The hereditary spastic paraplegias (HSPs), a group of neurodegenerative movement disorders, are amongst the genetically most heterogeneous clinical conditions. Still, the >50 forms known so far apparently explain <80% of cases. The present study identified two large HSP families which seemed to show an autosomal recessive and an X-linked inheritance pattern, respectively. A set of genetic analyses including exome sequencing revealed plausible mutations only when assuming incomplete/sex-dependent penetrance of adjacent alterations in the autosomal dominant HSP gene ATL1 (c.1243C>T and c.1244G>A, respectively). By screening of additional HSP patients for the presence of these alterations we identified three more cases and obtained additional evidence for reduced penetrance. Bisulphate sequencing and haplotype analysis indicated that c.1243C and c.1244G constitute a mutational hotspot. Our findings suggest that mis-interpretation of inheritance patterns and, consequently, mis-selection of candidate genes to be screened in gene-focused approaches contribute to the apparently missing heritability in HSP and, potentially, in other genetically heterogeneous disorders.