Kaushik K, Chapman G, Prakasam R, Batool F, Saleh M, Determan J, Huettner JE, Kroll KL. Requirements for the neurodevelopmental disorder-associated gene ZNF292 in human cortical interneuron development and function. Cell Rep. 2025 May 27;44(5):115597. doi: 10.1016/j.celrep.2025.115597. Epub 2025 Apr 20. PMID: 40257863; PMCID: PMC12283078.
Abstract
Pathogenic mutation of the zinc-finger transcription factor ZNF292 is a recently defined contributor to human neurodevelopmental disorders (NDDs). However, the gene's roles in cortical development and regulatory networks under its control were previously undefined. Here, human stem cell models of ZNF292 deficiency, resembling pathogenic haploinsufficiency, are used to derive cortical inhibitory neuron progenitors and neurons. ZNF292-deficient progenitors undergo precocious differentiation but subsequently exhibit compromised interneuron maturation and function. In progenitors, genome-wide occupancy and transcriptomic analyses identify direct target genes controlling neuronal differentiation and synapse formation that are upregulated upon ZNF292 deficiency. By contrast, deficiency in interneurons compromises ZNF292 genome-wide association with and causes downregulation of direct target genes promoting interneuron maturation and function, including other NDD genes. ZNF292-deficient interneurons also exhibit altered channel activities, elevated GABA responsiveness, and hallmarks of neuronal hyperactivity. Together, the results of this work define neurodevelopmental requirements for ZNF292, some of which may contribute to pathogenic ZNF292 mutation-related NDDs.
Mirzaa GM, Chong JX, Piton A, Popp B, Foss K, Guo H, Harripaul R, Xia K, Scheck J, Aldinger KA, Sajan SA, Tang S, Bonneau D, Beck A, White J, Mahida S, Harris J, Smith-Hicks C, Hoyer J, Zweier C, Reis A, Thiel CT, Jamra RA, Zeid N, Yang A, Farach LS, Walsh L, Payne K, Rohena L, Velinov M, Ziegler A, Schaefer E, Gatinois V, Geneviève D, Simon MEH, Kohler J, Rotenberg J, Wheeler P, Larson A, Ernst ME, Akman CI, Westman R, Blanchet P, Schillaci LA, Vincent-Delorme C, Gripp KW, Mattioli F, Guyader GL, Gerard B, Mathieu-Dramard M, Morin G, Sasanfar R, Ayub M, Vasli N, Yang S, Person R, Monaghan KG, Nickerson DA, van Binsbergen E, Enns GM, Dries AM, Rowe LJ, Tsai ACH, Svihovec S, Friedman J, Agha Z, Qamar R, Rodan LH, Martinez-Agosto J, Ockeloen CW, Vincent M, Sunderland WJ, Bernstein JA; Undiagnosed Diseases Network,; Eichler EE, Vincent JB; University of Washington Center for Mendelian Genomics (UW-CMG),; Bamshad MJ. De novo and inherited variants in ZNF292 underlie a neurodevelopmental disorder with features of autism spectrum disorder. Genet Med. 2020 Mar;22(3):538-546. doi: 10.1038/s41436-019-0693-9. Epub 2019 Nov 14. PMID: 31723249; PMCID: PMC7060121.
Abstract
Purpose: Intellectual disability (ID) and autism spectrum disorder (ASD) are genetically heterogeneous neurodevelopmental disorders. We sought to delineate the clinical, molecular, and neuroimaging spectrum of a novel neurodevelopmental disorder caused by variants in the zinc finger protein 292 gene (ZNF292).
Methods: We ascertained a cohort of 28 families with ID due to putatively pathogenic ZNF292 variants that were identified via targeted and exome sequencing. Available data were analyzed to characterize the canonical phenotype and examine genotype-phenotype relationships.
Results: Probands presented with ID as well as a spectrum of neurodevelopmental features including ASD, among others. All ZNF292 variants were de novo, except in one family with dominant inheritance. ZNF292 encodes a highly conserved zinc finger protein that acts as a transcription factor and is highly expressed in the developing human brain supporting its critical role in neurodevelopment.
Conclusion: De novo and dominantly inherited variants in ZNF292 are associated with a range of neurodevelopmental features including ID and ASD. The clinical spectrum is broad, and most individuals present with mild to moderate ID with or without other syndromic features. Our results suggest that variants in ZNF292 are likely a recurrent cause of a neurodevelopmental disorder manifesting as ID with or without ASD.
Dongxue L, Ruen Y, Ying Y, Liting C, Jie W, Chunjiao L, Wei L, Rikun C, Cuiyun L. Short Stature and Developmental Delay Associated With a Novel Frame-Shift Mutation in ZNF292: Case Report and Literature Review. Clin Case Rep. 2025 Aug 7;13(8):e70747. doi: 10.1002/ccr3.70747. PMID: 40777882; PMCID: PMC12329236.
Abstract
Pathogenic mutations in the ZNF292 gene are a significant genetic cause of Intellectual Developmental Disorder (IDD) in individuals, manifesting with a spectrum of clinical features including mild to severe intellectual impairment, speech delay, and co-occurring autism spectrum disorder (ASD). In this study, we present a novel clinical phenotype associated with a newly identified variant of ZNF292 and conduct a thorough review of relevant literature. A 4-year-old female patient displayed language developmental delays, short stature, and skeletal abnormalities. Trio whole-exome sequencing revealed a novel de novo heterozygous frameshift variant in exon 8 of the ZNF292 gene, c.5977_5978del, p.Gln1993fs. According to the ACMG guidelines, this variant is expected to be pathogenic. Our research unveils a novel variant in ZNF292-related disorders and expands the associated phenotypic spectrum. This study highlights the significance of employing next-generation sequencing for timely patient diagnosis, while further clinical phenotypic and genotypic investigations could improve the understanding of ZNF292-linked conditions.
Wang F, Qi N, Gao Y, Wu D, Zhang M, Zhang Q, Yang K, Peng H, Lei X, Liao S. [Genetic analysis of two children with developmental delay and intellectual disability]. Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2023 Jul 10;40(7):876-880. Chinese. doi: 10.3760/cma.j.cn511374-20220318-00181. PMID: 37368394.
Abstract
Objective: To explore the genetic etiology of two patients with developmental delay and intellectual disability.
Methods: Two children who were respectively admitted to Henan Provincial People's Hospital on August 29, 2021 and August 5, 2019 were selected as the study subjects. Clinical data were collected, and array comparative genomic hybridization (aCGH) was carried out on the children and their parents for the detection of chromosomal microduplication/microdeletions.
Results: Patient 1 was a 2-year-and-10-month female and patient 2 was a 3-year-old female. Both children had featured developmental delay, intellectual disability, and abnormal findings on cranial MRI. aCGH revealed that patient 1 has harbored arr[hg19] 6q14.2q15(84621837_90815662)×1, a 6.19 Mb deletion at 6q14.2q15, which encompassed ZNF292, the pathogenic gene for Autosomal dominant intellectual developmental disorder 64. Patient 2 has harbored arr[hg19] 22q13.31q13.33(46294326_51178264)×1, a 4.88 Mb deletion at 22q13.31q13.33 encompassing the SHANK3 gene, haploinsufficiency of which can lead to Phelan-McDermid syndrome. Both deletions were classified as pathogenic CNVs based on the guidelines of American College of Medical Genetics and Genomics (ACMG) and were not found in their parents.
Conclusion: The 6q14.2q15 deletion and 22q13-31q13.33 deletion probably underlay the developmental delay and intellectual disability in the two children, respectively. Haploinsufficiency of the ZNF292 gene may account for the key clinical features of the 6q14.2q15 deletion.
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