ClinVar Miner

Submissions for variant NM_000277.3(PAH):c.977G>C (p.Trp326Ser)

dbSNP: rs62514959
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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen PAH Variant Curation Expert Panel RCV001789822 SCV002032215 likely pathogenic Phenylketonuria 2024-09-06 reviewed by expert panel curation The NM_000277.3(PAH):c.977G>C (p.Trp326Ser) variant is a missense variant in exon 10/13 of PAH. This variant has been previously reported in at least one proband with hyperphenylalanemia (HPA; Palmieri, A. (2013). MOLECULAR ANALYSIS OF PHENYLALANINE HYDROXYLASE GENE IN SOUTH ITALY PATIENTS AFFECTED BY PHENYLKETONURIA) in whom BH4 deficiency was not formally excluded by normal urine pterins and normal DHPR activity, or sequencing of genes in the BH4 cofactor metabolism pathway to exclude a defect of BH4 cofactor metabolism (PP4_Supporting). This variant has been reported in at least one proband with the genotype p.Leu48Ser/p.Trp326Ser (phase not confirmed) phenotype (PMID: 32668217); the p.Leu48Ser variant is path in ClinVar by PAH VCEP (Var ID: 608) (PM3_Supporting). The variant is absent from ethnically diverse control databases, including gnomAD/ExAC, 1000 Genomes, and ESP (PM2). The variant is predicted damaging by multiple in-silico missense predictors, including REVEL (REVEL score 0.874) (PP3_Moderate). A different missense variant at the same site, p.Trp326Cys, has been previously reported in one patient with HPA (PMID: 36537053), BH4 deficiency not excluded, in presumed trans w/p.R408W (path by PAH VCEP, ClinVar ID 577); the p.W326C variant qualifies as likely path (PM3_Supp, PP3_Mod, PP4_Mod (hyperphenylalanemia, BH4 deficiency excluded by sequencing of genes in sequencing of genes in the BH4 cofactor metabolism pathway, PM2_Supp), such that PM5_Supporting is met. In summary, this variant meets criteria to be classified as Likely Pathogenic based on the ACMG/AMP criteria applied, as specified by the ClinGen Phenylketonuria Variant Curation Expert Panel (Specifications Version 2.0): PM2_Supporting, PM3_Supporting, PM5_Supporting, PP4_Supporting, PP3_Moderate.

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