{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T05:59:52Z","timestamp":1775541592398,"version":"3.50.1"},"reference-count":16,"publisher":"Cold Spring Harbor Laboratory","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Cold Spring Harb Mol Case Stud"],"published-print":{"date-parts":[[2020,6]]},"abstract":"<jats:p>Reticular dysgenesis is a form of severe combined immunodeficiency (SCID) caused by biallelic pathogenic variants in <jats:italic>AK2<\/jats:italic>. Here we present the case of a boy diagnosed with SCID following a positive newborn screen (NBS). Genetic testing revealed a homozygous variant: <jats:italic>AK2<\/jats:italic> c.330 + 5G &gt; A. In silico analyses predicted weakened native donor splice site. However, this variant was initially classified as a variant of uncertain significance (VUS) given lack of direct evidence. To determine the impact on splicing, we analyzed RNA from the proband and his parents, using massively parallel RNA-seq of cloned RT-PCR products. Analysis showed that c.330 + 5G &gt; A results in exon 3 skipping, which encodes a critical region of the AK2 protein. With these results, the variant was upgraded to pathogenic, and the patient was given a diagnosis of reticular dysgenesis. Interpretation of VUS at noncanonical splice site nucleotides presents a challenge. RNA sequencing provides an ideal platform to perform qualitative and quantitative assessment of intronic VUS, which can lead to reclassification if a significant impact on mRNA is observed. Genetic disorders of hematopoiesis and immunity represent fruitful areas to apply RNA-based analysis for variant interpretation given the high expression of RNA in blood.<\/jats:p>","DOI":"10.1101\/mcs.a005017","type":"journal-article","created":{"date-parts":[[2020,6,12]],"date-time":"2020-06-12T23:07:54Z","timestamp":1592003274000},"page":"a005017","source":"Crossref","is-referenced-by-count":5,"title":["Reticular dysgenesis caused by an intronic pathogenic variant in <i>AK2<\/i>"],"prefix":"10.1101","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6477-0520","authenticated-orcid":false,"given":"Shoji","family":"Ichikawa","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4175-5728","authenticated-orcid":false,"given":"Susan","family":"Prockop","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0725-0320","authenticated-orcid":false,"given":"Charlotte","family":"Cunningham-Rundles","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6334-1097","authenticated-orcid":false,"given":"Travis","family":"Sifers","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6295-8375","authenticated-orcid":false,"given":"Blair 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