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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...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2022
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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. |
format | Online Article Text |
id | pubmed-8984122 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
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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