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[Genetic analysis of a fetus with Short-rib thoracic dysplasia 8 with or without polydactyly due to variants of DYNC2I1 gene].

Yingwen Liu·Chunxiao Han·Yuxin Zhang·Lulu Yan·Jiangyang Xue·Haibo Li
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Abstract

OBJECTIVE: To investigate the clinical characteristics of a fetus with Short-rib thoracic dysplasia 8 with or without polydactyly (SRTD8) due to variants of DYNC2I1 gene. METHODS: A fetus identified to have short ribs, short long bones, and narrow thorax at 26+1 weeks of gestation at the Women and Children's Hospital of Ningbo University in September 2024 was selected as study subject. The fetus underwent termination of pregnancy at 35+5 weeks of gestation. Clinical data of the fetus were retrospectively collected. Whole exome sequencing (WES) was carried out on fetal tissue, and candidate variants were validated by Sanger sequencing. Difference between the wild type and variant DYNC2I1 proteins was analyzed using AlphaFold v3.0.1 and PyMOL v2.5.6 software. Pathogenicity of the variant was rated based on guidelines from the American College of Medical Genetics and Genomics (ACMG). Using keywords such as "DYNC2I1 gene", previous literature on patients due to biallelic DYNC2I1 gene variants were retrieved from the PubMed databases, CNKI, and Wanfang Data Knowledge Service Platform, and the genetic variant and clinical phenotypes of patients were analyzed. The literature retrieval time was set from the establishment of database to December 31, 2025. This study was approved by the Medical Ethics Committee of the hospital (Ethics No.: 2023-094). RESULTS: Prenatal ultrasound revealed that the fetus had short ribs, short long bones, and narrow thorax at 26+1 gestational weeks. WES and Sanger sequencing revealed that the fetus has harbored compound heterozygous variants of the DYNC2I1 gene, namely c.265_268 (p.Gln89GlyfsTer15) in exon 3 and c.1777C>T (p.Arg593Trp) in exon 14, which were inherited from his father and mother, respectively. Prediction of the DYNC2I1 protein structure suggested that the c.265_268del variant has formed a premature termination codon, which may significantly alter the protein's secondary structure. The c.1777C>T variant may disrupt the electrostatic interaction between Arg593 and Asp729. Based on the ACMG guidelines, the c.265_268del (p.Gln89GlyfsTer15) variant was predicted to be likely pathogenic (PM2_Supporting +PVS1), whilst the c.1777C>T(p.Arg593Trp) variant was rated as uncertain significance (PM2_Supporting+PM3+PP4). Literature search has identified five articles related to biallelic DYNC2I1 variants involving a total of 11 fetuses/patients. Together with the fetus from this study, typical phenotypes included short ribs (6 cases), narrow thorax (6 cases), short limb bones (6 cases), and hand polydactyly (6 cases), and foot polydactyly (5 cases), albeit with significant clinical heterogeneity. A total of 12 genetic variants were identified, among which c.44delC was the most common (16.7%, 4/24), followed by c.1777C>T, c.2246C>T, and c.2305G>A (each accounting for 12.5%). No mutational hotspot was identified. CONCLUSION: The c.265_268del (p.Gln89GlyfsTer15) and c.1777C>T (p.Arg593Trp) compound heterozygous variants of the DYNC2I1 gene probably underlay the pathogenesis of SRTD8 in this fetus. This study has enriched the mutational spectrum of the DYNC2I1 gene and facilitated etiological diagnosis and treatment of DYNC2I1-related diseases.

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HumansFemalePregnancyCytoplasmic DyneinsShort Rib-Polydactyly SyndromePolydactylyFetusExome SequencingMutationJournal ArticleCase ReportsEnglish Abstract

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Yingwen Liu, Chunxiao Han, Yuxin Zhang, Lulu Yan, Jiangyang Xue, Haibo Li. 2026-09-10. [Genetic analysis of a fetus with Short-rib thoracic dysplasia 8 with or without polydactyly due to variants of DYNC2I1 gene].. https://doi.org/10.3760/cma.j.cn511374-20250221-00099

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