{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T09:59:36Z","timestamp":1789207176945,"version":"build-2803163510"},"reference-count":20,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,2,27]],"date-time":"2023-02-27T00:00:00Z","timestamp":1677456000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Genet."],"abstract":"<jats:p><jats:bold>Introduction:<\/jats:bold> Alport syndrome (AS; OMIM#308940) is a progressive hereditary kidney disease characterized by hearing loss and ocular abnormalities. According to the mode of inheritance, AS has three subtypes: X-linked (XL; OMIM#301050), autosomal recessive (AR; OMIM#203780), and autosomal dominant (AD; OMIM#104200). XLAS is caused by a pathogenic variant in <jats:italic>COL4A5<\/jats:italic> (OMIM*303630) gene encoding type IV collagen (Col-IV) \u03b15 chain, while ADAS and ARAS are consequences of a variant in <jats:italic>COL4A3<\/jats:italic> (OMIM*120070) and <jats:italic>COL4A4<\/jats:italic> (OMIM*120131) genes that encode Col-IV \u03b13 and \u03b14 chains, respectively. Usually, diagnosis of AS requires hereditary or pathological examinations. Splicing variants are hard to be determined as pathogenic or non-pathogenic based on the results of gene sequencing.<\/jats:p><jats:p><jats:bold>Methods:<\/jats:bold> This study focused on a splicing variant in <jats:italic>COL4A5<\/jats:italic> gene, termed NM_000495.5: c.4298\u201320T&amp;gt;A, and to analyzed its authenticity and damaged \u03b15 chain. In vitro minigene splicing assay was applied to investigate the effect of splicing variant, c.4298\u201320T&amp;gt;A, on <jats:italic>COL4A5<\/jats:italic> mRNA synthesis. Molecular dynamics method was used to predict the capability of the responsible \u03b15(IV) to form a triple helix.<\/jats:p><jats:p><jats:bold>Results:<\/jats:bold> The intron 46 of <jats:italic>COL4A5<\/jats:italic> mRNA retained 18 bp, resulting in insertion of six amino acids behind the amino acid at position 1,433 of \u03b15(IV). The predicted protein effect of this variant: p. (Pro1432_Gly1433insAspTyrPheValGluIle). As a consequence, the stability of \u03b15(IV) secondary structure was impaired, probably leading to the unusual configuration of \u03b1345(IV).<\/jats:p><jats:p><jats:bold>Discussion:<\/jats:bold> Normally, splicing variant in <jats:italic>COL4A5<\/jats:italic> gene can lead to phenotypes of XLAS, and the effect is associated with the extent of splicing. The patient reported here carried a c.4298\u201320T&amp;gt;A splicing variant in COL4A5 gene, and AS was highly suspected based on the pathology results. However, the patient did not manifest any ocular or ear abnormalities. We therefore present the c.4298\u201320T&amp;gt;A splicing variant in <jats:italic>COL4A5<\/jats:italic> gene as likely-pathogenic splicing variant that leads to XLAS with mild phenotypes.<\/jats:p>","DOI":"10.3389\/fgene.2023.1059322","type":"journal-article","created":{"date-parts":[[2023,2,27]],"date-time":"2023-02-27T06:53:14Z","timestamp":1677480794000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":8,"title":["Molecular dynamics and minigene assay of new splicing variant c.4298-20T&gt;A of COL4A5 gene that cause Alport syndrome"],"prefix":"10.3389","volume":"14","author":[{"given":"Lei","family":"Liang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haotian","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zeyu","family":"Cai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianrong","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2023,2,27]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"876","DOI":"10.1681\/ASN.2009070784","article-title":"Genotype-phenotype correlation in X-linked Alport syndrome","volume":"21","author":"Bekheirnia","year":"2010","journal-title":"J. Am. Soc. Nephrol."},{"key":"B2","doi-asserted-by":"publisher","first-page":"699","DOI":"10.1007\/s10157-015-1197-9","article-title":"X-linked Alport syndrome associated with a synonymous p.Gly292Gly mutation alters the splicing donor site of the type IV collagen alpha chain 5 gene","volume":"20","author":"Fu","year":"2016","journal-title":"Clin. Exp. Nephrol."},{"key":"B3","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1159\/000502798","article-title":"A novel COL4A5 splicing mutation causes skipping of exon 14 in a Chinese family with Alport syndrome","volume":"6","author":"Gao","year":"2020","journal-title":"Kidney Dis. (Basel)"},{"key":"B4","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1056\/NEJMoa1806891","article-title":"Diagnostic utility of exome sequencing for kidney disease","volume":"380","author":"Groopman","year":"2019","journal-title":"N. Engl. J. Med."},{"key":"B5","doi-asserted-by":"publisher","first-page":"1218","DOI":"10.1093\/ndt\/17.7.1218","article-title":"Meta-analysis of genotype-phenotype correlation in X-linked Alport syndrome: Impact on clinical counselling","volume":"17","author":"Gross","year":"2002","journal-title":"Nephrol. Dial. Transpl."},{"key":"B6","doi-asserted-by":"publisher","first-page":"1208","DOI":"10.1038\/ki.2013.479","article-title":"Milder clinical aspects of X-linked Alport syndrome in men positive for the collagen IV \u03b15 chain","volume":"85","author":"Hashimura","year":"2014","journal-title":"Kidney Int."},{"key":"B7","doi-asserted-by":"publisher","first-page":"12696","DOI":"10.1038\/s41598-019-48990-9","article-title":"Determination of the pathogenicity of known COL4A5 intronic variants by in vitro splicing assay","volume":"9","author":"Horinouchi","year":"2019","journal-title":"Sci. Rep."},{"key":"B8","doi-asserted-by":"publisher","first-page":"e1342","DOI":"10.1002\/mgg3.1342","article-title":"Pathogenic evaluation of synonymous COL4A5 variants in X-linked Alport syndrome using a minigene assay","volume":"8","author":"Horinouchi","year":"2020","journal-title":"Mol. Genet. Genomic Med."},{"key":"B9","doi-asserted-by":"publisher","first-page":"940","DOI":"10.1111\/nep.13115","article-title":"Autosomal dominant form of type IV collagen nephropathy exists among patients with hereditary nephritis difficult to diagnose clinicopathologically","volume":"23","author":"Imafuku","year":"2018","journal-title":"Nephrol. Carlt."},{"key":"B10","doi-asserted-by":"publisher","first-page":"2603","DOI":"10.1097\/01.asn.0000090034.71205.74","article-title":"X-Linked Alport syndrome: Natural history and genotype-phenotype correlations in girls and women belonging to 195 families: A \"European community Alport syndrome concerted action\" study","volume":"14","author":"Jais","year":"2003","journal-title":"J. Am. Soc. Nephrol."},{"key":"B11","doi-asserted-by":"publisher","first-page":"649","DOI":"10.1681\/ASN.V114649","article-title":"X-Linked Alport syndrome: Natural history in 195 families and genotype-phenotype correlations in males","volume":"11","author":"Jais","year":"2000","journal-title":"J. Am. Soc. Nephrol."},{"key":"B12","doi-asserted-by":"publisher","first-page":"1441","DOI":"10.2215\/CJN.01000116","article-title":"Genetic, clinical, and pathologic backgrounds of patients with autosomal dominant Alport syndrome","volume":"11","author":"Kamiyoshi","year":"2016","journal-title":"Clin. J. Am. Soc. Nephrol."},{"key":"B13","doi-asserted-by":"publisher","first-page":"718","DOI":"10.1016\/j.ekir.2020.01.008","article-title":"Trimerization and genotype-phenotype correlation of COL4A5 mutants in Alport syndrome","volume":"5","author":"Kamura","year":"2020","journal-title":"Kidney Int. Rep."},{"key":"B14","doi-asserted-by":"publisher","first-page":"997","DOI":"10.1007\/s00467-016-3565-4","article-title":"Functional assessment of a novel COL4A5 splice region variant and immunostaining of plucked hair follicles as an alternative method of diagnosis in X-linked Alport syndrome","volume":"32","author":"Malone","year":"2017","journal-title":"Pediatr. Nephrol."},{"key":"B15","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1007\/s10157-018-1629-4","article-title":"A review of clinical characteristics and genetic backgrounds in Alport syndrome","volume":"23","author":"Nozu","year":"2019","journal-title":"Clin. Exp. Nephrol."},{"key":"B16","doi-asserted-by":"publisher","first-page":"1958","DOI":"10.2215\/CJN.04140414","article-title":"X-linked Alport syndrome caused by splicing mutations in COL4A5","volume":"9","author":"Nozu","year":"2014","journal-title":"Clin. J. Am. Soc. Nephrol."},{"key":"B17","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1016\/j.ekir.2016.09.056","article-title":"Negative staining for COL4A5 correlates with worse prognosis and more severe ultrastructural alterations in males with Alport syndrome","volume":"2","author":"Said","year":"2017","journal-title":"Kidney Int. Rep."},{"key":"B18","doi-asserted-by":"publisher","first-page":"3878","DOI":"10.1021\/ct400314y","article-title":"Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. Explicit solvent particle mesh ewald","volume":"9","author":"Salomon-Ferrer","year":"2013","journal-title":"J. Chem. Theory Comput."},{"key":"B19","doi-asserted-by":"publisher","first-page":"850","DOI":"10.1016\/j.ekir.2017.04.011","article-title":"Natural history and genotype-phenotype correlation in female X-linked Alport syndrome","volume":"2","author":"Yamamura","year":"2017","journal-title":"Kidney Int. Rep."},{"key":"B20","doi-asserted-by":"publisher","first-page":"e883","DOI":"10.1002\/mgg3.883","article-title":"Comparison between conventional and comprehensive sequencing approaches for genetic diagnosis of Alport syndrome","volume":"7","author":"Yamamura","year":"2019","journal-title":"Mol. Genet. Genomic Med."}],"container-title":["Frontiers in Genetics"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fgene.2023.1059322\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,27]],"date-time":"2023-02-27T06:53:17Z","timestamp":1677480797000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fgene.2023.1059322\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,2,27]]},"references-count":20,"alternative-id":["10.3389\/fgene.2023.1059322"],"URL":"https:\/\/doi.org\/10.3389\/fgene.2023.1059322","relation":{},"ISSN":["1664-8021"],"issn-type":[{"value":"1664-8021","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,2,27]]},"article-number":"1059322"}}