ClinVar Genomic variation as it relates to human health

DNA sequence analysis of the QDPR gene demonstrated a sequence change in the canonical splice donor site of intron 5, c.545+1G>A. This sequence change has been described in the gnomAD database with a low population frequency of 0.0016% (dbSNP rs761619802). This change has been previously reported in one patient in a homozygous state with dihydropteridine reductase deficiency (PMID: 10408783) and has also been predicted to affect normal splicing of the QDPR gene. Functional studies by Smooker et al., 1999 have also shown skipping of exon 5 for this variant with abnormal PCR products.

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 1335971). This variant is also known as IVS5G+1A, IVS4+1G>A. Disruption of this splice site has been observed in individual(s) with dihydropteridine reductase deficiency (PMID: 9744478, 32905092). This variant is present in population databases (rs761619802, gnomAD 0.004%). This sequence change affects a donor splice site in intron 5 of the QDPR gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in QDPR are known to be pathogenic (PMID: 7627180, 11153907).

A Homozygote Intron, Splice site donor variant c.545+1G>A in Exon 5 of the QDPR gene that results in the amino acid substitution was identified. The observed variant has a minor allele frequency of 0.0002% in gnomAD exomes and genomes, respectively. The severity of the impact of this variant on the protein is high, based on the effect of the protein and REVEL score. Rare Exome Variant Ensemble Learner (REVEL) is an ensembl method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, LRT, GERP++, SiPhy, phyloP, and phastCons. The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. The variant has been reported to ClinVar as Pathogenic with a status of (2 stars) criteria provided, multiple submitters, no conflicts (Variation ID 1335971 as of 2022-03-28). The variant in QDPR was identified previously in patients with Hyperphenylalaninemia, BH4-deficient, C (Romstad, A et al., 2000). This sequence change affects a donor splice site in intron 5 of the QDPR gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (Baralle, D, and M Baralle., 2005). Based on the above evidence this variant has been classified as Pathogenic according to the ACMG guidelines.

Variant summary: QDPR c.545+1G>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes a 5' splicing donor site. At least one publication reports experimental evidence that this variant affects mRNA splicing (Smooker_1999). The variant allele was found at a frequency of 1.6e-05 in 248736 control chromosomes. c.545+1G>A has been reported in the literature in multiple homozygous individuals affected with Dihydropteridine Reductase Deficiency (example: Smooker_199, Carducci_2020). These data indicate that the variant is very likely to be associated with disease. Homozygous individuals show almost no Dihydropteridine Reductase activity (Carducci_2020). The following publications have been ascertained in the context of this evaluation (PMID: 32905092, 10408783). Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.