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The adenosine diphosphate (ADP) ribosylation factors (ARF) are key proteins for regulating cargo sorting at the Golgi network. In this family, ARF3 mainly works at the trans-Golgi network (TGN), and no ARF3-related phenotypes have yet been described in humans. We here report the clinical and genetic evaluations of two unrelated children with de novo pathogenic variants in the ARF3 gene: c.200A\u2009&amp;gt;\u2009T (p.Asp67Val) and c.296G\u2009&amp;gt;\u2009T (p.Arg99Leu). Although the affected individuals presented commonly with developmental delay, epilepsy and brain abnormalities, there were differences in severity, clinical course and brain lesions. In vitro subcellular localization assays revealed that the p.Arg99Leu mutant localized to Golgi apparatus, similar to the wild-type, whereas the p.Asp67Val mutant tended to show a disperse cytosolic pattern together with abnormally dispersed Golgi localization, similar to that observed in a known dominant negative variant (p.Thr31Asn). Pull-down assays revealed that the p.Asp67Val had a loss-of-function effect and the p.Arg99Leu variant had increased binding of the adaptor protein, Golgi-localized, \u03b3-adaptin ear-containing, ARF-binding protein 1 (GGA1), supporting the gain of function. Furthermore, in vivo studies revealed that p.Asp67Val transfection led to lethality in flies. In contrast, flies expressing p.Arg99Leu had abnormal rough eye, as observed in the gain-of-function variant p.Gln71Leu. These data indicate that two ARF3 variants, the possibly loss-of-function p.Asp67Val and the gain-of-function p.Arg99Leu, both impair the Golgi transport system. Therefore, it may not be unreasonable that they showed different clinical features like diffuse brain atrophy (p.Asp67Val) and cerebellar hypoplasia (p.Arg99Leu).<\/jats:p>","DOI":"10.1093\/hmg\/ddab224","type":"journal-article","created":{"date-parts":[[2021,7,30]],"date-time":"2021-07-30T07:13:04Z","timestamp":1627629184000},"page":"69-81","source":"Crossref","is-referenced-by-count":26,"title":["<i>De novo ARF3<\/i>\n                    variants cause neurodevelopmental disorder with brain abnormality"],"prefix":"10.1093","volume":"31","author":[{"given":"Masamune","family":"Sakamoto","sequence":"first","affiliation":[{"name":"Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan"},{"name":"Department of Pediatrics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kazunori","family":"Sasaki","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan"},{"name":"Department of Cancer Biology, Institute for Diseases of Old Age, Juntendo University School of Medicine, Tokyo 113-8421, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Atsushi","family":"Sugie","sequence":"additional","affiliation":[{"name":"Brain Research Institute, Niigata University, Niigata, 951-8585, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yohei","family":"Nitta","sequence":"additional","affiliation":[{"name":"Brain Research Institute, Niigata University, Niigata, 951-8585, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tetsuaki","family":"Kimura","sequence":"additional","affiliation":[{"name":"Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, 411-8540, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Semra","family":"G\u00fcrsoy","sequence":"additional","affiliation":[{"name":"Department of Pediatric Genetics, S.B.\u00dc. Dr. Beh\u00e7et Uz Children's Education and Research Hospital, Izmir, 35210, Turkey"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tayfun","family":"Cinleti","sequence":"additional","affiliation":[{"name":"Department of Pediatric Genetics, Dokuz Eylul University, Faculty of Medicine, Izmir, 35340, Turkey"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mizue","family":"Iai","sequence":"additional","affiliation":[{"name":"Department of Neurology, Kanagawa Children's Medical Center, Yokohama, 232-8555, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Toru","family":"Sengoku","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kazuhiro","family":"Ogata","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Atsushi","family":"Suzuki","sequence":"additional","affiliation":[{"name":"Molecular Cellular Biology Laboratory, Yokohama City University Graduate School of Medical Life Science, Yokohama, 230-0045, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nobuhiko","family":"Okamoto","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, 594-1101, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kazuhiro","family":"Iwama","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan"},{"name":"Department of Pediatrics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naomi","family":"Tsuchida","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan"},{"name":"Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, 236-0004, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuri","family":"Uchiyama","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan"},{"name":"Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, 236-0004, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eriko","family":"Koshimizu","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Atsushi","family":"Fujita","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kohei","family":"Hamanaka","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Satoko","family":"Miyatake","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan"},{"name":"Clinical Genetics Department, Yokohama City University Hospital, Yokohama, 236-0004, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Takeshi","family":"Mizuguchi","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masataka","family":"Taguri","sequence":"additional","affiliation":[{"name":"Department of Data Science, Yokohama City University School of Data Science, Yokohama, 236-0027, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuuichi","family":"Ito","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hidehisa","family":"Takahashi","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Noriko","family":"Miyake","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan"},{"name":"Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naomichi","family":"Matsumoto","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,8,4]]},"reference":[{"key":"2021121717432092200_ref1","doi-asserted-by":"crossref","DOI":"10.3390\/cells8060531","article-title":"Cargo sorting at the trans-Golgi network for shunting into specific transport routes: role of Arf small G proteins and 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Rev. Mol. Cell Biol."},{"key":"2021121717432092200_ref3","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1016\/j.pneurobio.2017.03.007","article-title":"Golgi trafficking defects in postnatal microcephaly: the evidence for \"Golgipathies\"","volume":"153","author":"Passemard","year":"2017","journal-title":"Prog. Neurobiol."},{"key":"2021121717432092200_ref4","doi-asserted-by":"crossref","first-page":"1359","DOI":"10.1086\/375454","article-title":"Cohen syndrome is caused by mutations in a novel gene, COH1, encoding a transmembrane protein with a presumed role in vesicle-mediated sorting and intracellular protein transport","volume":"72","author":"Kolehmainen","year":"2003","journal-title":"Am. J. Hum. Genet."},{"key":"2021121717432092200_ref5","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1136\/jmedgenet-2013-101823","article-title":"VPS53 mutations cause progressive cerebello-cerebral atrophy type 2 (PCCA2)","volume":"51","author":"Feinstein","year":"2014","journal-title":"J. Med. Genet."},{"key":"2021121717432092200_ref6","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1002\/humu.22296","article-title":"Mutation spectrum in RAB3GAP1, RAB3GAP2, and RAB18 and genotype-phenotype correlations in Warburg micro syndrome and Martsolf syndrome","volume":"34","author":"Handley","year":"2013","journal-title":"Hum. Mutat."},{"key":"2021121717432092200_ref7","doi-asserted-by":"crossref","DOI":"10.1038\/npjgenmed.2016.36","article-title":"Missense-depleted regions in population exomes implicate ras superfamily nucleotide-binding protein alteration in patients with brain malformation","volume":"1","author":"Ge","year":"2016","journal-title":"NPJ Genom. Med."},{"key":"2021121717432092200_ref8","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1152\/physrev.2001.81.1.153","article-title":"Small GTP-binding proteins","volume":"81","author":"Takai","year":"2001","journal-title":"Physiol. Rev."},{"key":"2021121717432092200_ref9","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1083\/jcb.201103008","article-title":"The Ras protein superfamily: evolutionary tree and role of conserved amino acids","volume":"196","author":"Rojas","year":"2012","journal-title":"J. Cell Biol."},{"key":"2021121717432092200_ref10","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1146\/annurev.cellbio.23.090506.123209","article-title":"The small G proteins of the Arf family and their regulators","volume":"23","author":"Gillingham","year":"2007","journal-title":"Annu. Rev. Cell Dev. Biol."},{"key":"2021121717432092200_ref11","doi-asserted-by":"crossref","first-page":"1249","DOI":"10.1091\/mbc.E18-12-0820","article-title":"ARF GTPases and their GEFs and GAPs: concepts and challenges","volume":"30","author":"Sztul","year":"2019","journal-title":"Mol. Biol. Cell"},{"key":"2021121717432092200_ref12","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1042\/bj20020428","article-title":"GGA proteins associate with Golgi membranes through interaction between their GGAH domains and ADP-ribosylation factors","volume":"365","author":"Takatsu","year":"2002","journal-title":"Biochem. J."},{"key":"2021121717432092200_ref13","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1007\/s12565-019-00505-2","article-title":"Emerging roles of Golgi\/endosome-localizing monomeric clathrin adaptors GGAs","volume":"95","author":"Uemura","year":"2020","journal-title":"Anat. Sci. Int."},{"key":"2021121717432092200_ref14","doi-asserted-by":"crossref","first-page":"W452","DOI":"10.1093\/nar\/gks539","article-title":"SIFT web server: predicting effects of amino acid substitutions on proteins","volume":"40","author":"Sim","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2021121717432092200_ref15","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1038\/nmeth0410-248","article-title":"A method and server for predicting damaging missense mutations","volume":"7","author":"Adzhubei","year":"2010","journal-title":"Nat. Methods"},{"key":"2021121717432092200_ref16","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1038\/ng.2892","article-title":"A general framework for estimating the relative pathogenicity of human genetic variants","volume":"46","author":"Kircher","year":"2014","journal-title":"Nat. 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Cell"},{"key":"2021121717432092200_ref19","doi-asserted-by":"crossref","first-page":"5283","DOI":"10.1091\/mbc.e04-05-0388","article-title":"BIG2, a guanine nucleotide exchange factor for ADP-ribosylation factors: its localization to recycling endosomes and implication in the endosome integrity","volume":"15","author":"Shin","year":"2004","journal-title":"Mol. Biol. Cell"},{"key":"2021121717432092200_ref20","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.ajhg.2019.11.011","article-title":"Gain-of-function MN1 truncation variants cause a recognizable syndrome with craniofacial and brain abnormalities","volume":"106","author":"Miyake","year":"2020","journal-title":"Am. J. Hum. Genet."},{"key":"2021121717432092200_ref21","doi-asserted-by":"crossref","first-page":"1437","DOI":"10.1016\/S0021-9258(17)42277-0","article-title":"Dominant inhibitory mutants of ARF1 block endoplasmic reticulum to Golgi transport and trigger disassembly of the Golgi apparatus","volume":"269","author":"Dascher","year":"1994","journal-title":"J. Biol. Chem."},{"key":"2021121717432092200_ref22","doi-asserted-by":"crossref","first-page":"1836","DOI":"10.1091\/mbc.e10-01-0016","article-title":"Arf3 is activated uniquely at the trans-Golgi network by brefeldin A-inhibited guanine nucleotide exchange factors","volume":"21","author":"Manolea","year":"2010","journal-title":"Mol. Biol. 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J. Hum. Genet."},{"key":"2021121717432092200_ref32","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1016\/j.ajhg.2020.02.001","article-title":"De novo variants in SPOP cause two clinically distinct neurodevelopmental disorders","volume":"106","author":"Nabais Sa","year":"2020","journal-title":"Am. J. Hum. Genet."},{"key":"2021121717432092200_ref33","doi-asserted-by":"crossref","first-page":"108074","DOI":"10.1016\/j.celrep.2020.108074","article-title":"Real-time in-cell NMR reveals the intracellular modulation of GTP-bound levels of RAS","volume":"32","author":"Zhao","year":"2020","journal-title":"Cell Rep."},{"key":"2021121717432092200_ref34","doi-asserted-by":"crossref","first-page":"21949","DOI":"10.1038\/srep21949","article-title":"The structural basis of oncogenic mutations G12, G13 and Q61 in small GTPase K-Ras4B","volume":"6","author":"Lu","year":"2016","journal-title":"Sci. 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