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In this study, we aimed to uncover the genetic basis of severe CMD in Egypt and to determine the efficacy of whole exome sequencing (WES)-based genetic diagnosis in this population. We recruited twelve individuals from eleven families with a clinical diagnosis of CMD with brain malformations that fell into two groups: seven patients with suspected dystroglycanopathy and five patients with suspected merosin-deficient CMD. WES was analyzed by variant filtering using multiple approaches including splicing and copy number variant (CNV) analysis. We identified likely pathogenic variants in <jats:italic>FKRP<\/jats:italic> in two cases and variants in <jats:italic>POMT1<\/jats:italic>, <jats:italic>POMK<\/jats:italic>, and <jats:italic>B3GALNT2<\/jats:italic> in three individuals. All individuals with merosin-deficient CMD had truncating variants in <jats:italic>LAMA2<\/jats:italic>. Further analysis in one of the two unsolved cases showed a homozygous protein-truncating variant in <jats:italic>Feline Leukemia Virus subgroup C Receptor 1<\/jats:italic> (<jats:italic>FLVCR1<\/jats:italic>). <jats:italic>FLVCR1<\/jats:italic> loss of function has never been previously reported. Yet, loss of function of its paralog, <jats:italic>FLVCR2<\/jats:italic>, causes lethal hydranencephaly-hydrocephaly syndrome (Fowler Syndrome) which should be considered in the differential diagnosis for dystroglycanopathy. Overall, we reached a diagnostic rate of 86% (6\/7) for dystroglycanopathies and 100% (5\/5) for merosinopathy. In conclusion, our results provide further evidence that WES is an important diagnostic method in CMD in developing countries to improve the diagnostic rate, management plan, and genetic counseling for these disorders.<\/jats:p>","DOI":"10.1007\/s10048-024-00745-z","type":"journal-article","created":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T02:22:10Z","timestamp":1706754130000},"page":"93-102","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Genetic blueprint of congenital muscular dystrophies with brain malformations in Egypt: A report of 11 families"],"prefix":"10.1007","volume":"25","author":[{"given":"Sylvia","family":"Safwat","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kyle P.","family":"Flannery","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ahmed A.","family":"El Beheiry","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohamed M.","family":"Mokhtar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ebtesam","family":"Abdalla","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7175-1096","authenticated-orcid":false,"given":"M. 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