Animals with mutations in COL4a4 present with autosomal recessive Alport Syndrome (ARAS). Through sequencing of COL4a4, the mutation causative for ARAS in the English Cocker Spaniel (ECS) has been identified. The resulting protein is severely truncated due to a premature stop codon in exon 3. This nonsense mutation occurs in the 7S domain and also causes the loss of the entire collagenous and NC1 domains of the protein. Methods for the identification of animals that harbor a mutation in the COL4a4 gene are described. Mutations in the COL4a4 gene can be identified from any biological sample such as a cell or tissue that contains genomic DNA. Methods for identifying single nucleotide polymorphisms (SNPs) that are inherited with the disease are also described. A microsatellite marker that segregates with ARAS is also described that was identified using linkage disequilibrium mapping.