{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,27]],"date-time":"2026-01-27T14:19:20Z","timestamp":1769523560728,"version":"3.49.0"},"reference-count":21,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2021,12,8]],"date-time":"2021-12-08T00:00:00Z","timestamp":1638921600000},"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","award":["81970894 82000989"],"award-info":[{"award-number":["81970894 82000989"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100014206","name":"National Key Laboratory Foundation of China","doi-asserted-by":"publisher","award":["2017YFC1001804"],"award-info":[{"award-number":["2017YFC1001804"]}],"id":[{"id":"10.13039\/501100014206","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003399","name":"Science and Technology Commission of Shanghai Municipality","doi-asserted-by":"publisher","award":["14DZ2260300 20YF1428800"],"award-info":[{"award-number":["14DZ2260300 20YF1428800"]}],"id":[{"id":"10.13039\/501100003399","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003395","name":"Shanghai Municipal Education Commission","doi-asserted-by":"publisher","award":["20152519"],"award-info":[{"award-number":["20152519"]}],"id":[{"id":"10.13039\/501100003395","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Genet."],"abstract":"<jats:p>Splice site mutations contribute to a significant portion of the genetic causes for mendelian disorders including deafness. By next-generation sequencing of 4 multiplex, autosomal dominant families and 2 simplex, autosomal recessive families with hereditary deafness, we identified a variety of candidate pathogenic variants in noncanonical splice sites of known deafness genes, which include c.1616+3A &amp;gt; T and c.580G &amp;gt; A in <jats:italic>EYA4<\/jats:italic>, c.322-57_322-8del in <jats:italic>PAX3<\/jats:italic>, c.991-15_991-13del in <jats:italic>DFNA5<\/jats:italic>, c.6087-3T &amp;gt; G in <jats:italic>PTPRQ<\/jats:italic> and c.164+5G &amp;gt; A in <jats:italic>USH1G<\/jats:italic>. All six variants were predicted to affect the RNA splicing by at least one of the computational tools Human Splicing Finder, NNSPLICE and NetGene2. Phenotypic segregation of the variants was confirmed in all families and is consistent with previously reported genotype-phenotype correlations of the corresponding genes. Minigene analysis showed that those splicing site variants likely have various negative impact including exon-skipping (c.1616+3A &amp;gt; T and c.580G &amp;gt; A in <jats:italic>EYA4<\/jats:italic>, c.991-15_991-13del in <jats:italic>DFNA5<\/jats:italic>), intron retention (c.322-57_322-8del in <jats:italic>PAX3<\/jats:italic>), exon skipping and intron retention (c.6087-3T &amp;gt; G in <jats:italic>PTPRQ<\/jats:italic>) and shortening of exon (c.164+5G &amp;gt; A in <jats:italic>USH1G<\/jats:italic>). Our study showed that the cryptic, noncanonical splice site mutations may play an important role in the molecular etiology of hereditary deafness, whose diagnosis can be facilitated by modified filtering criteria for the next-generation sequencing data, functional verification, as well as segregation, bioinformatics, and genotype-phenotype correlation analysis.<\/jats:p>","DOI":"10.3389\/fgene.2021.773922","type":"journal-article","created":{"date-parts":[[2021,12,8]],"date-time":"2021-12-08T11:45:55Z","timestamp":1638963955000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":7,"title":["Detection and Functional Verification of Noncanonical Splice Site Mutations in Hereditary Deafness"],"prefix":"10.3389","volume":"12","author":[{"given":"Penghui","family":"Chen","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Longhao","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yongchuan","family":"Chai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hao","family":"Wu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tao","family":"Yang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2021,12,8]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1007\/s13353-018-0444-7","article-title":"Splicing Mutations in Human Genetic Disorders: Examples, Detection, and Confirmation","volume":"59","author":"Anna","year":"2018","journal-title":"J. Appl. Genet."},{"key":"B2","doi-asserted-by":"publisher","first-page":"433","DOI":"10.1002\/humu.23384","article-title":"Exonic Mutations and Exon Skipping: Lessons Learned from DFNA5","volume":"39","author":"Booth","year":"2018","journal-title":"Hum. Mutat."},{"key":"B3","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1038\/nrg775","article-title":"Listening to Silence and Understanding Nonsense: Exonic Mutations that Affect Splicing","volume":"3","author":"Cartegni","year":"2002","journal-title":"Nat. Rev. Genet."},{"key":"B4","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1016\/j.ijporl.2017.10.042","article-title":"A Novel Mutation of the EYA4 Gene Associated with post-lingual Hearing Loss in a Proband Is Co-segregating with a Novel PAX3 Mutation in Two Congenitally Deaf Family Members","volume":"104","author":"Cesca","year":"2018","journal-title":"Int. J. Pediatr. Otorhinolaryngol."},{"key":"B5","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2016\/3018132","article-title":"NLRP3 Is Expressed in the Spiral Ganglion Neurons and Associated with Both Syndromic and Nonsyndromic Sensorineural Deafness","volume":"2016","author":"Chen","year":"2016","journal-title":"Neural Plasticity"},{"key":"B6","doi-asserted-by":"publisher","first-page":"NP18","DOI":"10.1177\/1120672119879392","article-title":"Novel USH1G Homozygous Variant Underlying USH2-like Phenotype of Usher Syndrome","volume":"31","author":"D\u2019Esposito","year":"2021","journal-title":"Eur. J. Ophthalmol."},{"key":"B7","doi-asserted-by":"publisher","first-page":"1977","DOI":"10.1016\/j.febslet.2008.03.004","article-title":"RNA-binding Proteins and post-transcriptional Gene Regulation","volume":"582","author":"Glisovic","year":"2008","journal-title":"FEBS Lett."},{"key":"B8","doi-asserted-by":"publisher","first-page":"1599","DOI":"10.1002\/ajmg.a.31860","article-title":"A Novel Splice Site Mutation inEYA4 Causes DFNA10 Hearing Loss","author":"Hildebrand","year":"2007","journal-title":"Am. J. Med. Genet."},{"key":"B9","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1016\/j.heares.2019.01.003","article-title":"Hereditary Hearing Loss; about the Known and the Unknown","volume":"376","author":"Kremer","year":"2019","journal-title":"Hearing Res."},{"key":"B10","doi-asserted-by":"publisher","first-page":"e0126602","DOI":"10.1371\/journal.pone.0126602","article-title":"Exome Sequencing Identifies a Mutation in EYA4 as a Novel Cause of Autosomal Dominant Non-syndromic Hearing Loss","volume":"10","author":"Liu","year":"2015","journal-title":"PLoS ONE"},{"key":"B11","doi-asserted-by":"publisher","first-page":"1135","DOI":"10.1007\/s00438-014-0979-1","article-title":"Identification of a Novel Compound Heterozygous Mutation in PTPRQ in a DFNB84 Family with Prelingual Sensorineural Hearing Impairment","volume":"290","author":"Sang","year":"2015","journal-title":"Mol. Genet. Genomics"},{"key":"B12","doi-asserted-by":"publisher","first-page":"445","DOI":"10.1016\/j.ajhg.2014.09.001","article-title":"Utilizing Ethnic-specific Differences in Minor Allele Frequency to Recategorize Reported Pathogenic Deafness Variants","volume":"95","author":"Shearer","year":"2014","journal-title":"Am. J. Hum. Genet."},{"key":"B13","doi-asserted-by":"publisher","first-page":"a033258","DOI":"10.1101\/cshperspect.a033258","article-title":"The Epidemiology of Deafness","volume":"9","author":"Sheffield","year":"2019","journal-title":"Cold Spring Harb Perspect. Med."},{"key":"B14","doi-asserted-by":"publisher","first-page":"2951","DOI":"10.1002\/ajmg.a.61893","article-title":"Phenotypic Diversity and Genetic Complexity of PAX3 \u2010related Waardenburg Syndrome","volume":"182","author":"Somashekar","year":"2020","journal-title":"Am. J. Med. Genet."},{"key":"B15","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1038\/jhg.2015.19","article-title":"A Novel Mutation of EYA4 in a Large Chinese Family with Autosomal Dominant Middle-Frequency Sensorineural Hearing Loss by Targeted Exome Sequencing","volume":"60","author":"Sun","year":"2015","journal-title":"J. Hum. Genet."},{"key":"B16","doi-asserted-by":"publisher","first-page":"1467","DOI":"10.3892\/ijmm.2014.1939","article-title":"Identification of I411K, a Novel Missense EYA4 Mutation Causing Autosomal Dominant Non-syndromic Hearing Loss","volume":"34","author":"Tan","year":"2014","journal-title":"Int. J. Mol. Med."},{"key":"B17","doi-asserted-by":"publisher","first-page":"732","DOI":"10.3390\/genes10100732","article-title":"Aberrant Splicing Events Associated to CDH23 Noncanonical Splice Site Mutations in a Proband with Atypical Usher Syndrome 1","volume":"10","author":"Valero","year":"2019","journal-title":"Genes"},{"key":"B18","doi-asserted-by":"publisher","first-page":"1093","DOI":"10.1007\/s00439-017-1809-4","article-title":"Deep Intronic Mutations and Human Disease","volume":"136","author":"Vaz-Drago","year":"2017","journal-title":"Hum. Genet."},{"key":"B19","doi-asserted-by":"publisher","first-page":"D1055","DOI":"10.1093\/nar\/gkr1171","article-title":"SpliceDisease Database: Linking RNA Splicing and Disease","volume":"40","author":"Wang","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"B20","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2018\/9425725","article-title":"Autosomal Recessive Congenital Sensorineural Hearing Loss Due to a Novel Compound Heterozygous PTPRQ Mutation in a Chinese Family","volume":"2018","author":"Wu","year":"2018","journal-title":"Neural Plasticity"},{"key":"B21","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1007\/s10162-004-4044-3","article-title":"A Comparative Study of Eya1 and Eya4 Protein Function and its Implication in Branchio-Oto-Renal Syndrome and DFNA10","volume":"5","author":"Zhang","year":"2004","journal-title":"Jaro"}],"container-title":["Frontiers in Genetics"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fgene.2021.773922\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,12,8]],"date-time":"2021-12-08T11:45:58Z","timestamp":1638963958000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fgene.2021.773922\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,12,8]]},"references-count":21,"alternative-id":["10.3389\/fgene.2021.773922"],"URL":"https:\/\/doi.org\/10.3389\/fgene.2021.773922","relation":{},"ISSN":["1664-8021"],"issn-type":[{"value":"1664-8021","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,12,8]]},"article-number":"773922"}}