NR2F1 database: 112 variants and 84 patients support refining the clinical synopsis of Bosch-Boonstra-Schaaf optic atrophy syndrome.
BBSOAS
Bosch-Boonstra-Schaaf optic atrophy syndrome
COUP transcription factor 1 protein
COUP-TF1
NR2F1
database
neurodegenerative disorders
nuclear receptor subfamily 2 group F member 1
ontology
optic atrophy
Journal
Human mutation
ISSN: 1098-1004
Titre abrégé: Hum Mutat
Pays: United States
ID NLM: 9215429
Informations de publication
Date de publication:
02 2022
02 2022
Historique:
revised:
12
10
2021
received:
21
06
2021
accepted:
16
11
2021
pubmed:
28
11
2021
medline:
30
4
2022
entrez:
27
11
2021
Statut:
ppublish
Résumé
Pathogenic variants of the nuclear receptor subfamily 2 group F member 1 gene (NR2F1) are responsible for Bosch-Boonstra-Schaaf optic atrophy syndrome (BBSOAS), an autosomal dominant disorder characterized by optic atrophy associated with developmental delay and intellectual disability, but with a clinical presentation which appears to be multifaceted. We created the first public locus-specific database dedicated to NR2F1. All variants and clinical cases reported in the literature, as well as new unpublished cases, were integrated into the database using standard nomenclature to describe both molecular and phenotypic anomalies. We subsequently pursued a comprehensive approach based on computed representation and analysis suggesting a refinement of the BBSOAS clinical description with respect to neurological features and the inclusion of additional signs of hypotonia and feeding difficulties. This database is fully accessible for both clinician and molecular biologists and should prove useful in further refining the clinical synopsis of NR2F1 as new data is recorded.
Substances chimiques
COUP Transcription Factor I
0
NR2F1 protein, human
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
128-142Informations de copyright
© 2021 Wiley Periodicals LLC.
Références
Alfano, C., Viola, L., Heng, J. I., Pirozzi, M., Clarkson, M., Flore, G., de Maio, A., Schedl, A., Guillemot, F., & Studer, M. (2011). COUP-TFI promotes radial migration and proper morphology of callosal projection neurons by repressing Rnd2 expression. Development, 138(21), 4685-4697. https://doi.org/10.1242/dev.068031
Al-Kateb, H., Shimony, J. S., Vineyard, M., Manwaring, L., Kulkarni, S., & Shinawi, M. (2013). NR2F1 haploinsufficiency is associated with optic atrophy, dysmorphism and global developmental delay. American Journal of Medical Genetics. Part A, 161A(2), 377-381. https://doi.org/10.1002/ajmg.a.35650
Armentano, M., Filosa, A., Andolfi, G., & Studer, M. (2006). COUP-TFI is required for the formation of commissural projections in the forebrain by regulating axonal growth. Development, 133(21), 4151-4162. https://doi.org/10.1242/dev.02600
Balciuniene, J., DeChene, E. T., Akgumus, G., Romasko, E. J., Cao, K., Dubbs, H. A., Mulchandani, S., Spinner, N. B., Conlin, L. K., Marsh, E. D., Goldberg, E., Helbig, I., Sarmady, M., & Abou Tayoun, A. (2019). Use of a dynamic genetic testing approach for childhood-onset epilepsy. JAMA Network Open, 2(4), e192129. https://doi.org/10.1001/jamanetworkopen.2019.2129
Bertacchi, M., Parisot, J., & Studer, M. (2019). The pleiotropic transcriptional regulator COUP-TFI plays multiple roles in neural development and disease. Brain Research, 1705, 75-94. https://doi.org/10.1016/j.brainres.2018.04.024
Bertacchi, M., Romano, A. L., Loubat, A., Tran Mau-Them, F., Willems, M., Faivre, L., Khau van Kien, P., Perrin, L., Devillard, F., Sorlin, A., Kuentz, P., Philippe, C., Garde, A., Neri, F., Di Giaimo, R., Oliviero, S., Cappello, S., D'Incerti, L., Frassoni, C., & Studer, M. (2020). NR2F1 regulates regional progenitor dynamics in the mouse neocortex and cortical gyrification in BBSOAS patients. EMBO Journal, 39(13), e104163. https://doi.org/10.15252/embj.2019104163
Biesecker, L. G. (2004). Phenotype matters. Nature Genetics, 36(4), 323-324. https://doi.org/10.1038/ng0404-323
Blum, M., Chang, H. Y., Chuguransky, S., Grego, T., Kandasaamy, S., Mitchell, A., Nuka, G., Paysan-Lafosse, T., Qureshi, M., Raj, S., Richardson, L., Salazar, G. A., Williams, L., Bork, P., Bridge, A., Gough, J., Haft, D. H., Letunic, I., Marchler-Bauer, A., … Finn, R. D. (2021). The InterPro protein families and domains database: 20 years on. Nucleic Acids Research, 49(D1), D344-D354. https://doi.org/10.1093/nar/gkaa977
Bojanek, E. K., Mosconi, M. W., Guter, S., Betancur, C., Macmillan, C., & Cook, E. H. (2020). Clinical and neurocognitive issues associated with Bosch-Boonstra-Schaaf optic atrophy syndrome: A case study. American Journal of Medical Genetics. Part A, 182(1), 213-218. https://doi.org/10.1002/ajmg.a.61409
Bosch, D. G., Boonstra, F. N., Gonzaga-Jauregui, C., Xu, M., de Ligt, J., Jhangiani, S., Wiszniewski, W., Muzny, D. M., Yntema, H. G., Pfundt, R., Vissers, L. E., Spruijt, L., Blokland, E. A., Chen, C. A., Baylor-Hopkins Center for Mendelian, G., Lewis, R. A., Tsai, S. Y., Gibbs, R. A., Tsai, M. J., … Schaaf, C. P. (2014). NR2F1 mutations cause optic atrophy with intellectual disability. American Journal of Human Genetics, 94(2), 303-309. https://doi.org/10.1016/j.ajhg.2014.01.002
Bosch, D. G., Boonstra, F. N., de Leeuw, N., Pfundt, R., Nillesen, W. M., de Ligt, J., Gilissen, C., Jhangiani, S., Lupski, J. R., Cremers, F. P., & de Vries, B. B. (2016). Novel genetic causes for cerebral visual impairment. European Journal of Human Genetics, 24(5), 660-665. https://doi.org/10.1038/ejhg.2015.186
Brookes, A. J., & Robinson, P. N. (2015). Human genotype-phenotype databases: aims, challenges and opportunities. Nature Reviews Genetics, 16(12), 702-715. https://doi.org/10.1038/nrg3932
Brown, K. K., Alkuraya, F. S., Matos, M., Robertson, R. L., Kimonis, V. E., & Morton, C. C. (2009). NR2F1 deletion in a patient with a de novo paracentric inversion, inv(5)(q15q33.2), and syndromic deafness. American Journal of Medical Genetics. Part A, 149A(5), 931-938. https://doi.org/10.1002/ajmg.a.32764
Chen, C. A., Bosch, D. G., Cho, M. T., Rosenfeld, J. A., Shinawi, M., Lewis, R. A., Mann, J., Jayakar, P., Payne, K., Walsh, L., Moss, T., Schreiber, A., Schoonveld, C., Monaghan, K. G., Elmslie, F., Douglas, G., Boonstra, F. N., Millan, F., Cremers, F. P., … Schaaf, C. (2016). The expanding clinical phenotype of Bosch-Boonstra-Schaaf optic atrophy syndrome: 20 new cases and possible genotype-phenotype correlations. Genetics in Medicine, 18(11), 1143-1150. https://doi.org/10.1038/gim.2016.18
Cotton, R. G., Auerbach, A. D., Axton, M., Barash, C. I., Berkovic, S. F., Brookes, A. J., Burn, J., Cutting, G., den Dunnen, J. T., Flicek, P., Freimer, N., Greenblatt, M. S., Howard, H. J., Katz, M., Macrae, F. A., Maglott, D., Möslein, G., Povey, S., Ramesar, R. S., … Watson, M. (2008). Genetics. The Human Variome Project. Science, 322(5903), 861-862. https://doi.org/10.1126/science.1167363
Deans, A. R., Lewis, S. E., Huala, E., Anzaldo, S. S., Ashburner, M., Balhoff, J. P., Blackburn, D. C., Blake, J. A., Burleigh, J. G., Chanet, B., Cooper, L. D., Courtot, M., Csösz, S., Cui, H., Dahdul, W., Das, S., Dececchi, T. A., Dettai, A., Diogo, R., … Mabee, P. (2015). Finding our way through phenotypes. PLOS Biology, 13(1), e1002033. https://doi.org/10.1371/journal.pbio.1002033
Dimassi, S., Labalme, A., Ville, D., Calender, A., Mignot, C., Boutry-Kryza, N., de Bellescize, J., Rivier-Ringenbach, C., Bourel-Ponchel, E., Cheillan, D., Simonet, T., Maincent, K., Rossi, M., Till, M., Mougou-Zerelli, S., Edery, P., Saad, A., Heron, D., des Portes, V., … Lesca, G. (2016). Whole-exome sequencing improves the diagnosis yield in sporadic infantile spasm syndrome. Clinical Genetics, 89(2), 198-204. https://doi.org/10.1111/cge.12636
den Dunnen, J. T., Dalgleish, R., Maglott, D. R., Hart, R. K., Greenblatt, M. S., McGowan-Jordan, J., Roux, A. F., Smith, T., Antonarakis, S. E., & Taschner, P. E. (2016). HGVS recommendations for the description of sequence variants: 2016 Update. Human Mutation, 37(6), 564-569. https://doi.org/10.1002/humu.22981
Eldomery, M. K., Coban-Akdemir, Z., Harel, T., Rosenfeld, J. A., Gambin, T., Stray-Pedersen, A., Küry, S., Mercier, S., Lessel, D., Denecke, J., Wiszniewski, W., Penney, S., Liu, P., Bi, W., Lalani, S. R., Schaaf, C. P., Wangler, M. F., Bacino, C. A., Lewis, R. A., … Lupski, J. R. (2017). Lessons learned from additional research analyses of unsolved clinical exome cases. Genome Medicine, 9(1), 26. https://doi.org/10.1186/s13073-017-0412-6
Fokkema, I., van der Velde, K. J., Slofstra, M. K., Ruivenkamp, C., Vogel, M. J., Pfundt, R., Blok, M. J., Lekanne Deprez, R. H., Waisfisz, Q., Abbott, K. M., Sinke, R. J., Rahman, R., Nijman, I. J., de Koning, B., Thijs, G., Wieskamp, N., Moritz, R., Charbon, B., Saris, J. J., … van Gijn, M. E. (2019). Dutch genome diagnostic laboratories accelerated and improved variant interpretation and increased accuracy by sharing data. Human Mutation, 40, 2230-2238. https://doi.org/10.1002/humu.23896
Fokkema, I. F., Taschner, P. E., Schaafsma, G. C., Celli, J., Laros, J. F., & den Dunnen, J. T. (2011). LOVD v.2.0: the next generation in gene variant databases. Human Mutation, 32(5), 557-563. https://doi.org/10.1002/humu.21438
Global Alliance for Genomics and Health. (2016). Genomics. A federated ecosystem for sharing genomic, clinical data. Science, 352(6291), 1278-1280. https://doi.org/10.1126/science.aaf6162
Gray, K. A., Daugherty, L. C., Gordon, S. M., Seal, R. L., Wright, M. W., & Bruford, E. A. (2013). Genenames.org: The HGNC resources in 2013. Nucleic Acids Research, 41(Database issue), D545-D552. https://doi.org/10.1093/nar/gks1066
Greene, D., Richardson, S., & Turro, E. (2017). ontologyX: A suite of R packages for working with ontological data. Bioinformatics, 33(7), 1104-1106. https://doi.org/10.1093/bioinformatics/btw763
Hamosh, A., Scott, A. F., Amberger, J., Valle, D., & McKusick, V. A. (2000). Online Mendelian Inheritance in Man (OMIM). Human Mutation, 15(1), 57-61. https://doi.org/10.1002/(SICI)1098-1004(200001)15:1%3C57::AID-HUMU12%3E3.0.CO;2-G
Hino-Fukuyo, N., Kikuchi, A., Yokoyama, H., Iinuma, K., Hirose, M., Haginoya, K., Niihori, T., Nakayama, K., Aoki, Y., & Kure, S. (2017). Long-term outcome of a 26-year-old woman with West syndrome and an nuclear receptor subfamily 2 group F member 1 gene (NR2F1) mutation. Seizure, 50, 144-146. https://doi.org/10.1016/j.seizure.2017.06.018
Hobbs, M. M., Wolters, W. C., & Rayapati, A. O. (2020). Bosch-Boonstra-Schaaf optic atrophy syndrome presenting as new-onset psychosis in a 32-year-old man: A case report and literature review. Journal of Psychiatric Practice, 26(1), 58-62. https://doi.org/10.1097/PRA.0000000000000440
INSERM. (1997). Orphanet: an online database of rare diseases and orphan drugs. Retrieved May 21, 2021, from http://www.orpha.net
Jezela-Stanek, A., Ciara, E., Jurkiewicz, D., Kucharczyk, M., Jędrzejowska, M., Chrzanowska, K. H., Krajewska-Walasek, M., & Żemojtel, T. (2020). The phenotype-driven computational analysis yields clinical diagnosis for patients with atypical manifestations of known intellectual disability syndromes. Molecular Genetics & Genomic Medicine, 8(9), e1263. https://doi.org/10.1002/mgg3.1263
Kaiwar, C., Zimmermann, M. T., Ferber, M. J., Niu, Z., Urrutia, R. A., Klee, E. W., & Babovic-Vuksanovic, D. (2017). Novel NR2F1 variants likely disrupt DNA binding: molecular modeling in two cases, review of published cases, genotype-phenotype correlation, and phenotypic expansion of the Bosch-Boonstra-Schaaf optic atrophy syndrome. Cold Spring Harbor Molecular Case Studies, 3(6), https://doi.org/10.1101/mcs.a002162
Karczewski, K. J., Francioli, L. C., Tiao, G., Cummings, B. B., Alföldi, J., Wang, Q., Collins, R. L., Laricchia, K. M., Ganna, A., Birnbaum, D. P., Gauthier, L. D., Brand, H., Solomonson, M., Watts, N. A., Rhodes, D., Singer-Berk, M., England, E. M., Seaby, E. G., Kosmicki, J. A., … MacArthur, D. G. (2020). The mutational constraint spectrum quantified from variation in 141,456 humans. Nature, 581(7809), 434-443. https://doi.org/10.1038/s41586-020-2308-7
Köhler, S., Carmody, L., Vasilevsky, N., Jacobsen, J., Danis, D., Gourdine, J. P., Gargano, M., Harris, N. L., Matentzoglu, N., McMurry, J. A., Osumi-Sutherland, D., Cipriani, V., Balhoff, J. P., Conlin, T., Blau, H., Baynam, G., Palmer, R., Gratian, D., Dawkins, H., … Robinson, P. N. (2019). Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic Acids Research, 47(D1), D1018-D1027. https://doi.org/10.1093/nar/gky1105
Martín-Hernández, E., Rodríguez-García, M. E., Chen, C. A., Cotrina-Vinagre, F. J., Carnicero-Rodríguez, P., Bellusci, M., Schaaf, C. P., & Martínez-Azorín, F. (2018). Mitochondrial involvement in a Bosch-Boonstra-Schaaf optic atrophy syndrome patient with a novel de novo NR2F1 gene mutation. Journal of Human Genetics, 63(4), 525-528. https://doi.org/10.1038/s10038-017-0398-3
Mio, C., Fogolari, F., Pezzoli, L., D'Elia, A. V., Iascone, M., & Damante, G. (2020). Missense NR2F1 variant in monozygotic twins affected with the Bosch-Boonstra-Schaaf optic atrophy syndrome. Molecular Genetics & Genomic Medicine, 8(7), e1278. https://doi.org/10.1002/mgg3.1278
O'Leary, N. A., Wright, M. W., Brister, J. R., Ciufo, S., Haddad, D., McVeigh, R., Rajput, B., Robbertse, B., Smith-White, B., Ako-Adjei, D., Astashyn, A., Badretdin, A., Bao, Y., Blinkova, O., Brover, V., Chetvernin, V., Choi, J., Cox, E., Ermolaeva, O., … Pruitt, K. D. (2016). Reference sequence (RefSeq) database at NCBI: Current status, taxonomic expansion, and functional annotation. Nucleic Acids Research, 44(D1), D733-D745. https://doi.org/10.1093/nar/gkv1189
Park, S. E., Lee, J. S., Lee, S. T., Kim, H. Y., Han, S. H., & Han, J. (2019). Targeted panel sequencing identifies a novel NR2F1 mutations in a patient with Bosch-Boonstra-Schaaf optic atrophy syndrome. Ophthalmic Genetics, 40(4), 359-361. https://doi.org/10.1080/13816810.2019.1650074
R Core Team. (2020). R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. https://www.R-project.org/
Rech, M. E., McCarthy, J. M., Chen, C. A., Edmond, J. C., Shah, V. S., Bosch, D., Berry, G. T., Williams, L., Madan-Khetarpal, S., Niyazov, D., Shaw-Smith, C., Kovar, E. M., Lupo, P. J., & Schaaf, C. P. (2020). Phenotypic expansion of Bosch-Boonstra-Schaaf optic atrophy syndrome and further evidence for genotype-phenotype correlations. American Journal of Medical Genetics. Part A, 182(6), 1426-1437. https://doi.org/10.1002/ajmg.a.61580
Richards, S., Aziz, N., Bale, S., Bick, D., Das, S., Gastier-Foster, J., Grody, W. W., Hegde, M., Lyon, E., Spector, E., Voelkerding, K., Rehm, H. L., & ACMG Laboratory Quality Assurance, C. (2015). 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. Genetics in Medicine, 17(5), 405-424. https://doi.org/10.1038/gim.2015.30
Robinson, P. N. (2012). Deep phenotyping for precision medicine. Human Mutation, 33(5), 777-780. https://doi.org/10.1002/humu.22080
Sayers, E. W., Barrett, T., Benson, D. A., Bolton, E., Bryant, S. H., Canese, K., Chetvernin, V., Church, D. M., Dicuccio, M., Federhen, S., Feolo, M., Geer, L. Y., Helmberg, W., Kapustin, Y., Landsman, D., Lipman, D. J., Lu, Z., Madden, T. L., Madej, T., … Ye, J. (2010). Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, 38(Database issue), D5-D16. https://doi.org/10.1093/nar/gkp967
Starosta, R. T., Tarnowski, J., Vairo, F. P. E., Raymond, K., Preston, G., & Morava, E. (2020). Bosch-Boonstra-Schaaf optic atrophy syndrome (BBSOAS) initially diagnosed as ALG6-CDG: Functional evidence for benignity of the ALG6 c.391T>C (p.Tyr131His) variant and further expanding the BBSOAS phenotype. European Journal of Medical Genetics, 63(7), 103941. https://doi.org/10.1016/j.ejmg.2020.103941
Vihinen, M., den Dunnen, J. T., Dalgleish, R., & Cotton, R. G. (2012). Guidelines for establishing locus-specific databases. Human Mutation, 33(2), 298-305. https://doi.org/10.1002/humu.21646
Vissers, L., van Nimwegen, K., Schieving, J. H., Kamsteeg, E. J., Kleefstra, T., Yntema, H. G., Pfundt, R., van der Wilt, G. J., Krabbenborg, L., Brunner, H. G., van der Burg, S., Grutters, J., Veltman, J. A., & Willemsen, M. (2017). A clinical utility study of exome sequencing versus conventional genetic testing in pediatric neurology. Genetics in Medicine, 19(9), 1055-1063. https://doi.org/10.1038/gim.2017.1
Walsh, S., Gösswein, S. S., Rump, A., von der Hagen, M., Hackmann, K., Schröck, E., Di Donato, N., & Kahlert, A. K. (2020). Novel dominant-negative NR2F1 frameshift mutation and a phenotypic expansion of the Bosch-Boonstra-Schaaf optic atrophy syndrome. European Journal of Medical Genetics, 63(10), 104019. https://doi.org/10.1016/j.ejmg.2020.104019
Wildeman, M., van Ophuizen, E., den Dunnen, J. T., & Taschner, P. E. (2008). Improving sequence variant descriptions in mutation databases and literature using the Mutalyzer sequence variation nomenclature checker. Human Mutation, 29(1), 6-13. https://doi.org/10.1002/humu.20654
Zou, W., Cheng, L., Lu, S., & Wu, Z. (2020). A de novo nonsense mutation in the N-terminal of ligand-binding domain of NR2F1 gene provoked a milder phenotype of BBSOAS. Ophthalmic Genetics, 41(1), 88-89. https://doi.org/10.1080/13816810.2020.1719520