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Case Report: Novel Splicing Variant in SH2D1A in a Patient With X-Linked Lymphoproliferative Syndrome Type 1

X-linked lymphoproliferative disease type 1 (XLP1), an X-linked recessive genetic disorder, is associated with primary immunodeficiency. Patients with XLP1 are susceptible to Epstein–Barr virus (EBV) infection. SH2D1A gene is known as the causative gene. We found a novel hemizygous variant of SH2D1A...

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Autores principales: Kwon, Won Kyung, Kim, Jee Ah, Park, Jong-Ho, Kim, Doo Ri, Park, Su Eun, Kim, Yae Jean, Yoo, Keon Hee, Jang, Ja-Hyun, Kang, Eun Suk
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8984122/
https://www.ncbi.nlm.nih.gov/pubmed/35402355
http://dx.doi.org/10.3389/fped.2022.812590
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author Kwon, Won Kyung
Kim, Jee Ah
Park, Jong-Ho
Kim, Doo Ri
Park, Su Eun
Kim, Yae Jean
Yoo, Keon Hee
Jang, Ja-Hyun
Kang, Eun Suk
author_facet Kwon, Won Kyung
Kim, Jee Ah
Park, Jong-Ho
Kim, Doo Ri
Park, Su Eun
Kim, Yae Jean
Yoo, Keon Hee
Jang, Ja-Hyun
Kang, Eun Suk
author_sort Kwon, Won Kyung
collection PubMed
description X-linked lymphoproliferative disease type 1 (XLP1), an X-linked recessive genetic disorder, is associated with primary immunodeficiency. Patients with XLP1 are susceptible to Epstein–Barr virus (EBV) infection. SH2D1A gene is known as the causative gene. We found a novel hemizygous variant of SH2D1A, c.162_201+31delinsTACAAGGACATATACA, from a 5-year-old male patient who had been diagnosed with EBV infection and Hodgkin's lymphoma. In targeted next-generation sequencing (NGS), complex variants at exon 2 were not consistently identified with two software programs. They showed a soft-clipped read pattern. The variant had a 71-bp deletion and a 16-bp insertion across exon 2 as confirmed by direct sequencing. As the variant was located within the exon–intron boundary, two aberrant transcripts were shown by RNA study. Although NGS method has a limitation in detecting large deletion/duplication variants, proper bioinformatics pipeline and careful review of data might enable the detection of complex variants.
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spelling pubmed-89841222022-04-07 Case Report: Novel Splicing Variant in SH2D1A in a Patient With X-Linked Lymphoproliferative Syndrome Type 1 Kwon, Won Kyung Kim, Jee Ah Park, Jong-Ho Kim, Doo Ri Park, Su Eun Kim, Yae Jean Yoo, Keon Hee Jang, Ja-Hyun Kang, Eun Suk Front Pediatr Pediatrics X-linked lymphoproliferative disease type 1 (XLP1), an X-linked recessive genetic disorder, is associated with primary immunodeficiency. Patients with XLP1 are susceptible to Epstein–Barr virus (EBV) infection. SH2D1A gene is known as the causative gene. We found a novel hemizygous variant of SH2D1A, c.162_201+31delinsTACAAGGACATATACA, from a 5-year-old male patient who had been diagnosed with EBV infection and Hodgkin's lymphoma. In targeted next-generation sequencing (NGS), complex variants at exon 2 were not consistently identified with two software programs. They showed a soft-clipped read pattern. The variant had a 71-bp deletion and a 16-bp insertion across exon 2 as confirmed by direct sequencing. As the variant was located within the exon–intron boundary, two aberrant transcripts were shown by RNA study. Although NGS method has a limitation in detecting large deletion/duplication variants, proper bioinformatics pipeline and careful review of data might enable the detection of complex variants. Frontiers Media S.A. 2022-03-23 /pmc/articles/PMC8984122/ /pubmed/35402355 http://dx.doi.org/10.3389/fped.2022.812590 Text en Copyright © 2022 Kwon, Kim, Park, Kim, Park, Kim, Yoo, Jang and Kang. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Pediatrics
Kwon, Won Kyung
Kim, Jee Ah
Park, Jong-Ho
Kim, Doo Ri
Park, Su Eun
Kim, Yae Jean
Yoo, Keon Hee
Jang, Ja-Hyun
Kang, Eun Suk
Case Report: Novel Splicing Variant in SH2D1A in a Patient With X-Linked Lymphoproliferative Syndrome Type 1
title Case Report: Novel Splicing Variant in SH2D1A in a Patient With X-Linked Lymphoproliferative Syndrome Type 1
title_full Case Report: Novel Splicing Variant in SH2D1A in a Patient With X-Linked Lymphoproliferative Syndrome Type 1
title_fullStr Case Report: Novel Splicing Variant in SH2D1A in a Patient With X-Linked Lymphoproliferative Syndrome Type 1
title_full_unstemmed Case Report: Novel Splicing Variant in SH2D1A in a Patient With X-Linked Lymphoproliferative Syndrome Type 1
title_short Case Report: Novel Splicing Variant in SH2D1A in a Patient With X-Linked Lymphoproliferative Syndrome Type 1
title_sort case report: novel splicing variant in sh2d1a in a patient with x-linked lymphoproliferative syndrome type 1
topic Pediatrics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8984122/
https://www.ncbi.nlm.nih.gov/pubmed/35402355
http://dx.doi.org/10.3389/fped.2022.812590
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