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We report an 8-year-old boy with a strikingly similar phenotype including facial asymmetry, microtia with preauricular tags and bilateral hearing loss, cleft lip and palate, cardiac dysrhythmia, and undescended testes. Joint contracture, no finger flexion creases, and large halluces were the same as those of a previously reported patient with homozygous <jats:italic>CDK9<\/jats:italic> variants. The ocular phenotype included blepharophimosis, lacrimal duct obstruction, eyelid dermoids, Duane syndrome-like abduction deficit, and congenital cataracts. Optical coherence tomography and electroretinography evaluations revealed severe retinal dystrophy had developed at an early age. Trio-based whole-exome sequencing identified compound heterozygous variants in <jats:italic>CDK9<\/jats:italic> [p.(A288T) of maternal origin and p.(R303C) of paternal origin] in the patient. Variants\u2019 kinase activities were reduced compared with wild type. We concluded that <jats:italic>CDK9<\/jats:italic> biallelic variants cause a CHARGE-like malformation syndrome with retinal dystrophy as a distinguishing feature.<\/jats:p>","DOI":"10.1038\/s10038-021-00909-x","type":"journal-article","created":{"date-parts":[[2021,2,27]],"date-time":"2021-02-27T14:03:04Z","timestamp":1614434584000},"page":"1021-1027","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Biallelic CDK9 variants as a cause of a new multiple-malformation syndrome with retinal dystrophy mimicking the CHARGE syndrome"],"prefix":"10.1038","volume":"66","author":[{"given":"Sachiko","family":"Nishina","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7480-6133","authenticated-orcid":false,"given":"Katsuhiro","family":"Hosono","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shizuka","family":"Ishitani","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kenjiro","family":"Kosaki","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tadashi","family":"Yokoi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tomoyo","family":"Yoshida","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kaoru","family":"Tomita","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9971-4035","authenticated-orcid":false,"given":"Maki","family":"Fukami","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0723-0960","authenticated-orcid":false,"given":"Hirotomo","family":"Saitsu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7178-9991","authenticated-orcid":false,"given":"Tsutomu","family":"Ogata","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tohru","family":"Ishitani","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4052-5066","authenticated-orcid":false,"given":"Yoshihiro","family":"Hotta","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Noriyuki","family":"Azuma","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2021,2,27]]},"reference":[{"key":"909_CR1","doi-asserted-by":"publisher","first-page":"1273","DOI":"10.1002\/jcb.26293","volume":"119","author":"LC Franco","year":"2018","unstructured":"Franco LC, Morales F, Boffo S, Giordano A. 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The parents of the current patient provided written informed consent for ophthalmic examinations under general anesthesia, genetic analysis including whole-exome sequencing, and publication of this report.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics statement"}}]}}