Classifying DDC Variants Will Help Interpret Genetic Test Results
Researchers identified 422 variants and mapped them to their location in the gene
Researchers classified variants of the DDC gene that causes AADC deficiency according to their disease-causing potential, a study reported, the first study to identify and characterize previously unknown DDC variants.
“Given that genetic testing is a core diagnostic test for AADC deficiency, a comprehensive catalogue of the genetic variants associated with the disorder is critical for interpreting genetic testing results,” researchers wrote.
The variant study, “Spectrum of DDC variants causing aromatic l-amino acid decarboxylase (AADC) deficiency and pathogenicity interpretation using ACMG-AMP/ACGS recommendations,” was published in the journal Molecular Genetics and Metabolism.
AADC deficiency is caused by variants of the DDC gene that result in reduced activity of the AADC enzyme, which is vital for producing several neurotransmitters, molecules that nerve cells use to communicate.
DDC variants can give rise to an inactive AADC enzyme, or too little enzyme, ultimately lowering the production of neurotransmitters. Because different variants lead to enzymes with different activities, and in turn, a range of neurotransmitter levels, symptoms, and their severity, vary substantially from person to person.
Therefore, understanding the molecular characteristics associated with different DDC variants will help support an accurate AADC deficiency diagnosis.
“The ability to accurately diagnose aromatic l-amino acid decarboxylase (AADC) deficiency depends on a more complete understanding of DDC gene variants, their molecular effects, and their link to AADC deficiency [characteristics],” wrote a research team in Europe and the U.S.
422 variants identified and located
Researchers first identified 422 variants from three databases and mapped them to their location in the human DDC gene. Variants were found across the whole gene, including in segments containing instructions for proteins, called exons, and introns, segments removed before protein production. Variants also occurred immediately adjacent to the gene’s start and end.
All variants were then classified based on their disease-causing potential, or pathogenicity, according to the modified American College of Medical Genetics and Genomics/Association for Molecular Pathology/Association for Clinical Genomic Science (ACMG-AMP/ACGS) criteria.
The largest number of variants, totaling 348, were classified as having moderate pathogenicity by ACMG and not found in a healthy population. This was followed by 176 variants deemed supporting pathogenicity by computer analysis.
Based on published reports, 108 unique DDC variants cause confirmed AADC deficiency. At least one allele was classified in this study as pathogenic or likely pathogens in 101 of the 108 different gene types (genotypes). An allele is a variation of the same gene present at the same part of the DNA. People inherit one allele from each parent.
At the same time, the remaining were a combination of two so-called variants of uncertain significance. No variants were found to be benign or likely benign.
Among the 422 variants, 204 (48%) were missense variants, whereby a single change within the DDC gene leads to an AADC enzyme marked by a single change in an amino acid, a protein building block. Sixty-two variants (15%) were synonymous, meaning they do not change amino acids but still may affect protein function, and 53 (13%) were considered intronic splice site variants. These changes occur at the boundary of an exon and an intron.
The impact of 68 variants (16%) on AADC enzyme production was unknown, and among these, 47 (69%) were deep intronic variants that occur far from the exon-intron boundary.
Frameshift, extension, nonsense, and inframe variants
The remaining variants in this group were classified as frameshift variants due to DNA insertion or deletions, and extension variants, which extend the protein size. These were also a few nonsense variants, leading to a shortened enzyme, and inframe variants, resulting in an enzyme with missing or changed sections.
Computer algorithms (CADD, PolyPhen2, and SIFT) were used to predict the impact of the identified DDC missense variants, that change single amino acids, on AADC enzyme function. This included an analysis of the three-dimensional (3D) structure of pig kidney AADC enzyme to map these amino acid changes.
Among the 204 missense variants, 14 (7%) were classified as pathogenic and 66 (32%) as likely pathogenic.
Uncharacterized variants deemed as “hot” variants of uncertain significance (VUS), which were predicted to be more pathogenic, occurred in 11 variants (5%), with 32 (16%) as warm VUSs, and 36 (18%) as tepid VUSs. Also classified were cool VUSs in 25 (12%), 10 (5%) as cold VUSs, five (2%) as ice cold VUSs, and two each (1%) as likely benign and benign.
Statistical analysis found ACMG classification was highly associated with the severity of the VUS. Computer tools, including CADD plus the three-dimensional AADC enzyme structure, correlated more with likely benign or likely pathogenic classifications. Last, the algorithms PolyPhen2 and SIFT were mainly associated with benign or pathogenic classifications.
“The use of [computer] variant interpretation tools, combined with structural 3D modeling of variant proteins and applied comparative analysis, improved the current DDC variant interpretation recommendations, particularly of VUSs,” the researchers concluded.