Total submissions: 4
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
Clin |
RCV000411640 | SCV002032222 | pathogenic | Phenylketonuria | 2020-06-08 | reviewed by expert panel | curation | The c.830A>G (p.Tyr277Cys) variant in PAH has been reported in multiple individuals with PKU (PMID:24350308). This variant has an extremely low allele frequency (MAF=0.00006) in gnomAD. It was detected with multiple pathogenic variants: p.R408W in 2 patients; p.L194P (PMID: 24350308); c.842+1G>A in 2 patients (PMID: 25952249). Computational prediction tools and conservation analysis support a deleterious effect. Another missense change at the same amino acid (p.Y277D), is pathogenic by 8 submitters. In summary, this variant meets criteria to be classified as pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PM3_strong, PM2, PM5, PP3, PP4 |
Counsyl | RCV000411640 | SCV000486807 | likely pathogenic | Phenylketonuria | 2016-08-16 | criteria provided, single submitter | clinical testing | |
Invitae | RCV000411640 | SCV003441218 | pathogenic | Phenylketonuria | 2022-08-31 | criteria provided, single submitter | clinical testing | For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Tyr277 amino acid residue in PAH. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 2035532, 8268925, 8632937, 12173030, 12655546). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt PAH protein function. ClinVar contains an entry for this variant (Variation ID: 102860). This missense change has been observed in individuals with phenylketonuria (PMID: 32668217). This variant is present in population databases (rs62516155, gnomAD 0.006%). This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 277 of the PAH protein (p.Tyr277Cys). |
De |
RCV000089121 | SCV000119729 | not provided | not provided | no assertion provided | not provided |