Advertisement

A novel pathogenic variant in an Iranian Ataxia telangiectasia family revealed by next-generation sequencing followed by in silico analysis

      Highlights

      • A pathogenic frameshift variant in ATM gene was detected in an Iranian proband with classical phenotype of A-T.
      • Frameshift and missense variants are among the majority types of ATM variants.
      • Truncating variants which result in complete absence of ATM kinase activity lead to severe phenotype of A-T.
      • This variant was classified as pathogenic based on some line of evidence according to ACMG guideline.
      • In this proof-of-concept study, NGS was applied to the genetic diagnostics of a genetic disease with a large gene

      Abstract

      Ataxia telangiectasia (A-T) is a neurodegenerative autosomal recessive disorder with the main characteristics of progressive cerebellar degeneration, sensitivity to ionizing radiation, immunodeficiency, telangiectasia, premature aging, recurrent sinopulmonary infections, and increased risk of malignancy, especially of lymphoid origin. Ataxia Telangiectasia Mutated gene, ATM, as a causative gene for the A-T disorder, encodes the ATM protein, which plays an important role in the activation of cell-cycle checkpoints and initiation of DNA repair in response to DNA damage. Targeted next-generation sequencing (NGS) was performed on an Iranian 5-year-old boy presented with truncal and limb ataxia, telangiectasia of the eye, Hodgkin lymphoma, hyper pigmentation, total alopecia, hepatomegaly, and dysarthria. Sanger sequencing was used to confirm the candidate pathogenic variants. Computational docking was done using the HEX software to examine how this change affects the interactions of ATM with the upstream and downstream proteins. Three different variants were identified comprising two homozygous SNPs and one novel homozygous frameshift variant (c.80468047delTA, p.Thr2682ThrfsX5), which creates a stop codon in exon 57 leaving the protein truncated at its C-terminal portion. Therefore, the activation and phosphorylation of target proteins are lost. Moreover, the HEX software confirmed that the mutated protein lost its interaction with upstream and downstream proteins. The variant was classified as pathogenic based on the American College of Medical Genetics and Genomics guideline. This study expands the spectrum of ATM pathogenic variants in Iran and demonstrates the utility of targeted NGS in genetic diagnostics.

      Keywords

      To read this article in full you will need to make a payment

      Purchase one-time access:

      Academic & Personal: 24 hour online accessCorporate R&D Professionals: 24 hour online access
      One-time access price info
      • For academic or personal research use, select 'Academic and Personal'
      • For corporate R&D use, select 'Corporate R&D Professionals'

      Subscribe:

      Subscribe to Journal of the Neurological Sciences
      Already a print subscriber? Claim online access
      Already an online subscriber? Sign in
      Institutional Access: Sign in to ScienceDirect

      References

        • Anheim M.
        • Tranchant C.
        • Koenig M.
        The autosomal recessive cerebellar ataxias.
        New Engl. J. Med. 2012; 366: 636-646
        • Nissenkorn A.
        • Levy-Shraga Y.
        • Banet-Levi Y.
        • Lahad A.
        • Sarouk I.
        • Modan-Moses D.
        Endocrine abnormalities in ataxia telangiectasia: findings from a national cohort.
        Pediatr. Res. 2016; 79: 889-894
        • Swift M.
        • Morrell D.
        • Cromartie E.
        • Chamberlin A.R.
        • Skolnick M.H.
        • Bishop D.T.
        The incidence and gene frequency of ataxia-telangiectasia in the United States.
        Am. J. Hum. Genet. 1986; 39: 573-583
        • Gatti R.A.
        • Berkel I.
        • Boder E.
        • Braedt G.
        • Charmley P.
        • Concannon P.
        • Ersoy F.
        • Foroud T.
        • Jaspers N.G.
        • Lange K.
        • et al.
        Localization of an ataxia-telangiectasia gene to chromosome 11q22-23.
        Nature. 1988; 336: 577-580
        • Savitsky K.
        • Bar-Shira A.
        • Gilad S.
        • Rotman G.
        A single ataxia telangiectasia gene with a product similar to Pl-3 kinase.
        Science. 1995; 268: 1749
        • Uziel T.
        • Savitsky K.
        • Platzer M.
        • Ziv Y.
        • Helbitz T.
        • Nehls M.
        • Boehm T.
        • Rosenthal A.
        • Shiloh Y.
        • Rotman G.
        Genomic organization of the ATM gene.
        Genomics. 1996; 33: 317-320
        • Platzer M.
        • Rotman G.
        • Bauer D.
        • Uziel T.
        • Savitsky K.
        • Bar-Shira A.
        • Gilad S.
        • Shiloh Y.
        • Rosenthal A.
        Ataxia-telangiectasia locus: sequence analysis of 184 kb of human genomic DNA containing the entire ATM gene.
        Genome Res. 1997; 7: 592-605
        • Watters D.
        • Kedar P.
        • Spring K.
        • Bjorkman J.
        • Chen P.
        • Gatei M.
        • Birrell G.
        • Garrone B.
        • Srinivasa P.
        • Crane D.I.
        • Lavin M.F.
        Localization of a portion of extranuclear ATM to peroxisomes.
        J. Biol. Chem. 1999; 274: 34277-34282
        • Sun Y.
        • Jiang X.
        • Chen S.
        • Fernandes N.
        • Price B.D.
        A role for the Tip60 histone acetyltransferase in the acetylation and activation of ATM.
        Proc. Natl. Acad. Sci. U. S. A. 2005; 102: 13182-13187
        • Kitagawa R.
        • Kastan M.B.
        The ATM-dependent DNA damage signaling pathway.
        Cold Spring Harb. Symp. Quant. Biol. 2005; 70: 99-109
        • Li A.
        • Swift M.
        Mutations at the ataxia-telangiectasia locus and clinical phenotypes of A–T patients.
        Am. J. Med. Genet. 2000; 92: 170-177
        • Sandoval N.
        • Platzer M.
        • Rosenthal A.
        • Dörk T.
        • Bendix R.
        • Skawran B.
        • Stuhrmann M.
        • Wegner R.-D.
        • Sperling K.
        • Banin S.
        Characterization of ATM gene mutations in 66 ataxia telangiectasia families.
        Hum. Mol. Genet. 1999; 8: 69-79
        • Telatar M.
        • Teraoka S.
        • Wang Z.
        • Chun H.H.
        • Liang T.
        • Castellvi-Bel S.
        • Udar N.
        • Borresen-Dale A.-L.
        • Chessa L.
        • Bernatowska-Matuszkiewicz E.
        Ataxia-telangiectasia: identification and detection of founder-effect mutations in the ATM gene in ethnic populations.
        Am. J. Hum. Genet. 1998; 62: 86-97
        • Mardis E.R.
        The impact of next-generation sequencing technology on genetics.
        Trends Genet. 2008; 24: 133-141
        • De Keulenaer S.
        • Hellemans J.
        • Lefever S.
        • Renard J.-P.
        • De Schrijver J.
        • Van de Voorde H.
        • Tabatabaiefar M.A.
        • Van Nieuwerburgh F.
        • Flamez D.
        • Pattyn F.
        Molecular diagnostics for congenital hearing loss including 15 deafness genes using a next generation sequencing platform.
        BMC Med. Genet. 2012; 5: 17
        • Babaei M.
        • Mitui M.
        • Olson E.R.
        • Gatti R.A.
        ATM haplotypes and associated mutations in Iranian patients with ataxia–telangiectasia: recurring homozygosity without a founder haplotype.
        Hum. Genet. 2005; 117: 101-106
        • Li H.
        • Durbin R.
        Fast and accurate short read alignment with Burrows-Wheeler transform.
        Bioinformatics. 2009; 25: 1754-1760
        • Macindoe G.
        • Mavridis L.
        • Venkatraman V.
        • Devignes M.D.
        • Ritchie D.W.
        HexServer: an FFT-based protein docking server powered by graphics processors.
        Nucleic Acids Res. 2010; 38: W445-W449
        • Richards S.
        • Aziz N.
        • Bale S.
        • Bick D.
        • Das S.
        • Gastier-Foster J.
        • Grody W.W.
        • Hegde M.
        • Lyon E.
        • Spector E.
        • Voelkerding K.
        • Rehm H.L.
        • Committee A.L.Q.A.
        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. 2015; 17: 405-424
        • Heikkinen K.
        • Rapakko K.
        • Karppinen S.M.
        • Erkko H.
        • Nieminen P.
        • Winqvist R.
        Association of common ATM polymorphism with bilateral breast cancer.
        Int. J. Cancer. 2005; 116: 69-72
        • Zhang Y.
        • Liu Z.
        • Wang M.
        • Tian H.
        • Su K.
        • Cui J.
        • Dong L.
        • Han F.
        Single nucleotide polymorphism rs1801516 in ataxia telangiectasia-mutated gene predicts late fibrosis in cancer patients after radiotherapy: a PRISMA-compliant systematic review and meta-analysis.
        Medicine. 2016; 95
        • Fernandes N.
        • Sun Y.
        • Chen S.
        • Paul P.
        • Shaw R.J.
        • Cantley L.C.
        • Price B.D.
        DNA damage-induced association of ATM with its target proteins requires a protein interaction domain in the N terminus of ATM.
        J. Biol. Chem. 2005; 280: 15158-15164
        • Jiang X.
        • Sun Y.
        • Chen S.
        • Roy K.
        • Price B.D.
        The FATC domains of PIKK proteins are functionally equivalent and participate in the Tip60-dependent activation of DNA-PKcs and ATM.
        J. Biol. Chem. 2006; 281: 15741-15746
        • Barone G.
        • Groom A.
        • Reiman A.
        • Srinivasan V.
        • Byrd P.J.
        • Taylor A.M.
        Modeling ATM mutant proteins from missense changes confirms retained kinase activity.
        Hum. Mutat. 2009; 30: 1222-1230
        • Becker-Catania S.G.
        • Chen G.
        • Hwang M.J.
        • Wang Z.
        • Sun X.
        • Sanal O.
        • Bernatowska-Matuszkiewicz E.
        • Chessa L.
        • Lee E.Y.
        • Gatti R.A.
        Ataxia-telangiectasia: phenotype/genotype studies of ATM protein expression, mutations, and radiosensitivity.
        Mol. Genet. Metab. 2000; 70: 122-133
        • Cavalieri S.
        • Funaro A.
        • Porcedda P.
        • Turinetto V.
        • Migone N.
        • Gatti R.A.
        • Brusco A.
        ATM mutations in Italian families with ataxia telangiectasia include two distinct large genomic deletions.
        Hum. Mutat. 2006; 27: 1061
        • Demuth I.
        • Dutrannoy V.
        • Marques W.
        • Neitzel H.
        • Schindler D.
        • Dimova P.S.
        • Chrzanowska K.H.
        • Bojinova V.
        • Gregorek H.
        • Graul-Neumann L.M.
        New mutations in the ATM gene and clinical data of 25 AT patients.
        Neurogenetics. 2011; 12: 273-282
        • Gilad S.
        • Khosravi R.
        • Shkedy D.
        • Uziel T.
        • Ziv Y.
        • Savitsky K.
        • Rotman G.
        • Smith S.
        • Chessa L.
        • Jorgensen T.J.
        • Harnik R.
        • Frydman M.
        • Sanal O.
        • Portnoi S.
        • Goldwicz Z.
        • Jaspers N.G.
        • Gatti R.A.
        • Lenoir G.
        • Lavin M.F.
        • Tatsumi K.
        • Wegner R.D.
        • Shiloh Y.
        • Bar-Shira A.
        Predominance of null mutations in ataxia-telangiectasia.
        Hum. Mol. Genet. 1996; 5: 433-439
        • Heinrich T.
        • Prowald C.
        • Friedl R.
        • Gottwald B.
        • Kalb R.
        • Neveling K.
        • Herterich S.
        • Hoehn H.
        • Schindler D.
        Exclusion/confirmation of ataxia-telangiectasia via cell-cycle testing.
        Eur. J. Pediatr. 2006; 165: 250-257
        • Mitui M.
        • Campbell C.
        • Coutinho G.
        • Sun X.
        • Lai C.H.
        • Thorstenson Y.
        • Castellvi-Bel S.
        • Fernandez L.
        • Monros E.
        • Carvalho B.T.
        • Porras O.
        • Fontan G.
        • Gatti R.A.
        Independent mutational events are rare in the ATM gene: haplotype prescreening enhances mutation detection rate.
        Hum. Mutat. 2003; 22: 43-50
        • Saviozzi S.
        • Saluto A.
        • Taylor A.
        • Last J.
        • Trebini F.
        • Paradiso M.
        • Grosso E.
        • Funaro A.
        • Ponzio G.
        • Migone N.
        A late onset variant of ataxia-telangiectasia with a compound heterozygous genotype, A8030G/7481insA.
        J. Med. Genet. 2002; 39: 57-61
        • Scott S.P.
        • Bendix R.
        • Chen P.
        • Clark R.
        • Dörk T.
        • Lavin M.F.
        Missense mutations but not allelic variants alter the function of ATM by dominant interference in patients with breast cancer.
        Proc. Natl. Acad. Sci. 2002; 99: 925-930
        • Concannon P.
        • Gatti R.A.
        Diversity of ATM gene mutations detected in patients with ataxia-telangiectasia.
        Hum. Mutat. 1997; 10: 100-107
        • Wright J.
        • Teraoka S.
        • Onengut S.
        • Tolun A.
        • Gatti R.A.
        • Ochs H.D.
        • Concannon P.
        A high frequency of distinct ATM gene mutations in ataxia-telangiectasia.
        Am. J. Hum. Genet. 1996; 59: 839-846
        • Micol R.
        • Ben Slama L.
        • Suarez F.
        • Le Mignot L.
        • Beaute J.
        • Mahlaoui N.
        • Dubois d'Enghien C.
        • Lauge A.
        • Hall J.
        • Couturier J.
        • Vallee L.
        • Delobel B.
        • Rivier F.
        • Nguyen K.
        • Billette de Villemeur T.
        • Stephan J.L.
        • Bordigoni P.
        • Bertrand Y.
        • Aladjidi N.
        • Pedespan J.M.
        • Thomas C.
        • Pellier I.
        • Koenig M.
        • Hermine O.
        • Picard C.
        • Moshous D.
        • Neven B.
        • Lanternier F.
        • Blanche S.
        • Tardieu M.
        • Debre M.
        • Fischer A.
        • Stoppa-Lyonnet D.
        • Investigators C.N.
        Morbidity and mortality from ataxia-telangiectasia are associated with ATM genotype.
        J. Allergy Clin. Immunol. 2011; 128 (e381): 382-389
        • Lakin N.D.
        • Weber P.
        • Stankovic T.
        • Rottinghaus S.T.
        • Taylor A.M.
        • Jackson S.P.
        Analysis of the ATM protein in wild-type and ataxia telangiectasia cells.
        Oncogene. 1996; 13: 2707-2716
        • Stewart G.S.
        • Last J.I.
        • Stankovic T.
        • Haites N.
        • Kidd A.M.
        • Byrd P.J.
        • Taylor A.M.
        Residual ataxia telangiectasia mutated protein function in cells from ataxia telangiectasia patients, with 5762ins137 and 7271T-->G mutations, showing a less severe phenotype.
        J. Biol. Chem. 2001; 276: 30133-30141
        • Verhagen M.M.
        • Abdo W.F.
        • Willemsen M.A.
        • Hogervorst F.B.
        • Smeets D.F.
        • Hiel J.A.
        • Brunt E.R.
        • van Rijn M.A.
        • Majoor Krakauer D.
        • Oldenburg R.A.
        • Broeks A.
        • Last J.I.
        • van't Veer L.J.
        • Tijssen M.A.
        • Dubois A.M.
        • Kremer H.P.
        • Weemaes C.M.
        • Taylor A.M.
        • van Deuren M.
        Clinical spectrum of ataxia-telangiectasia in adulthood.
        Neurology. 2009; 73: 430-437
        • Ross C.A.
        • Truant R.
        DNA repair: a unifying mechanism in neurodegeneration.
        Nature. 2017; 541: 34-35
        • Huang Y.
        • Yang L.
        • Wang J.
        • Yang F.
        • Xiao Y.
        • Xia R.
        • Yuan X.
        • Yan M.
        Twelve novel Atm mutations identified in Chinese ataxia telangiectasia patients.
        NeuroMolecular Med. 2013; 15: 536-540
        • Laake K.
        • Telatar M.
        • Geitvik G.A.
        • Hansen R.Ø.
        • Heiberg A.
        • Andresen A.M.
        • Gatti R.
        • Børresen-Dale A.-L.
        Identical mutation in 55% of the ATM alleles in 11 Norwegian AT families: evidence for a founder effect.
        Eur. J. Hum. Genet. 1998; 6: 235-244
        • Saadat M.
        • Ansari-Lari M.
        • Farhud D.
        Short report consanguineous marriage in Iran.
        Ann. Hum. Biol. 2004; 31: 263-269