ClinVar Genomic variation as it relates to human health

Variant summary: PAH c.60+5G>T alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Five predict the variant weakens a 5' donor site. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 7.2e-05 in 251412 control chromosomes (gnomAD). This frequency is not higher than expected for a pathogenic variant in PAH causing Phenylalanine Hydroxylase Deficiency (Phenylketonuria) (7.2e-05 vs 0.0079), allowing no conclusion about variant significance. c.60+5G>T has been reported in the literature in multiple individuals affected with Phenylalanine Hydroxylase Deficiency (Phenylketonuria) (Sarkissian_2011, Bueno_2013). These data indicate that the variant is very likely to be associated with disease. PAH activity in vitro was null according to PAHdb (http://www.pahdb.mcgill.ca) via Bueno_2013. Four ClinVar submitters (evaluation after 2014) cite the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

This sequence change falls in intron 1 of the PAH gene. It does not directly change the encoded amino acid sequence of the PAH protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs62514895, gnomAD 0.02%). This variant has been observed in individuals with phenylketonuria or hyperphenylalaninemia (PMID: 24368688, 24941924; Invitae). ClinVar contains an entry for this variant (Variation ID: 102751). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.

Reduces the quality of the splice donor site in intron 1, and is expected to cause abnormal gene splicing (PMID: 24941924); In silico analysis is inconclusive as to whether the variant alters gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.; This variant is associated with the following publications: (PMID: 25596310, 24368688, 23430918, 34828281, 25525159, 27121329, 18937047, 17935162, 17443661, 15171997, 23792259, 22112818, 20188615, 11180595, 10598814, 9399896, 31589614, 32778825, 32668217, 22841515, 24941924, 23514811, 8406445)

The PAH c.60+5G>T variant is predicted to interfere with splicing. This sequence variant, which lies near the junction of exon 1 and intron 1, has been reported as causative for phenylalanine hydroxylase deficiency (e.g., Guldberg et al. 1993. PubMed ID: 8406445, referred to as IVS-1nt5(g-->t); Vela-Amieva et al. 2015. PubMed ID: 24941924). Available splicing prediction programs predict that this variant would weaken the canonical splice donor site at this location (Alamut Visual v2.11), although to our knowledge this prediction has not been confirmed with functional studies. In the BioPKU database, the c.60+5G>T variant has been reported to have a severe phenotypic effect and is listed as a variant associated with classic phenylketonuria (PKU) (see the PAHvdb page at www.biopku.org). This variant is reported in 0.023% of alleles in individuals of Latino descent in gnomAD (http://gnomad.broadinstitute.org/variant/12-103310844-C-A), which is consistent with it being reported as a founder variant in the Mexican population (Vela-Amieva et al. 2021. PubMed ID: 34828281). Multiple independent submitters to ClinVar interpret this variant as pathogenic (https://www.ncbi.nlm.nih.gov/clinvar/variation/102751). Based on the collective evidence, this variant is interpreted as pathogenic.