Compound heterozygous variants including a novel copy number variation in a child with atypical ataxia-telangiectasia: a case report
Abstract Background Ataxia-telangiectasia is a rare autosomal recessive, neurodegenerative disorder caused by alterations in the ATM gene. The majority of ATM pathogenic variants are frameshift or nonsense variants which are predicted to truncate the whole ATM protein. Herein, we report on an ataxia...
Main Authors: | , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
BMC
2021-08-01
|
Series: | BMC Medical Genomics |
Subjects: | |
Online Access: | https://doi.org/10.1186/s12920-021-01053-3 |
id |
doaj-f54a1212751c4ac2a8e0252b981cc5b8 |
---|---|
record_format |
Article |
spelling |
doaj-f54a1212751c4ac2a8e0252b981cc5b82021-08-22T11:08:27ZengBMCBMC Medical Genomics1755-87942021-08-0114111010.1186/s12920-021-01053-3Compound heterozygous variants including a novel copy number variation in a child with atypical ataxia-telangiectasia: a case reportHoo Young Lee0Dae-Hyun Jang1Jae-Won Kim2Dong-Woo Lee3Ja-Hyun Jang4Joungsu Joo5TBI Rehabilitation Center, National Traffic Injury Rehabilitation HospitalDepartment of Rehabilitation Medicine, Incheon St. Mary’s Hospital, College of Medicine, The Catholic University of KoreaDepartment of Rehabilitation Medicine, Incheon St. Mary’s Hospital, College of Medicine, The Catholic University of KoreaDepartment of Rehabilitation Medicine, Incheon St. Mary’s Hospital, College of Medicine, The Catholic University of KoreaDepartment of Laboratory Medicine and Genetics, Samsung Medical CenterEONE-DIAGNOMICS Genome CenterAbstract Background Ataxia-telangiectasia is a rare autosomal recessive, neurodegenerative disorder caused by alterations in the ATM gene. The majority of ATM 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 ATM variants involving a previously described pathogenic single nucleotide variation (SNV) and a novel copy number variation (CNV). Case presentation 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 ATM, c.742C > T (p.Arg248Ter) inherited from the father. Single-nucleotide polymorphism array revealed a compound heterozygous CNV, arr[GRCh37] 11q22.3(10851766–108183226) × 1, 31460 bp (exons 24–40 deletion of ATM) 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 24–40 of ATM (p.Ser1135_Gln2002del). Conclusions The compound heterozygosity for ATM 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 ATM 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.https://doi.org/10.1186/s12920-021-01053-3Case reportAtaxia telangiectasiaDNA copy number variationPathologic variants |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Hoo Young Lee Dae-Hyun Jang Jae-Won Kim Dong-Woo Lee Ja-Hyun Jang Joungsu Joo |
spellingShingle |
Hoo Young Lee Dae-Hyun Jang Jae-Won Kim Dong-Woo Lee Ja-Hyun Jang Joungsu Joo Compound heterozygous variants including a novel copy number variation in a child with atypical ataxia-telangiectasia: a case report BMC Medical Genomics Case report Ataxia telangiectasia DNA copy number variation Pathologic variants |
author_facet |
Hoo Young Lee Dae-Hyun Jang Jae-Won Kim Dong-Woo Lee Ja-Hyun Jang Joungsu Joo |
author_sort |
Hoo Young Lee |
title |
Compound heterozygous variants including a novel copy number variation in a child with atypical ataxia-telangiectasia: a case report |
title_short |
Compound heterozygous variants including a novel copy number variation in a child with atypical ataxia-telangiectasia: a case report |
title_full |
Compound heterozygous variants including a novel copy number variation in a child with atypical ataxia-telangiectasia: a case report |
title_fullStr |
Compound heterozygous variants including a novel copy number variation in a child with atypical ataxia-telangiectasia: a case report |
title_full_unstemmed |
Compound heterozygous variants including a novel copy number variation in a child with atypical ataxia-telangiectasia: a case report |
title_sort |
compound heterozygous variants including a novel copy number variation in a child with atypical ataxia-telangiectasia: a case report |
publisher |
BMC |
series |
BMC Medical Genomics |
issn |
1755-8794 |
publishDate |
2021-08-01 |
description |
Abstract Background Ataxia-telangiectasia is a rare autosomal recessive, neurodegenerative disorder caused by alterations in the ATM gene. The majority of ATM 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 ATM variants involving a previously described pathogenic single nucleotide variation (SNV) and a novel copy number variation (CNV). Case presentation 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 ATM, c.742C > T (p.Arg248Ter) inherited from the father. Single-nucleotide polymorphism array revealed a compound heterozygous CNV, arr[GRCh37] 11q22.3(10851766–108183226) × 1, 31460 bp (exons 24–40 deletion of ATM) 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 24–40 of ATM (p.Ser1135_Gln2002del). Conclusions The compound heterozygosity for ATM 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 ATM 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. |
topic |
Case report Ataxia telangiectasia DNA copy number variation Pathologic variants |
url |
https://doi.org/10.1186/s12920-021-01053-3 |
work_keys_str_mv |
AT hooyounglee compoundheterozygousvariantsincludinganovelcopynumbervariationinachildwithatypicalataxiatelangiectasiaacasereport AT daehyunjang compoundheterozygousvariantsincludinganovelcopynumbervariationinachildwithatypicalataxiatelangiectasiaacasereport AT jaewonkim compoundheterozygousvariantsincludinganovelcopynumbervariationinachildwithatypicalataxiatelangiectasiaacasereport AT dongwoolee compoundheterozygousvariantsincludinganovelcopynumbervariationinachildwithatypicalataxiatelangiectasiaacasereport AT jahyunjang compoundheterozygousvariantsincludinganovelcopynumbervariationinachildwithatypicalataxiatelangiectasiaacasereport AT joungsujoo compoundheterozygousvariantsincludinganovelcopynumbervariationinachildwithatypicalataxiatelangiectasiaacasereport |
_version_ |
1721200147703005184 |