{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T03:06:57Z","timestamp":1760238417485,"version":"build-2065373602"},"reference-count":67,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2020,8,7]],"date-time":"2020-08-07T00:00:00Z","timestamp":1596758400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000072","name":"National Institute of Dental and Craniofacial Research","doi-asserted-by":"publisher","award":["U01 DE024443"],"award-info":[{"award-number":["U01 DE024443"]}],"id":[{"id":"10.13039\/100000072","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Missense, nonsense, splice site and regulatory region variants in interferon regulatory factor 6 (IRF6) have been shown to contribute to both syndromic and non-syndromic forms of cleft lip and\/or palate (CL\/P). We report the diagnostic evaluation of a complex multigeneration family of Honduran ancestry with a pedigree structure consistent with autosomal-dominant inheritance with both incomplete penetrance and variable expressivity. The proband\u2019s grandmother bore children with two partners and CL\/P segregates on both sides of each lineage. Through whole-exome sequencing of five members of the family, we identified a single shared synonymous variant, located in the middle of exon 7 of IRF6 (p.Ser307Ser; g.209963979 G&gt;A; c.921C&gt;T). The variant was shown to segregate in the seven affected individuals and through three unaffected obligate carriers, spanning both sides of this pedigree. This variant is very rare, only being found in three (all of Latino ancestry) of 251,352 alleles in the gnomAD database. While the variant did not create a splice acceptor\/donor site, in silico analysis predicted it to impact an exonic splice silencer element and the binding of major splice regulatory factors. In vitro splice assays supported this by revealing multiple abnormal splicing events, estimated to impact &gt;60% of allelic transcripts. Sequencing of the alternate splice products demonstrated the unmasking of a cryptic splice site six nucleotides 5\u2032 of the variant, as well as variable utilization of cryptic splice sites in intron 6. The ectopic expression of different splice regulatory proteins altered the proportion of abnormal splicing events seen in the splice assay, although the alteration was dependent on the splice factor. Importantly, each alternatively spliced mRNA is predicted to result in a frame shift and prematurely truncated IRF6 protein. This is the first study to identify a synonymous variant as a likely cause of NS-CL\/P and highlights the care that should be taken by laboratories when considering and interpreting variants.<\/jats:p>","DOI":"10.3390\/genes11080903","type":"journal-article","created":{"date-parts":[[2020,8,10]],"date-time":"2020-08-10T07:25:03Z","timestamp":1597044303000},"page":"903","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["A Synonymous Exonic Splice Silencer Variant in IRF6 as a Novel and Cryptic Cause of Non-Syndromic Cleft Lip and Palate"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4917-408X","authenticated-orcid":false,"given":"Beau","family":"Sylvester","sequence":"first","affiliation":[{"name":"Division of Plastic and Maxillofacial Surgery, Children\u2019s Hospital Los Angeles, Los Angeles, CA 90027, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Frederick","family":"Brindopke","sequence":"additional","affiliation":[{"name":"Operation Smile Global Headquarters, Virginia Beach, WV 23453, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3163-8093","authenticated-orcid":false,"given":"Akiko","family":"Suzuki","sequence":"additional","affiliation":[{"name":"Department of Oral &amp; Craniofacial Sciences, University of Missouri-Kansas City School of Dentistry, Kansas City, MO 64108, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Melissa","family":"Giron","sequence":"additional","affiliation":[{"name":"Operaci\u00f3n Sonrisa Honduras, Tegucigalpa 11101, Honduras"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Allyn","family":"Auslander","sequence":"additional","affiliation":[{"name":"Division of Plastic and Maxillofacial Surgery, Children\u2019s Hospital Los Angeles, Los Angeles, CA 90027, USA"},{"name":"Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard L.","family":"Maas","sequence":"additional","affiliation":[{"name":"Division of Genetics, Department of Medicine, Brigham and Women\u2019s Hospital, Harvard Medical School, Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1995-802X","authenticated-orcid":false,"given":"Becky","family":"Tsai","sequence":"additional","affiliation":[{"name":"Fulgent Genetics, Temple City, CA 91780, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hanlin","family":"Gao","sequence":"additional","affiliation":[{"name":"Fulgent Genetics, Temple City, CA 91780, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"suffix":"III","given":"William","family":"Magee","sequence":"additional","affiliation":[{"name":"Division of Plastic and Maxillofacial Surgery, Children\u2019s Hospital Los Angeles, Los Angeles, CA 90027, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8015-5528","authenticated-orcid":false,"given":"Timothy C.","family":"Cox","sequence":"additional","affiliation":[{"name":"Department of Oral &amp; Craniofacial Sciences, University of Missouri-Kansas City School of Dentistry, Kansas City, MO 64108, USA"},{"name":"Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1181-7828","authenticated-orcid":false,"given":"Pedro A.","family":"Sanchez-Lara","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Cedars-Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2020,8,7]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1038\/nrg2933","article-title":"Cleft lip and palate: Understanding genetic and environmental influences","volume":"12","author":"Dixon","year":"2011","journal-title":"Nat. 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