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Pulmonary surfactant metabolism dysfunction caused by variants in the<jats:italic>ABCA3<\/jats:italic>gene is a rare disease with very poor prognosis. Currently, the mechanisms associated with some<jats:italic>ABCA3<\/jats:italic>variants have been determined, including protein mistrafficking and impaired phospholipid transport. However, some novel variants and their underlying pathogenesis has not been fully elucidated yet. In this study we aimed to identify the genetic features in a family with lethal respiratory failure.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>We studied members of two generations of a Chinese family, including a female proband, her parents, her monozygotic twin sister, and her older sister. Trio whole exome sequencing (WES) were used on the proband and her parents to identify the<jats:italic>ABCA3<\/jats:italic>variants. Sanger sequencing and real-time quantitative polymerase chain reaction (PCR) were used on the monozygotic twin sister of proband to validate the<jats:italic>ABCA3<\/jats:italic>synonymous variant and exon deletion, respectively. The potential pathogenicity of the identified synonymous variant was predicted using the splice site algorithms dbscSNV11_AdaBoost, dbscSNV11_RandomForest, and Human Splicing Finder (HSF).<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>All patients showed severe respiratory distress, which could not be relieved by mechanical ventilation, supplementation of surfactant, or steroid therapy, and died at an early age. WES analysis revealed that the proband had compound heterozygous<jats:italic>ABCA3<\/jats:italic>variants, including a novel synonymous variant c.G873A (p.Lys291Lys) in exon 8 inherited from the mother, and a heterozygous deletion of exons 4\u20137 inherited from the father. The synonymous variant was consistently predicted to be a cryptic splice donor site that may lead to aberrant splicing of the pre-mRNA by three different splice site algorithms. The deletion of exons 4\u20137 of the<jats:italic>ABCA3<\/jats:italic>gene was determined to be a likely pathogenic variant. The variants were confirmed in the monozygotic twin sister of proband by Sanger sequencing and qPCR respectively. The older sister of proband was not available to determine if she also carried both<jats:italic>ABCA3<\/jats:italic>variants, but it is highly likely based on her clinical course.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>We identified a novel synonymous variant and a deletion in the<jats:italic>ABCA3<\/jats:italic>gene that may be responsible for the pathogenesis in patients in this family. These results add to the known mutational spectrum of the<jats:italic>ABCA3<\/jats:italic>gene. The study of<jats:italic>ABCA3<\/jats:italic>variants may be helpful for the implementation of patient-specific therapies.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s12920-021-01098-4","type":"journal-article","created":{"date-parts":[[2021,10,29]],"date-time":"2021-10-29T18:02:48Z","timestamp":1635530568000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["A novel synonymous ABCA3 variant identified in a Chinese family with lethal neonatal respiratory failure"],"prefix":"10.1186","volume":"14","author":[{"given":"Weifeng","family":"Zhang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhiyong","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yiming","family":"Lin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruiquan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinglin","family":"Xu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ying","family":"He","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fengfeng","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lianqiang","family":"Wu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dongmei","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2021,10,29]]},"reference":[{"issue":"4","key":"1098_CR1","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1016\/j.siny.2017.03.003","volume":"22","author":"LM Nogee","year":"2017","unstructured":"Nogee LM. 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The parents of the patients signed written informed consent and agreed to themselves and their children taking part in this study, and the use of the relevant data and information for scientific research. We confirm that all methods were performed in accordance with the relevant guidelines and regulations.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"We confirm that the parents of the patients signed written informed consent for publication of their own and children\u2019s genetic data, clinical details and\/or any accompanying images.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"256"}}