{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,11]],"date-time":"2026-08-11T20:30:19Z","timestamp":1786480219711,"version":"build-2736575974"},"reference-count":38,"publisher":"Ovid Technologies (Wolters Kluwer Health)","issue":"3","funder":[{"name":"The Japan Foundation for Pediatric Research","award":["19-002"],"award-info":[{"award-number":["19-002"]}]},{"DOI":"10.13039\/501100001691","name":"Grants-in-Aid for Scientific Research","doi-asserted-by":"crossref","award":["20K16892"],"award-info":[{"award-number":["20K16892"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001691","name":"Grants-in-Aid for Scientific Research","doi-asserted-by":"crossref","award":["19K08726"],"award-info":[{"award-number":["19K08726"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001691","name":"Grants-in-Aid for Scientific Research","doi-asserted-by":"crossref","award":["19K17710"],"award-info":[{"award-number":["19K17710"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001691","name":"Grants-in-Aid for Scientific Research","doi-asserted-by":"crossref","award":["20H03698"],"award-info":[{"award-number":["20H03698"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["lww.com","ovid.com"],"crossmark-restriction":true},"short-container-title":["Kidney360"],"published-print":{"date-parts":[[2022,3,31]]},"abstract":"<jats:sec>\n                    <jats:title>Key Points<\/jats:title>\n                    <jats:p>\n                      <jats:list list-type=\"bullet\">\n                        <jats:list-item>\n                          <jats:p>Mutations registered in the database for autosomal Alport syndrome do not include synonymous variants.<\/jats:p>\n                        <\/jats:list-item>\n                        <jats:list-item>\n                          <jats:p>Certain synonymous variants can affect pre-mRNA splicing, and transcript analysis should be carried out to evaluate synonymous variants.<\/jats:p>\n                        <\/jats:list-item>\n                        <jats:list-item>\n                          <jats:p>\n                            Our\n                            <jats:italic toggle=\"yes\">in vivo<\/jats:italic>\n                            and\n                            <jats:italic toggle=\"yes\">in vitro<\/jats:italic>\n                            splicing assays showed that two of the four synonymous variants cause exon skipping.\n                          <\/jats:p>\n                        <\/jats:list-item>\n                      <\/jats:list>\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      Alport syndrome is an inherited disorder characterized by progressive renal disease, variable sensorineural hearing loss, and ocular abnormalities. Although many pathogenic variants in\n                      <jats:italic toggle=\"yes\">COL4A3<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">COL4A4<\/jats:italic>\n                      have been identified in patients with autosomal Alport syndrome, synonymous mutations in these genes have rarely been identified.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      We conducted\n                      <jats:italic toggle=\"yes\">in silico<\/jats:italic>\n                      splicing analysis using Human Splicing Finder (HSF) and Alamut to predict splicing domain strength and disruption of the sites. Furthermore, we performed\n                      <jats:italic toggle=\"yes\">in vitro<\/jats:italic>\n                      splicing assays using minigene constructs and mRNA analysis of patient samples to determine the pathogenicity of four synonymous variants detected in four patients with suspected autosomal dominant Alport syndrome (\n                      <jats:italic toggle=\"yes\">COL4A3<\/jats:italic>\n                      [c.693G&gt;A (p.Val231=)] and\n                      <jats:italic toggle=\"yes\">COL4A4<\/jats:italic>\n                      [c.1353C&gt;T (p.Gly451=), c.735G&gt;A (p.Pro245=), and c.870G&gt;A (p.Lys290=)]).\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Both\n                      <jats:italic toggle=\"yes\">in vivo<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">in vitro<\/jats:italic>\n                      splicing assays showed exon skipping in two out of the four synonymous variants identified (c.735G&gt;A and c.870G&gt;A in\n                      <jats:italic toggle=\"yes\">COL4A4<\/jats:italic>\n                      ). Prediction analysis of wild-type and mutated\n                      <jats:italic toggle=\"yes\">COL4A4<\/jats:italic>\n                      sequences using HSF and Alamut suggested these two variants may lead to the loss of binding sites for several splicing factors,\n                      <jats:italic toggle=\"yes\">e.g.<\/jats:italic>\n                      , in acceptor sites and exonic splicing enhancers. The other two variants did not induce aberrant splicing.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>This study highlights the pitfalls of classifying the functional consequences of variants by a simple approach. Certain synonymous variants, although they do not alter the amino acid sequence of the encoded protein, can dramatically affect pre-mRNA splicing, as shown in two of our patients. Our findings indicate that transcript analysis should be carried out to evaluate synonymous variants detected in patients with autosomal dominant Alport syndrome.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.34067\/kid.0005252021","type":"journal-article","created":{"date-parts":[[2021,10,14]],"date-time":"2021-10-14T14:02:54Z","timestamp":1634220174000},"page":"497-505","update-policy":"https:\/\/doi.org\/10.1097\/lww.0000000000001000","source":"Crossref","is-referenced-by-count":7,"title":["Evaluation of Suspected Autosomal Alport Syndrome Synonymous Variants"],"prefix":"10.34067","volume":"3","author":[{"given":"Rini","family":"Rossanti","sequence":"first","affiliation":[{"name":"Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan"},{"name":"Department of Child Health, Nephrology Division, Dr. Hasan Sadikin General Hospital\/Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1655-6030","authenticated-orcid":false,"given":"Tomoko","family":"Horinouchi","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6107-1169","authenticated-orcid":false,"given":"Tomohiko","family":"Yamamura","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4946-1345","authenticated-orcid":false,"given":"China","family":"Nagano","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, 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Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yoshifumi","family":"Ubara","sequence":"additional","affiliation":[{"name":"Nephrology Center, Okinaka Memorial Institute for Medical Research, Tokyo, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masahiko","family":"Nagahama","sequence":"additional","affiliation":[{"name":"Internal Medicine, St. Luke\u2019s International Hospital, Tokyo, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuko","family":"Shima","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Wakayama Medical University, Wakayama, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8681-9129","authenticated-orcid":false,"given":"Koichi","family":"Nakanishi","sequence":"additional","affiliation":[{"name":"Department of Child Health and Welfare (Pediatrics), Graduate School of Medicine, University of the Ryukyus, Okinawa, 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