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The majority of\n                      <jats:italic>ATM<\/jats:italic>\n                      pathogenic variants are frameshift or nonsense variants which are predicted to truncate the whole ATM protein. Herein, we report on an ataxia telangiectasia child with atypical phenotype who was identified as compound heterozygous for two\n                      <jats:italic>ATM<\/jats:italic>\n                      variants involving a previously described pathogenic single nucleotide variation (SNV) and a novel copy number variation (CNV).\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Case presentation<\/jats:title>\n                    <jats:p>\n                      A 6-year-old boy presented with delayed development and oculomotor apraxia. Brain magnetic resonance imaging showed interval development of mild atrophy in the cerebellum. Serum alpha fetoprotein level was in normal range. Next-generation sequencing and single-nucleotide polymorphism array tests were performed. Next-generation sequencing revealed a heterozygous nonsense pathogenic variant in\n                      <jats:italic>ATM<\/jats:italic>\n                      , c.742C\u2009&gt;\u2009T (p.Arg248Ter) inherited from the father. Single-nucleotide polymorphism array revealed a compound heterozygous CNV, arr[GRCh37] 11q22.3(10851766\u2013108183226)\u2009\u00d7\u20091, 31460\u00a0bp (exons 24\u201340 deletion of\n                      <jats:italic>ATM<\/jats:italic>\n                      ) inherited from the mother, which was validated by reverse transcription-polymerase chain reaction analysis (RT-PCR). We demonstrated that this variant (NM_000051.4:c.3403_6006del) generated a product of in-frame deletion of exon 24\u201340 of\n                      <jats:italic>ATM<\/jats:italic>\n                      (p.Ser1135_Gln2002del).\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      The compound heterozygosity for\n                      <jats:italic>ATM<\/jats:italic>\n                      variants involving a previously described pathogenic SNV and a novel CNV may be associated with the atypical clinical manifestations. This clinical report extends the genetic and phenotypic spectrum of\n                      <jats:italic>ATM<\/jats:italic>\n                      pathogenic variants in atypical ataxia-telangiectasia, thus making implementation of advanced analysis beyond the routine next-generation sequencing an important consideration in diagnosis and rehabilitation services for children with ataxia-telangiectasia.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12920-021-01053-3","type":"journal-article","created":{"date-parts":[[2021,8,17]],"date-time":"2021-08-17T08:21:23Z","timestamp":1629188483000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Compound heterozygous variants including a novel copy number variation in a child with atypical ataxia-telangiectasia: a case report"],"prefix":"10.1186","volume":"14","author":[{"given":"Hoo Young","family":"Lee","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dae-Hyun","family":"Jang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jae-Won","family":"Kim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dong-Woo","family":"Lee","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ja-Hyun","family":"Jang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joungsu","family":"Joo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2021,8,17]]},"reference":[{"issue":"5","key":"1053_CR1","first-page":"573","volume":"39","author":"M Swift","year":"1986","unstructured":"Swift M, Morrell D, Cromartie E, Chamberlin A, Skolnick M, Bishop D. 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The parents of the patient gave written informed consent in accordance with the Declaration of Helsinki. The protocol was approved by the institutional research review board of the Catholic University of Korea, Incheon St. Mary\u2019s Hospital.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Written informed consent for publication of identifying images or other personal or clinical details of the patient that compromise anonymity was obtained from the parents of the patient.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"Author Joungsu Joo was employed by company EONE-Diagnomics Genome Center. The remaining authors declare that they have no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"204"}}