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Mol Genet Genomic Med. 2019 Jul;7(7):e00789. doi: 10.1002/mgg3.789. Epub 2019 Jun 14.

Pathogenic missense mutation pattern of forkhead box genes in neurodevelopmental disorders.

Author information

Center for Medical Genetics & Hunan Provincial Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China.
Center of Children Psychology and Behavior, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
Child Psychobehavioural Rehabilitation Department, Shenzhen Baoan Maternal and Child Health Hospital, Shenzhen, China.
Key Laboratory of Medical Information Research, Central South University, Changsha, China.
CAS Center for Excellence in Brain Science and Intelligences Technology (CEBSIT), Shanghai, China.



Forkhead box (FOX) proteins are a family of transcription factors. Mutations of three FOX genes, including FOXP1, FOXP2, and FOXG1, have been reported in neurodevelopmental disorders (NDDs). However, due to the lack of site-specific statistical significance, the pathogenicity of missense mutations of these genes is difficult to determine.


DNA and RNA were extracted from peripheral blood lymphocytes. The mutation was detected by single-molecule molecular inversion probe-based targeted sequencing, and the variant was validated by Sanger sequencing. Real-time quantitative PCR and western blot were performed to assay the expression of the mRNA and protein. To assess the pattern of disorder-related missense mutations of NDD-related FOX genes, we manually curated de novo and inherited missense or inframeshift variants within FOXP1, FOXP2, and FOXG1 that co-segregated with phenotypes in NDDs. All variants were annotated by ANNOVAR.


We detected a novel de novo missense mutation (NM_001244815: c.G1444A, p.E482K) of FOXP1 in a patient with intellectual disability and severe speech delay. Real-time PCR and western blot revealed a dramatic reduction of mRNA and protein expression in patient-derived lymphocytes, indicating a loss-of-function mechanism. We observed that the majority of the de novo or transmitted missense variants were located in the FOX domains, and 95% were classified as pathogenic mutations. However, 10 variants were located outside of the FOX domain and were classified as likely pathogenic or variants of uncertain significance.


Our study shows the pathogenicity of missense and inframeshift variants of NDD-related FOX genes, which is important for clinical diagnosis and genetic counseling. Functional analysis is needed to determine the pathogenicity of the variants with uncertain clinical significance.


FOXG1 ; FOXP1 ; FOXP2 ; de novo; forkhead box domain; missense variant; neurodevelopmental disorders

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