Microtubule associated proteins (MAPs) are widely expressed in the central nervous system, and have established roles in cell proliferation, myelination, neurite formation, axon specification, outgrowth, dendrite, and synapse formation. We report eleven individuals from seven families harboring predicted pathogenic biallelic, de novo, and heterozygous variants in the NAV3 gene, which encodes the microtubule positive tip protein neuron navigator 3 (NAV3). All affected individuals have intellectual disability (ID), microcephaly, skeletal deformities, ocular anomalies, and behavioral issues. In mouse brain, Nav3 is expressed throughout the nervous system, with more prominent signatures in postmitotic, excitatory, inhibiting, and sensory neurons. When overexpressed in HEK293T and COS7 cells, pathogenic variants impaired NAV3 ability to stabilize microtubules. Further, knocking-down nav3 in zebrafish led to severe morphological defects, microcephaly, impaired neuronal growth, and behavioral impairment, which were rescued with co-injection of WT NAV3 mRNA and not by transcripts encoding the pathogenic variants. Our findings establish the role of NAV3 in neurodevelopmental disorders, and reveal its involvement in neuronal morphogenesis, and neuromuscular responses.

1st Department of Neurology Faculty of Medicine St Anne's University Hospital and CEITEC Masaryk University Brno Czech Republic

Alexander von Humboldt Fellowship Foundation Berlin 10117 Germany

Centre of Excellence in Molecular Biology University of the Punjab Lahore Pakistan

Department of Life Sciences School of Science University of Management and Technology Lahore Pakistan

Department of Medical Genetics Oslo University Hospital and University of Oslo Oslo Norway

Department of Medical Genetics University of Calgary Calgary Alberta Canada

Department of Neurology Charles University 1st Faculty of Medicine and General University Hospital Prague Prague Czech Republic

Department of Otorhinolaryngology Head and Neck Surgery School of Medicine University of Maryland Baltimore MD USA

Department of Pediatrics CHU de Nice Fondation Lenval Nice France

Division of Pediatric and Adolescent Medicine Oslo University Hospital and University of Oslo Oslo Norway

Faculty of Biological Sciences Department of Zoology University of Lakki Marwat 28420 Khyber Pakhtunkhwa Pakistan

INSERM UMR1231 GAD Génétique des Anomalies du Développement FHU TRANSLAD Université de Bourgogne Franche Comté Dijon France

Institute for Advanced Study Technical University of Munich Lichtenbergstrasse 2 a D 85748 Garching Germany

Institute for Medical Genetics and Applied Genomics University of Tübingen Tübinge 72076 Germany

Institute of Human Genetics Technical University of Munich School of Medicine Munich Germany

Institute of Neurogenomics Helmholtz Munich Neuherberg Germany

Jinnah Burn and Reconstructive Surgery Centre Allama Iqbal Medical Research University of Health Sciences Lahore Pakistan

Nantes Université CHU Nantes Service de Génétique Médicale 44000 Nantes France

National Center of Genetics 1 rue Louis Rech L 3555 Dudelange Luxembourg

See more in PubMed

van de Willige D, Hoogenraad CC, Akhmanova A. Microtubule plus-end tracking proteins in neuronal development. Cell. Mol. Life Sci. 2016;73:2053–2077. doi: 10.1007/s00018-016-2168-3. PubMed DOI PMC

Kumar P, Wittmann T. +TIPs: SxIPping along microtubule ends. Trends Cell Biol. 2012;22:418–428. doi: 10.1016/j.tcb.2012.05.005. PubMed DOI PMC

Honnappa S, et al. An EB1-binding motif acts as a microtubule tip localization signal. Cell. 2009;138:366–376. doi: 10.1016/j.cell.2009.04.065. PubMed DOI

Cohen‐Dvashi H, et al. Navigator‐3, a modulator of cell migration, may act as a suppressor of breast cancer progression. EMBO Mol. Med. 2015;7:299–314. doi: 10.15252/emmm.201404134. PubMed DOI PMC

Stringham, E., Pujol, N., Vandekerckhove, J. & Bogaert, T. unc-53 controls longitudinal migration in C. elegans. Development129, 3367–3379 (2002). PubMed

Martínez-López MJ, et al. Mouse neuron navigator 1, a novel microtubule-associated protein involved in neuronal migration. Mol. Cell. Neurosci. 2005;28:599–612. doi: 10.1016/j.mcn.2004.09.016. PubMed DOI

Accogli A, et al. Loss of neuron navigator 2 impairs brain and cerebellar development. Cerebellum. 2023;22:206–222. doi: 10.1007/s12311-022-01379-3. PubMed DOI PMC

Peeters PJ, et al. Sensory deficits in mice hypomorphic for a mammalian homologue of unc-53. Dev. Brain Res. 2004;150:89–101. doi: 10.1016/j.devbrainres.2004.03.004. PubMed DOI

Maes T, Barceló A, Buesa C. Neuron navigator: a human gene family with homology to unc-53, a cell guidance gene from Caenorhabditis elegans. Genomics. 2002;80:21–30. doi: 10.1006/geno.2002.6799. PubMed DOI

Coy JF, et al. Pore membrane and/or filament interacting like protein 1 (POMFIL1) is predominantly expressed in the nervous system and encodes different protein isoforms. Gene. 2002;290:73–94. doi: 10.1016/S0378-1119(02)00567-X. PubMed DOI

Lv F, et al. Neuron navigator 3 (NAV3) is required for heart development in zebrafish. Fish. Physiol. Biochem. 2022;48:173–183. doi: 10.1007/s10695-022-01049-5. PubMed DOI

Klein C, et al. Neuron navigator 3a regulates liver organogenesis during zebrafish embryogenesis. Development. 2011;138:1935–1945. doi: 10.1242/dev.056861. PubMed DOI PMC

Zhou X, et al. Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes. Nat. Genet. 2022;54:1305–1319. doi: 10.1038/s41588-022-01148-2. PubMed DOI PMC

Sobreira N, Schiettecatte F, Valle D, Hamosh A. GeneMatcher: a matching tool for connecting investigators with an interest in the same gene. Hum. Mutat. 2015;36:928–930. doi: 10.1002/humu.22844. PubMed DOI PMC

Karczewski KJ, et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020;581:434–443. doi: 10.1038/s41586-020-2308-7. PubMed DOI PMC

Mueller T, Wullimann MF. Expression domains of neuroD (nrd) in the early postembryonic zebrafish brain. Brain Res. Bull. 2002;57:377–379. doi: 10.1016/S0361-9230(01)00694-3. PubMed DOI

Kurolap A, et al. Bi-allelic variants in neuronal cell adhesion molecule cause a neurodevelopmental disorder characterized by developmental delay, hypotonia, neuropathy/spasticity. Am. J. Hum. Genet. 2022;109:518–532. doi: 10.1016/j.ajhg.2022.01.004. PubMed DOI PMC

Tsai P, Shinar S. Agenesis of the corpus callosum: What to tell expecting parents? Prenat. Diagn. 2023;43:1527–1535. doi: 10.1002/pd.6447. PubMed DOI

Barth PG. Disorders of neuronal migration. Can. J. Neurol. Sci. 1987;14:1–16. doi: 10.1017/S031716710002610X. PubMed DOI

Prasad T, Iyer S, Chatterjee S, Kumar M. In vivo models to study neurogenesis and associated neurodevelopmental disorders—Microcephaly and autism spectrum disorder. WIREs Mech. Dis. 2023;15:e1603. doi: 10.1002/wsbm.1603. PubMed DOI

Papaioannou G, Garel C. The fetal brain: migration and gyration anomalies—pre-and postnatal correlations. Pediatr. Radiol. 2023;53:589–601. doi: 10.1007/s00247-022-05458-9. PubMed DOI

Kahn OI, Baas PW. Microtubules and growth cones: motors drive the turn. Trends Neurosci. 2016;39:433–440. doi: 10.1016/j.tins.2016.04.009. PubMed DOI PMC

Yang K-M, et al. Co-chaperone BAG2 determines the pro-oncogenic role of cathepsin B in triple-negative breast cancer cells. Cell Rep. 2017;21:2952–2964. doi: 10.1016/j.celrep.2017.11.026. PubMed DOI

van Haren J, et al. Mammalian Navigators are microtubule plus‐end tracking proteins that can reorganize the cytoskeleton to induce neurite‐like extensions. Cell Motil. Cytoskeleton. 2009;66:824–838. doi: 10.1002/cm.20370. PubMed DOI

Schwarz JM, Cooper DN, Schuelke M, Seelow D. MutationTaster2: mutation prediction for the deep-sequencing age. Nat. Methods. 2014;11:361–362. doi: 10.1038/nmeth.2890. PubMed DOI

Robinson PN, et al. The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease. Am. J. Hum. Genet. 2008;83:610–615. doi: 10.1016/j.ajhg.2008.09.017. PubMed DOI PMC

Riazuddin S, et al. Exome sequencing of Pakistani consanguineous families identifies 30 novel candidate genes for recessive intellectual disability. Mol. Psychiatry. 2017;22:1604–1614. doi: 10.1038/mp.2016.109. PubMed DOI PMC

Adzhubei IA, et al. A method and server for predicting damaging missense mutations. Nat. Methods. 2010;7:248–249. doi: 10.1038/nmeth0410-248. PubMed DOI PMC

Ioannidis NM, et al. REVEL: an ensemble method for predicting the pathogenicity of rare missense variants. Am. J. Hum. Genet. 2016;99:877–885. doi: 10.1016/j.ajhg.2016.08.016. PubMed DOI PMC

Jagadeesh KA, et al. M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity. Nat. Genet. 2016;48:1581–1586. doi: 10.1038/ng.3703. PubMed DOI

Rentzsch P, Schubach M, Shendure J, Kircher M. CADD-Splice—improving genome-wide variant effect prediction using deep learning-derived splice scores. Genome Med. 2021;13:1–12. doi: 10.1186/s13073-021-00835-9. PubMed DOI PMC

Kopanos C, et al. VarSome: the human genomic variant search engine. Bioinformatics. 2019;35:1978. doi: 10.1093/bioinformatics/bty897. PubMed DOI PMC

Wiel L, et al. MetaDome: pathogenicity analysis of genetic variants through aggregation of homologous human protein domains. Hum. Mutat. 2019;40:1030–1038. PubMed PMC

Silk M, Petrovski S, Ascher DB. MTR-Viewer: identifying regions within genes under purifying selection. Nucleic Acids Res. 2019;47:W121–W126. doi: 10.1093/nar/gkz457. PubMed DOI PMC

Madeira F, et al. Search and sequence analysis tools services from EMBL-EBI in 2022. Nucleic Acids Res. 2022;50:W276–W279. doi: 10.1093/nar/gkac240. PubMed DOI PMC

Cao J, et al. The single-cell transcriptional landscape of mammalian organogenesis. Nature. 2019;566:496–502. doi: 10.1038/s41586-019-0969-x. PubMed DOI PMC

Speir ML, et al. UCSC Cell Browser: visualize your single-cell data. Bioinformatics. 2021;37:4578–4580. doi: 10.1093/bioinformatics/btab503. PubMed DOI PMC

Yang J, Zhang Y. I-TASSER server: new development for protein structure and function predictions. Nucleic Acids Res. 2015;43:W174–W181. doi: 10.1093/nar/gkv342. PubMed DOI PMC

Schrodinger, L. The AxPyMOL molecular graphics plugin for Microsoft PowerPoint, version 1.8. (Schrödinger, LLC, New York, NY, 2015).

Venselaar H, Te Beek TA, Kuipers RK, Hekkelman ML, Vriend G. Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces. BMC Bioinform. 2010;11:1–10. doi: 10.1186/1471-2105-11-548. PubMed DOI PMC