., Halley D., van der Sluijs P. Interaction between hamartin and tuberin, the TSC1 and TSC2 gene products. Hum Mol Genet. 1998 Jun;7(6):1053–1057. doi: 10.1093/hmg/7.6.1053. [DOI] [PubMed] [Google Scholar]
  42. 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]

Articles from American Journal of Human Genetics are provided here courtesy of American Society of Human Genetics

RESOURCES