Neurol Sci (2014) 35:1487–1489 DOI 10.1007/s10072-014-1803-8
LETTER TO THE EDITOR
A novel TSC2 mutation in a Korean patient with tuberous sclerosis complex Hae-Jin Hu • Yeun-Jun Chung • Han-Wook Yoo Young-Hoon Kim • Tae-Hoon Eom
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Received: 25 February 2014 / Accepted: 14 April 2014 / Published online: 26 April 2014 Ó Springer-Verlag Italia 2014
Sir, A 20-month-old girl presented with five seizures since the previous day. She experienced her first seizure at 10 months of age. In the past month, she began having recurrent seizures, with a frequency of about one every 4–5 days. She showed a normal pattern of development. Otherwise, past medical and family history were unremarkable. On examination, she had one hypomelanotic macule and three cafe´-au-lait spots. Brain MRI revealed multifocal cortical tubers and multiple subependymal nodules along the right lateral ventricle (Fig. 1). And EEG revealed intermittent spike and slow waves on the right temporal area during interictal period (Fig. 2). We performed a chest radiography, echocardiogram, renal sonogram and ophthalmic examination, which all showed no abnormalities. According to the clinical diagnostic criteria for tuberous sclerosis complex (TSC) [1], she was diagnosed with definite TSC. Subsequently, vigabatrin was
H.-J. Hu and Y.-J. Chung contributed equally for this paper. H.-J. Hu Y.-J. Chung Department of Microbiology and Integrated Research Center for Genome Polymorphism, College of Medicine, Catholic University of Korea, Songeui Campus, 222 Banpo-daero, Seocho-gu, Seoul 137-701, Republic of Korea H.-W. Yoo Department of Pediatrics and Medical Genetics Center, Asan Medical Center Children’s Hospital, University of Ulsan College of Medicine, Seoul 138-736, Republic of Korea Y.-H. Kim T.-H. Eom (&) Department of Pediatrics, College of Medicine, Catholic University of Korea, Songeui Campus, 222 Banpo-daero, Seocho-gu, Seoul 137-701, Republic of Korea e-mail:
[email protected]
prescribed (1,000 mg/day) and she did not develop additional seizure. We performed PCR sequencing of 23 exons on TSC1, 41 exons on TSC2 and their exon–intron boundaries and identified a novel heterozygous missense mutation (c.3379C[T: R1127 W) on exon 29 of the TSC2 (Fig. 3a). This variant has not been reported in dbSNP137 (http:// www.ncbi.nlm.nih.gov/SNP/, build 137), the 1,000 Genomes Project (http://www.1000genomes.org/, April 2012 release), nor 54 databases of normal Korean genomes (http://tiara.gmi.ac.kr/ and http://opengenome.net/index. php/Korean). Variant conservation was observed with phastCons and phyloP scores, which are part of the MutationTaster program [2]. MutationTaster calculates these scores based on pre-computed values from UCSC. The values from phastCons are calculated from multiple genome sequences of 46 different species and scaled to a range of 0–1: values close to 1 indicate that the nucleotide is likely highly conserved. PhastCons values are estimated from each aligned column and flanking columns. In contrast, phyloP estimates each column separately without considering the effects of flanking columns. PhyloP values range from -14 to ?6, where positive scores indicate conserved sites and negative scores indicate fast-evolving sites. According to the phastCons and phyloP scores (1 and 1.547, respectively), this mutation occurs in a conserved region (Fig. 3b). Subsequently, we applied in silico methods, such as SIFT [3], PolyPhen-2 [4] and MutationTaster [2]. These methods predict where a single amino-acid substitution affects protein function, and thus is a disease-causing mutation. SIFT defines a mutation as deleterious if the substitution has a score \0.05 while PolyPhen-2 predicts it to be probably damaging if the probability score of the substitution is [0.85. Using MutationTaster, a probability
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Fig. 1 MRI images T1 and T2 with contrast. a–c Multifocal subcortical T2 high signal intensity lesions in the frontal, right temporal, and parietal lobes, respectively. d–f An approximately 1.0 9 0.5 cm sized T1 high signal intensity tubular lesion with
Fig. 2 Interictal EEG revealed intermittent spike and slow waves on the right temporal area
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contrast enhancement in the anterior horn of the left lateral ventricle subependymal layer and diffuse prominent leptomeningeal enhancement in both the cerebral hemispheres
Neurol Sci (2014) 35:1487–1489
Fig. 3 a Sequence of exon 29 on TSC2 showing a heterozygous mutation (c.3379C[T) and b R1127W missense mutation on TSC2 is evolutionary conserved. Alignment was obtained from MultiZ and other tools in the UCSC comparative genomics alignment pipeline, based on 46 vertebrate species
value close to 1 indicates high reliability of the prediction. SIFT, PolyPhen-2, and MutationTaster predicted the mutation to be damaging (0.01), probably damaging (0.99), and disease causing (0.99), respectively. These results indicate that the mutation is likely to be functionally damaging. TSC is a multisystem genetic disorder that results in hamartomatous lesions primarily involving the skin, brain, kidney, eye, heart and lung. The clinical findings and severity of TSC are highly variable [5]. By the clinical diagnostic criteria for TSC, diagnosis of definite, probable, or possible TSC is based on the presence of major and/or minor features [1]. The recent discovery of the genetic defects underlying TSC has extended our understanding of this complex genetic disorder and genotype–phenotype correlations. Two causative genes, TSC1 and TSC2, have been identified for TSC. The interaction between tuberin from TSC2 and hamartin from TSC1—the tuberin–hamartin complex is critical to multiple intracellular-signaling pathways, especially those associated with cell growth [5]. TSC occurs by a spontaneous mutation in approximately 70 % of affected individuals and a large number of mutations have been identified including 1,241 mutations in TSC1 and 3,528 in TSC2, locus-specific mutation databases (http://chromium.liacs.nl/LOVD2/TSC/home.php?select_
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db=TSC1 and http://chromium.liacs.nl/LOVD2/TSC/ home.php?select_db=TSC2, August 29, 2013 updated version). In our patient, the heterozygous missense mutation on exon 29 of the TSC2 changes arginine to tryptophan at the 1,127th locus on the amino acid. Interestingly, in the locusspecific mutation databases, neighboring 1,125, 1,126, and 1,128th loci on TSC2 have been reported to be involved in frame shift or non-frame shift mutations for TSC, such as p.Arg1125Glyfs*66, p.Arg1125Profs*43, p.Asp1126Glyfs*42, p.Asp1126Val, and p.Val1128Alafs*63. Due to a lack of known 3D-structure models for this locus, we could not assess potential structural changes associated with this mutation. However, we concluded that the novel mutation reported here may be functionally damaging based on the following observations: the mutation occurred at an evolutionarily conserved locus; in silico methods predicted it to be damaging; mutations in neighboring loci are also associated with TSC. Acknowledgments This study was supported by a grant from the Ministry of Health, Welfare and Family Affairs, Republic of Korea (A120175).
References 1. Roach ES, Gomez MR, Northrup H (1998) Tuberous sclerosis complex consensus conference: revised clinical diagnostic criteria. J Child Neurol 13:624–628 2. Schwarz JM, Rodelsperger C, Schuelke M et al (2012) MutationTaster evaluates disease causing potential of sequence alterations. Nat Methods 7:575–576 3. Kumar P, Henikoff S, Ng PC (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 4:1073–1081 4. Adzhubei IA, Schmidt S, Peshkin L et al (2010) A method and server for predicting damaging missense mutations. Nat Methods 7:248–249 5. Rosser T, Panigrahy A, McClintock W (2006) The diverse clinical manifestations of tuberous sclerosis complex: a review. Semin Pediatr Neurol 13:27–36
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