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Although investigation with human induced pluripotent stem cell models has confirmed disruption of neuronal development in 16p11.2del neuronal cells, which genes are responsible for abnormal cellular phenotypes and what determines the penetrance of neurodevelopmental abnormalities are unknown. We performed haplotype phasing of the 16p11.2 region in a 16p11.2del neurodevelopmental disorders cohort and generated human induced pluripotent stem cells for two 16p11.2del families with distinct residual haplotypes and variable neurodevelopmental disorder phenotypes.<\/jats:p>\n               <jats:p>Using transcriptomic profiles and cellular phenotypes of the human induced pluripotent stem cell-differentiated cortex neuronal cells, we revealed MAPK3 to be a contributor to dysfunction in multiple pathways related to early neuronal development, with altered soma and electrophysiological properties in mature neuronal cells. Notably, MAPK3 expression in 16p11.2del neuronal cells varied on the basis of a 132 kb 58 single nucleotide polymorphism (SNP) residual haplotype, with the version composed entirely of minor alleles associated with reduced MAPK3 expression. Ten SNPs on the residual haplotype were mapped to enhancers of MAPK3. We functionally validated six of these SNPs by luciferase assay, implicating them in the residual haplotype-specific differences in MAPK3 expression via cis-regulation. Finally, the analysis of three different cohorts of 16p11.2del subjects showed that this minor residual haplotype is associated with neurodevelopmental disorder phenotypes in 16p11.2del carriers.<\/jats:p>","DOI":"10.1093\/brain\/awad071","type":"journal-article","created":{"date-parts":[[2023,3,1]],"date-time":"2023-03-01T22:06:08Z","timestamp":1677708368000},"page":"3347-3363","source":"Crossref","is-referenced-by-count":18,"title":["Haplotype-specific <i>MAPK3<\/i> expression in 16p11.2 deletion contributes to variable neurodevelopment"],"prefix":"10.1093","volume":"146","author":[{"given":"Fang","family":"Liu","sequence":"first","affiliation":[{"name":"Department of Medical Genetics, Capital Institute of Pediatrics , Beijing 100020 , China"},{"name":"Department of Medical Genetics, Graduate School of Peking Union Medical College , Beijing 100730 , 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and Chinese Academy of Medical Sciences , Beijing 100730 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haiming","family":"Yuan","sequence":"additional","affiliation":[{"name":"Affiliated Dongguan Maternal and Child Health Care Hospital, Southern Medical University , Dongguan 523120 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruen","family":"Yao","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics, Shanghai Children\u2019s Medical Center, Shanghai Jiao Tong University School of Medicine , Shanghai 200127 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zailong","family":"Qin","sequence":"additional","affiliation":[{"name":"Genetic and Metabolic Central Laboratory, Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region , Nanning 530003 , 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