Fukuyama type congenital muscular dystrophy (FCMD), the second most common form of childhood muscular dystrophy in Japan, is an autosomal recessive severe muscular dystrophy, associated with brain anomalies due to neuronal overmigration. By taking advantages of the presence of a consanguineous patient with both FCMD and xeroderma pigmentosum group A, we performed homozygosity mapping using consanguineous FCMD families mainly, and localized the FCMD locus to chromosome 9q31-33. Subsequently, we have identified the gene responsible for FCMD on 9q31, which encodes a novel 461-amino-acid protein termed fukutin. Most FCMD-bearing chromosomes are derived from a single ancestral founder (87%), and a 3kb-retrotransposal insertion was found to be a founder mutation. Two independent point mutations in this gene have also been detected on chromosomes carrying the non-founder haplotype. FCMD is the first human disease to be caused by an ancient retrotransposal integration. We further identified the gene for muscle-eye-brain (MEB) disease, which encodes POMGnT1. Recent studies have revealed that posttranslational modification of alpha-dystroglycan is associated with congenital muscular dystrophy with brain malformations. Since hypoglycosylation of alpha-dystroglycan is common amongst several other disorders, a new clinical entity called alpha-dystroglycanopathy is proposed. However, only POMGnT1 (MEB) and POMT1 (WWS) are shown to have a definite enzymatic activity, and no enzymatic activity has been detected in fukutin. We show positive interactions between fukutin and POMGnT1. Fukutin may form a protein complex with POMGnT1 and modulate POMGnT1's enzymatic activity. Through cDNA microarray, we also show aberrant neuromuscular junction formation and delayed muscle fiber maturation in alpha-dystroglycanopathies, suggesting a new pathomechanism.