Pseudogene Variants May Interfere with the Genetic Testing of CAH-X.

CAH-X is a hypermobility-type Ehlers-Danlos syndrome connective tissue dysplasia affecting approximately 15% of patients with 21-hydroxylase deficiency (21-OHD) congenital adrenal hyperplasia (CAH) due to contiguous deletion of and genes. The two most common genetic causes of CAH-X are chimeras with pseudogene substitution for exons 35-44 (CAH-X CH-1) and exons 40-44 (CAH-X CH-2). A total of 45 subjects (40 families) from a cohort of 278 subjects (135 families of 21-OHD and 11 families of other conditions) were found to have excessive exon 40 copy number as measured by digital PCR. Here, we report that 42 subjects (37 families) had at least one copy of a variant allele carrying a exon 40 sequence, whose overall allele frequency was 10.3% (48/467). Most of the variant alleles were in with either a normal (22/48) or an In2G (12/48) allele. There is potential interference with CAH-X molecular genetic testing based on copy number assessment, such as with digital PCR and multiplex ligation-dependent probe amplification, since this variant allele might mask a real copy number loss in exon 40. This interference most likely happens amongst genotypes of CAH-X CH-2 with an in normal or In2G allele.