Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Clinical profiling of MRD48 and functional characterization of two novel pathogenic RAC1 variants

European Journal of Human Genetics volume 31, pages 805–814 (2023)Cite this article

Subjects

Abstract

RAC1 is a member of the Rac/Rho GTPase subfamily within the RAS superfamily of small GTP-binding proteins, comprising 3 paralogs playing a critical role in actin cytoskeleton remodeling, cell migration, proliferation and differentiation. De novo missense variants in RAC1 are associated with a rare neurodevelopmental disorder (MRD48) characterized by DD/ID and brain abnormalities coupled with a wide range of additional features. Structural and functional studies have documented either a dominant negative or constitutively active behavior for a subset of mutations. Here, we describe two individuals with previously unreported de novo missense RAC1 variants. We functionally demonstrate their pathogenicity proving a gain-of-function (GoF) effect for both. By reviewing the clinical features of these two individuals and the previously published MRD48 subjects, we further delineate the clinical profile of the disorder, confirming its phenotypic variability. Moreover, we compare the main features of MRD48 with the neurodevelopmental disease caused by GoF variants in the paralog RAC3, highlighting similarities and differences. Finally, we review all previously reported variants in RAC proteins and in the closely related CDC42, providing an updated overview of the spectrum and hotspots of pathogenic variants affecting these functionally related GTPases.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: RAC1 mutations variably affect protein stability and GTP binding in COS-1 transfected cells.
Fig. 2: RAC1 mutations affect cytoskeletal rearrangement and cell shape.
Fig. 3: Structural impact of the pathogenic RAC1 amino acid substitutions and clinical pictures of affected individuals.
Fig. 4: Mutation spectrum in RAC1 and related GTPases.

Similar content being viewed by others

Data availability

The exome sequencing data that support the findings of this work are available on request from the corresponding author (MT). The data are not publicly available due to due to privacy/ethical restrictions. The pathogenic variants identified in this work have been submitted to ClinVar (c.475G>A, SCV002605544; c.184G>A, SCV002605545).

References

  1. Hall A. Rho family GTPases. Biochem Soc Trans. 2012;40:1378–82. https://doi.org/10.1042/BST20120103.

    Article  CAS  PubMed  Google Scholar 

  2. Aspenström P, Fransson A, Saras J. Rho GTPases have diverse effects on the organization of the actin filament system. Biochem J. 2004;377:327–37. https://doi.org/10.1042/BJ20031041.

    Article  PubMed  PubMed Central  Google Scholar 

  3. Scala M, Nishikawa M, Ito H, Tabata H, Khan T, Accogli A, et al. Variant-specific changes in RAC3 function disrupt corticogenesis in neurodevelopmental phenotypes. Brain. 2022;145:3308–27. https://doi.org/10.1093/brain/awac106.

    Article  PubMed  PubMed Central  Google Scholar 

  4. Porter AP, Papaioannou A, Malliri A. Deregulation of Rho GTPases in cancer. Small GTPases. 2016;7:123–38. https://doi.org/10.1080/21541248.2016.1173767.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Stankiewicz TR, Linseman DA. Rho family GTPases: key players in neuronal development, neuronal survival, and neurodegeneration. Front Cell Neurosci. 2014;8:314. https://doi.org/10.3389/fncel.2014.00314.

    Article  PubMed  PubMed Central  Google Scholar 

  6. Scala M, Nishikawa M, Nagata KI, Striano P. Pathophysiological mechanisms in neurodevelopmental disorders caused by RacGTPases dysregulation: what’s behind Neuro-RACopathies. Cells. 2021;10:3395. https://doi.org/10.3390/cells10123395.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Reijnders MRF, Ansor NM, Kousi M, Yue WW, Tan PL, Clarkson K, et al. RAC1 missense mutations in developmental disorders with diverse phenotypes. Am J Hum Genet. 2017;101:466–77. https://doi.org/10.1016/j.ajhg.2017.08.007.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Barbosa S, Greville-Heygate S, Bonnet M, Godwin A, Fagotto-Kaufmann C, Kajava AV, et al. Opposite modulation of RAC1 by mutations in TRIO is associated with distinct, domain-specific neurodevelopmental disorders. Am J Hum Genet. 2020;106:338–55. https://doi.org/10.1016/j.ajhg.2020.01.018.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Moll J, Sansig G, Fattori E, van der Putten H. The murine rac1 gene: cDNA cloning, tissue distribution and regulated expression of rac1 mRNA by disassembly of actin microfilaments. Oncogene. 1991;6:863–6. PMID: 1905006.

    CAS  PubMed  Google Scholar 

  10. Shirsat NV, Pignolo RJ, Kreider BL, Rovera G. A member of the ras gene superfamily is expressed specifically in T, B and myeloid hemopoietic cells. Oncogene. 1990;5:769–72. PMID: 2189110.

    CAS  PubMed  Google Scholar 

  11. Malosio ML, Gilardelli D, Paris S, Albertinazzi C, de Curtis I. Differential expression of distinct members of Rho family GTP-binding proteins during neuronal development: identification of Rac1B, a new neural-specific member of the family. J Neurosci. 1997;17:6717–28. https://doi.org/10.1523/JNEUROSCI.17-17-06717.1997.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Costain G, Callewaert B, Gabriel H, Tan TY, Walker S, Christodoulou J, et al. De novo missense variants in RAC3 cause a novel neurodevelopmental syndrome. Genet Med. 2019;21:1021–6. https://doi.org/10.1038/s41436-018-0323-y.

    Article  CAS  PubMed  Google Scholar 

  13. Lougaris V, Baronio M, Gazzurelli L, Benvenuto A, Plebani A. RAC2 and primary human immune deficiencies. J Leukoc Biol. 2020;108:687–96. https://doi.org/10.1002/JLB.5MR0520-194RR.

    Article  CAS  PubMed  Google Scholar 

  14. Lelieveld SH, Reijnders MR, Pfundt R, Yntema HG, Kamsteeg EJ, de Vries P, et al. Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability. Nat Neurosci. 2016;19:1194–6. https://doi.org/10.1038/nn.4352.

    Article  CAS  PubMed  Google Scholar 

  15. Haugh IM, Pineider JL, Agim NG. Ichthyosiform changes in a patient with RAC1 mutation. Pediatr Dermatol. 2021;38:1590–1. https://doi.org/10.1111/pde.14844.

    Article  PubMed  Google Scholar 

  16. Tian C, Kay Y, Sadybekov A, Rao S, Katritch V, Herring BE. An intellectual disability-related missense mutation in Rac1 prevents LTP induction. Front Mol Neurosci. 2018;11:223 https://doi.org/10.3389/fnmol.2018.00223.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Martinelli S, Krumbach OHF, Pantaleoni F, Coppola S, Amin E, Pannone L, et al. Functional dysregulation of CDC42 causes diverse developmental phenotypes. Am J Hum Genet. 2018;102:309–20. https://doi.org/10.1016/j.ajhg.2017.12.015.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Lam MT, Coppola S, Krumbach OHF, Prencipe G, Insalaco A, Cifaldi C, et al. A novel disorder involving dyshematopoiesis, inflammation, and HLH due to aberrant CDC42 function. J Exp Med. 2019;216:2778–99. https://doi.org/10.1084/jem.20190147.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Coppola S, Insalaco A, Zara E, Di Rocco M, Marafon DP, Spadaro F, et al. Mutations at the C-terminus of CDC42 cause distinct hematopoietic and autoinflammatory disorders. J Allergy Clin Immunol. 2022;150:223–8. https://doi.org/10.1016/j.jaci.2022.01.024.

    Article  CAS  PubMed  Google Scholar 

  20. Daimon E, Shibukawa Y, Thanasegaran S, Yamazaki N, Okamoto N. Macrothrombocytopenia of Takenouchi-Kosaki syndrome is ameliorated by CDC42 specific- and lipidation inhibitors in MEG-01 cells. Sci Rep. 2021;11:17990. https://doi.org/10.1038/s41598-021-97478-y.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Schneider CA, Rasband WS, Eliceiri KW. NIH Image to ImageJ: 25 years of image analysis. Nat Methods. 2012;9:671–5. https://doi.org/10.1038/nmeth.2089.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17:405–24. https://doi.org/10.1038/gim.2015.30.

    Article  PubMed  PubMed Central  Google Scholar 

  23. Frazer J, Notin P, Dias M, Gomez A, Min JK, Brock K, et al. Disease variant prediction with deep generative models of evolutionary data. Nature. 2021;599:91–95. https://doi.org/10.1038/s41586-021-04043-8.

    Article  CAS  PubMed  Google Scholar 

  24. Chang MT, Asthana S, Gao SP, Lee BH, Chapman JS, Kandoth C, et al. Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity. Nat Biotechnol. 2016;34:155–63. https://doi.org/10.1038/nbt.3391.

    Article  CAS  PubMed  Google Scholar 

  25. Majole´e J, Podieh F, Hordijk PL, Kovačević I. The interplay of Rac1 activity, ubiquitination and GDI binding and its consequences for endothelial cell spreading. PLoS One. 2021;16:e0254386. https://doi.org/10.1371/journal.pone.0254386.

    Article  CAS  PubMed  Google Scholar 

  26. Ridley AJ, Paterson HF, Johnston CL, Diekmann D, Hall A. The small GTP-binding protein rac regulates growth factor-induced membrane ruffling. Cell. 1992;70:401–10. https://doi.org/10.1016/0092-8674(92)90164-8.

    Article  CAS  PubMed  Google Scholar 

  27. Carta C, Pantaleoni F, Bocchinfuso G, Stella L, Vasta I, Sarkozy A, et al. Germline missense mutations affecting KRAS Isoform B are associated with a severe Noonan syndrome phenotype. Am J Hum Genet. 2006;79:129–35. https://doi.org/10.1086/504394.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Janakiraman M, Vakiani E, Zeng Z, Pratilas CA, Taylor BS, Chitale D, et al. Genomic and biological characterization of exon 4 KRAS mutations in human cancer. Cancer Res. 2010;70:5901–11. https://doi.org/10.1158/0008-5472.CAN-10-0192.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Gremer L, Merbitz-Zahradnik T, Dvorsky R, Cirstea IC, Kratz CP, Zenker M, et al. Germline KRAS mutations cause aberrant biochemical and physical properties leading to developmental disorders. Hum Mutat. 2011;32:33–43. https://doi.org/10.1002/humu.21377.

    Article  CAS  PubMed  Google Scholar 

  30. Sanghavi HM, Rashmi R, Dasgupta A, Majumdar S. G-domain prediction across the diversity of G protein families. bioRxiv. 2019;24:888222. https://doi.org/10.1101/2019.12.24.888222.

    Article  Google Scholar 

  31. Hiraide T, KabaYasui H, Kato M, Nakashima M, Saitsu H. A de novo variant in RAC3 causes severe global developmental delay and a middle interhemispheric variant of holoprosencephaly. J Hum Genet. 2019;64:1127–32. https://doi.org/10.1038/s10038-019-0656-7.

    Article  CAS  PubMed  Google Scholar 

  32. Sugihara K, Nakatsuji N, Nakamura K, Nakao K, Hashimoto R, Otani H, et al. Rac1 is required for the formation of three germ layers during gastrulation. Oncogene. 1998;17:3427–33. https://doi.org/10.1038/sj.onc.1202595.

    Article  CAS  PubMed  Google Scholar 

  33. He F, Soriano P. A critical role for PDGFRα signaling in medial nasal process development. PLoS Genet. 2013;9:e1003851. https://doi.org/10.1371/journal.pgen.1003851.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Chai Y, Jiang X, Ito Y, Bringas P Jr, Han J, Rowitch DH, et al. Fate of the mammalian cranial neural crest during tooth and mandibular morphogenesis. Development. 2000;127:1671–9. https://doi.org/10.1242/dev.127.8.1671.

    Article  CAS  PubMed  Google Scholar 

  35. Leung C, Engineer A, Kim MY, Lu X, Feng Q. Myocardium-specific deletion of Rac1 causes ventricular noncompaction and outflow tract defects. J Cardiovasc Dev Dis. 2021;8:29. https://doi.org/10.3390/jcdd8030029.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Allanson JE, Cunniff C, Hoyme HE, McGaughran J, Muenke M, Neri G. Elements of morphology: standard terminology for the head and face. Am J Med Genet A. 2009;149A:6–28. https://doi.org/10.1002/ajmg.a.32612.

    Article  PubMed  PubMed Central  Google Scholar 

  37. Pennucci R, Talpo F, Astro V, Montinaro V, Morè L, Cursi M, et al. Loss of either Rac1 or Rac3 GTPase differentially affects the behavior of mutant mice and the development of functional GABAergic networks. Cereb Cortex. 2016;26:873–90. https://doi.org/10.1093/cercor/bhv274.

    Article  PubMed  Google Scholar 

  38. Mosaddeghzadeh N, Ahmadian MR. The RHO family GTPases: mechanisms of regulation and signaling. Cells. 2021;10:1831. https://doi.org/10.3390/cells10071831.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Fiegen D, Haeusler LC, Blumenstein L, Herbrand U, Dvorsky R, Vetter IR, et al. Alternative splicing of Rac1 generates Rac1b, a self-activating GTPase. J Biol Chem. 2004;279:4743–9. https://doi.org/10.1074/jbc.M310281200.

    Article  CAS  PubMed  Google Scholar 

  40. Asiri A, Alwadaani D, Umair M, Alhamoudi KM, Almuhanna MH, Nasir A, et al. Pancytopenia, recurrent infection, poor wound healing, heterotopia of the brain probably associated with a candidate novel de novo CDC42 gene defect: expanding the molecular and phenotypic spectrum. Genes 2021;12:294. https://doi.org/10.3390/genes12020294.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Tartaglia M, Gelb BD. Disorders of dysregulated signal traffic through the RAS-MAPK pathway: phenotypic spectrum and molecular mechanisms. Ann N Y Acad Sci. 2010;1214:99–121. https://doi.org/10.1111/j.1749-6632.2010.05790.x.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Niihori T, Aoki Y, Okamoto N, Kurosawa K, Ohashi H, Mizuno S, et al. HRAS mutants identified in Costello syndrome patients can induce cellular senescence: possible implications for the pathogenesis of Costello syndrome. J Hum Genet. 2011;56:707–15. https://doi.org/10.1038/jhg.2011.85.

    Article  CAS  PubMed  Google Scholar 

  43. Zampino G, Pantaleoni F, Carta C, Cobellis G, Vasta I, Neri C, et al. Diversity, parental germline origin, and phenotypic spectrum of de novo HRAS missense changes in Costello syndrome. Hum Mutat. 2007;28:265–72. https://doi.org/10.1002/humu.20431.

    Article  CAS  PubMed  Google Scholar 

  44. Gripp KW, Lin AE. Costello syndrome: a Ras/mitogen activated protein kinase pathway syndrome (rasopathy) resulting from HRAS germline mutations. Genet Med. 2012;14:285–92. https://doi.org/10.1038/gim.0b013e31822dd91f.

    Article  CAS  PubMed  Google Scholar 

  45. Harms FL, Kloth K, Bley A, Denecke J, Santer R, Lessel D, et al. Activating mutations in PAK1, encoding p21-activated kinase 1, cause a neurodevelopmental disorder. Am J Hum Genet. 2018;103:579–91. https://doi.org/10.1016/j.ajhg.2018.09.005.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Hori K, Shimaoka K, Hoshino M. AUTS2 gene: keys to understanding the pathogenesis of neurodevelopmental disorders. Cells. 2021;11:11. https://doi.org/10.3390/cells11010011.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Duffney LJ, Wei J, Cheng J, Liu W, Smith KR, Kittler JT, et al. Shank3 deficiency induces NMDA receptor hypofunction via an actin-dependent mechanism. J Neurosci. 2013;33:15767–78. https://doi.org/10.1523/JNEUROSCI.1175-13.2013.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Dong T, He J, Wang S, Wang L, Cheng Y, Zhong Y. Inability to activate Rac1-dependent forgetting contributes to behavioral inflexibility in mutants of multiple autism-risk genes. Proc Natl Acad Sci USA. 2016;113:7644–9. https://doi.org/10.1073/pnas.1602152113.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Jones KL, Jones MC, and Del Campo M. Smith’s recognizable patterns of human malformation. Philadelphia, PA: Elsevier Health Sciences; 2013.

Download references

Acknowledgements

We are grateful to the families who participated in this study.

Funding

This work was supported by the Italian Ministry of Health (5×1000_2019 and CCR-2017-23669081 to MT, and RF-2018-12366931 and GR-2019-12371203 to FCR), Istituto Superiore di Sanità (Bando Ricerca Indipendente ISS 2020-2022-ISS20-39c812dd2b3c to SC), Fondazione AIRC per la Ricerca sul Cancro (IG 21614, to MT), and Italian Ministry of Research (FOE_2019 to MT).

Author information

Author notes

  1. These authors contributed equally: Manuela Priolo, Erika Zara.

Authors and Affiliations

  1. USD Genetica Medica, Grande Ospedale Metropolitano Bianchi-Melacrino-Morelli, 89124, Reggio Calabria, Italy

    Manuela Priolo, Luigi Chiriatti & Corrado Mammì

  2. Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy

    Erika Zara, Francesca Clementina Radio, Andrea Ciolfi, Emanuele Bellacchio, Cecilia Mancini, Francesca Pantaleoni, Marcello Niceta & Marco Tartaglia

  3. Department of Biology and Biotechnology, Sapienza University, 00185, Rome, Italy

    Erika Zara

  4. Core Facilities, Istituto Superiore di Sanità, 00161, Rome, Italy

    Francesca Spadaro

  5. Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161, Rome, Italy

    Viviana Cordeddu

  6. USD Neuroradiologia, Grande Ospedale Metropolitano Bianchi-Melacrino-Morelli, 89124, Reggio Calabria, Italy

    Emilio Africa

  7. Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, Università di Salerno, 84084, Salerno, Italy

    Daniela Melis

  8. National Center for Rare Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy

    Simona Coppola

Authors
  1. Manuela Priolo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Erika Zara
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Francesca Clementina Radio
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Andrea Ciolfi
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Francesca Spadaro
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Emanuele Bellacchio
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Cecilia Mancini
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Francesca Pantaleoni
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Viviana Cordeddu
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Luigi Chiriatti
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Marcello Niceta
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Emilio Africa
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Corrado Mammì
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Daniela Melis
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Simona Coppola
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. Marco Tartaglia
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

MP and MT conceived the work, and wrote the manuscript. AC, CM, FP, VC, LC and MN performed the genomic analyses and analyzed and validated the genomic data. EB performed the structural analyses. MP, FCR, EA, CM and DM collected the clinical data and contributed to the clinical data analyses. EZ, FS, and SC designed and performed the functional analyses. All coauthors helped write and revise the manuscript.

Corresponding authors

Correspondence to Manuela Priolo or Marco Tartaglia.

Ethics declarations

Competing interests

The authors declare no competing interests.

Ethical approval

The study was approved by the local Institutional Ethical Committee (ref. 1702_OPBG_2018). Clinical data, pictures, DNA samples and other biological specimens were collected, used, and stored after signed informed consents from the participating subjects/families were secured. Permission to publish the clinical pictures and the clinical details was obtained for both individuals.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Priolo, M., Zara, E., Radio, F.C. et al. Clinical profiling of MRD48 and functional characterization of two novel pathogenic RAC1 variants. Eur J Hum Genet 31, 805–814 (2023). https://doi.org/10.1038/s41431-023-01351-7

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41431-023-01351-7

This article is cited by

Search

Advanced search

Quick links