24While rare pathogenic CNVs are associated with both neuronal and non-neuronal phenotypes, 25 functional studies evaluating these regions have focused on the molecular basis of neuronal 26 defects. We report a systematic functional analysis of non-neuronal phenotypes for 59 homologs 27 of genes within ten CNVs and 20 neurodevelopmental genes in Drosophila. Using wing-specific 28 knockdown of 136 RNA interference lines, we identify phenotypes in 72/79 homologs including 29 six lines with lethality and 21 lines with severe phenotypes. We find no correlation between 30 severity of these phenotypes and neuronal defects due to eye-specific knockdown. We observe 31 disruptions in cell proliferation and apoptosis for 23/27 homologs, and altered Wnt, Hedgehog 32 and Notch signaling for 9/14 homologs, including AATF/Aatf, PPP4C/Pp4-19C, and 33 KIF11/Klp61F, validated with differences in human tissue-specific expression and network 34 connectivity. Our findings suggest that multiple genes within each CNV differentially affect both 35 global and tissue-specific developmental processes, contributing to non-neuronal phenotypes of 36 CNV disorders. 37 38 39 40Rare copy-number variants (CNVs), or deletions and duplications in the genome, are associated 41 with neurodevelopmental disorders such as autism, intellectual disability (ID), and 42 schizophrenia 1,2 . While dosage alteration of CNV regions contribute predominantly to defects in 43 nervous system development, several CNV disorders also lead to early developmental features 44 involving other organ systems 3,4 , including cardiac defects 5,6 , kidney malformations 7 , 45 craniofacial features 3 , and skeletal abnormalities 8 . In fact, an overall survey of ten rare disease-46 associated CNVs among individuals within the DECIPHER database 9 showed a wide range of 47 non-neuronal phenotypes across multiple organ systems for each CNV disorder ( Fig. 1). For 48 example, the 1q21.1 deletion causes variable expression of multiple neuronal and non-neuronal 49 phenotypes, including developmental delay, autism, and schizophrenia as well as craniofacial 50 features, cataracts, cardiac defects, and skeletal abnormalities 10-12 . Additionally, while the 51 7q11.23 deletion associated with Williams-Beuren syndrome (WBS) causes neuropsychiatric and 52 behavioral features, other non-neuronal phenotypes, including supravalvular aortic stenosis, 53 auditory defects, hypertension, diabetes mellitus, and musculoskeletal and connective tissue 54 anomalies, are also observed among the deletion carriers 13 . In fact, individual genes within the 55 WBS region are associated with specific features of the deletion, such as ELN and supravalvular 56 aortic stenosis 14 , STX1A and impaired glucose tolerance 15 , LIMK1 and impaired visuospatial 57 abilities 16 , and GTF2IRD1 and craniofacial abnormalities 17 . Furthermore, TBX1 was identified to 58 cause the pharyngeal arch cardiac defects associated with the 22q11.2 deletion (DiGeorge 59 syndrome) 18 , while HNF1B within the 17q12 delet...