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Jouret G, Egloff M, Landais E, Tassy O, Giuliano F, Karmous-Benailly H, Coutton C, Satre V, Devillard F, Dieterich K, Vieville G, Kuentz P, le Caignec C, Beneteau C, Isidor B, Nizon M, Callier P, Marquet V, Bieth E, Lévy J, Tabet AC, Lyonnet S, Baujat G, Rio M, Cartault F, Scheidecker S, Gouronc A, Schalk A, Jacquin C, Spodenkiewicz M, Angélini C, Pennamen P, Rooryck C, Doco-Fenzy M, Poirsier C. Clinical and genomic delineation of the new proximal 19p13.3 microduplication syndrome. Am J Med Genet A 2023; 191:52-63. [PMID: 36196855 DOI: 10.1002/ajmg.a.62983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/16/2022] [Accepted: 09/20/2022] [Indexed: 12/14/2022]
Abstract
A small but growing body of scientific literature is emerging about clinical findings in patients with 19p13.3 microdeletion or duplication. Recently, a proximal 19p13.3 microduplication syndrome was described, associated with growth delay, microcephaly, psychomotor delay and dysmorphic features. The aim of our study was to better characterize the syndrome associated with duplications in the proximal 19p13.3 region (prox 19p13.3 dup), and to propose a comprehensive analysis of the underlying genomic mechanism. We report the largest cohort of patients with prox 19p13.3 dup through a collaborative study. We collected 24 new patients with terminal or interstitial 19p13.3 duplication characterized by array-based Comparative Genomic Hybridization (aCGH). We performed mapping, phenotype-genotype correlations analysis, critical region delineation and explored three-dimensional chromatin interactions by analyzing Topologically Associating Domains (TADs). We define a new 377 kb critical region (CR 1) in chr19: 3,116,922-3,494,377, GRCh37, different from the previously described critical region (CR 2). The new 377 kb CR 1 includes a TAD boundary and two enhancers whose common target is PIAS4. We hypothesize that duplications of CR 1 are responsible for tridimensional structural abnormalities by TAD disruption and misregulation of genes essentials for the control of head circumference during development, by breaking down the interactions between enhancers and the corresponding targeted gene.
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Affiliation(s)
- Guillaume Jouret
- Department of Genetics, Reims University Hospital, Reims, France.,National Center of Genetics (NCG), Laboratoire national de santé (LNS), Dudelange, Luxembourg
| | - Matthieu Egloff
- Department of Genetics, Necker-Enfants malades, AP-HP, Institut Imagine, Paris, France
| | - Emilie Landais
- Department of Genetics, Reims University Hospital, Reims, France
| | | | | | | | - Charles Coutton
- Service de Génétique et Procréation, Hôpital Couple-Enfant, CHU Grenoble Alpes, Université Grenoble-Alpes, La Tronche, France.,ACLF (Association des Cytogénéticiens de Langue Française, French Society of Cytogenetics) Member, Grenoble cedex, France
| | - Véronique Satre
- Service de Génétique et Procréation, Hôpital Couple-Enfant, CHU Grenoble Alpes, Université Grenoble-Alpes, La Tronche, France
| | - Françoise Devillard
- Service de Génétique et Procréation, Hôpital Couple-Enfant, CHU Grenoble Alpes, Université Grenoble-Alpes, La Tronche, France
| | - Klaus Dieterich
- Service de Génétique et Procréation, Hôpital Couple-Enfant, CHU Grenoble Alpes, Université Grenoble-Alpes, La Tronche, France
| | - Gaëlle Vieville
- Service de Génétique et Procréation, Hôpital Couple-Enfant, CHU Grenoble Alpes, Université Grenoble-Alpes, La Tronche, France
| | - Paul Kuentz
- Génétique Biologique, PCBio, Besançon University Hospital, Besançon, France
| | - Cédric le Caignec
- ACLF (Association des Cytogénéticiens de Langue Française, French Society of Cytogenetics) Member, Grenoble cedex, France.,Department of Genetics, Nantes University Hospital, Nantes, France
| | - Claire Beneteau
- Department of Genetics, Nantes University Hospital, Nantes, France
| | - Bertrand Isidor
- Department of Genetics, Nantes University Hospital, Nantes, France
| | - Mathilde Nizon
- Department of Genetics, Nantes University Hospital, Nantes, France
| | - Patrick Callier
- ACLF (Association des Cytogénéticiens de Langue Française, French Society of Cytogenetics) Member, Grenoble cedex, France.,Department of Genetics, Dijon University Hospital, Dijon, France
| | - Valentine Marquet
- ACLF (Association des Cytogénéticiens de Langue Française, French Society of Cytogenetics) Member, Grenoble cedex, France.,Department of Genetics, Limoges University Hospital, Limoges, France
| | - Eric Bieth
- Department of Genetics, Toulouse University Hospital, Toulouse, France
| | - Jonathan Lévy
- Department of Genetics, Robert-Debré University Hospital, Paris, France
| | - Anne-Claude Tabet
- Department of Genetics, Robert-Debré University Hospital, Paris, France
| | - Stanislas Lyonnet
- Department of Genetics, Necker-Enfants malades, AP-HP, Institut Imagine, Paris, France.,INSERM U-1163, Université de Paris, Paris, France
| | - Geneviève Baujat
- Department of Genetics, Necker-Enfants malades, AP-HP, Institut Imagine, Paris, France
| | - Marlène Rio
- Department of Genetics, Necker-Enfants malades, AP-HP, Institut Imagine, Paris, France
| | - François Cartault
- Department of Genetics, La Réunion University Hospital, Saint Denis, France
| | | | | | | | - Clémence Jacquin
- Department of Genetics, Reims University Hospital, Reims, France
| | | | - Chloé Angélini
- CHU Bordeaux, Service de Génétique Médicale, Bordeaux, France
| | | | | | - Martine Doco-Fenzy
- Department of Genetics, Reims University Hospital, Reims, France.,ACLF (Association des Cytogénéticiens de Langue Française, French Society of Cytogenetics) Member, Grenoble cedex, France.,EA3801, SFR CAPSANTE, Reims, France
| | - Céline Poirsier
- Department of Genetics, Reims University Hospital, Reims, France
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Tenorio J, Nevado J, González-Meneses A, Arias P, Dapía I, Venegas-Vega CA, Calvente M, Hernández A, Landera L, Ramos S, Cigudosa JC, Pérez-Jurado LA, Lapunzina P. Further definition of the proximal 19p13.3 microdeletion/microduplication syndrome and implication of PIAS4 as the major contributor. Clin Genet 2020; 97:467-476. [PMID: 31972898 DOI: 10.1111/cge.13689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/24/2019] [Accepted: 11/01/2019] [Indexed: 12/15/2022]
Abstract
The proximal 19p13.3 microdeletion/microduplication (prox19p13.3del/dup) syndrome is a recently described disorder with common clinical features including developmental delay, intellectual disability, speech delay, facial dysmorphic features with ear defects, anomalies of the hands and feet, umbilical hernia and hypotonia. While deletions are associated with macrocephaly, patients with duplications have microcephaly. The smallest region of overlap in multiple patients (113.5 kb) included three genes and one pseudogene, with a suggested major role of PIAS4 in determination of the phenotype and head size in these patients. Here, we refine the prox19p13.3del/dup with four additional patients: two with microdeletions, one with microduplication and one family with single-nucleotide nonsense variant in PIAS4. The patient with the PIAS4 loss of function variant displayed a phenotype quite similar to deletion patients -including the macrocephaly and many other core features of the syndrome. Patient's SNV was inherited from her mother who is similarly affected. Thus, our data indicate that PIAS4 is a major contributor to the proximal 19p13.3del/dup syndrome phenotype. In summary, we report the first patient with a pathogenic variant in PIAS4- and three additional rearrangements at the proximal 19p13.3 locus. These observations add further evidence about the molecular basis of this microdeletion/microduplication syndrome.
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Affiliation(s)
- Jair Tenorio
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario LaPaz-UAM, Paseo de La Castellana, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Callede Melchor Fernández Almagro, Madrid, Spain.,ERN-ITHACA, ITHACA European Reference Network
| | - Julián Nevado
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario LaPaz-UAM, Paseo de La Castellana, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Callede Melchor Fernández Almagro, Madrid, Spain.,ERN-ITHACA, ITHACA European Reference Network
| | - Antonio González-Meneses
- Dysmorphology and Metabolism unit, Hospital Universitario Virgen del Rocío, Av. Manuel Siurot, Sevilla, Spain
| | - Pedro Arias
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario LaPaz-UAM, Paseo de La Castellana, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Callede Melchor Fernández Almagro, Madrid, Spain
| | - Irene Dapía
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario LaPaz-UAM, Paseo de La Castellana, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Callede Melchor Fernández Almagro, Madrid, Spain
| | - Carlos A Venegas-Vega
- Unidadde Genética, Hospital General de México, México City, Mexico, Facultad deMedicina, Universidad Nacional Autónoma de México, México City, Mexico
| | - María Calvente
- NIMGENETICS, c/ Faraday, 7 Parque Científico de Madrid, Madrid, Spain
| | - Alicia Hernández
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario LaPaz-UAM, Paseo de La Castellana, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Callede Melchor Fernández Almagro, Madrid, Spain
| | - Leandro Landera
- Congenital Malformations Laboratory, Federal University of Rio de Janeiro, Avenida Carlos Chagas Filho, Rio deJaneiro, Brazil
| | - Sergio Ramos
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario LaPaz-UAM, Paseo de La Castellana, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Callede Melchor Fernández Almagro, Madrid, Spain
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- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario LaPaz-UAM, Paseo de La Castellana, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Callede Melchor Fernández Almagro, Madrid, Spain
| | | | - Luis A Pérez-Jurado
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Callede Melchor Fernández Almagro, Madrid, Spain.,Genetics Unit, Universitat Pompeu Fabra, and IMIM-Hospital del Mar, Barcelona, Spain.,Women's and Children's Hospital, South Australian Health and Medical Research Institute (SAHMRI), The University of Adelaide, Adelaide, Australia
| | - Pablo Lapunzina
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario LaPaz-UAM, Paseo de La Castellana, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Callede Melchor Fernández Almagro, Madrid, Spain.,ERN-ITHACA, ITHACA European Reference Network
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