ClinVar Miner

Submissions for variant NM_000277.3(PAH):c.975C>G (p.Tyr325Ter)

dbSNP: rs62508573
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen PAH Variant Curation Expert Panel RCV000410321 SCV001370855 pathogenic Phenylketonuria 2020-04-13 reviewed by expert panel curation The c.975C>G (p.Tyr325Ter) is a variant in PAH is a null variant (nonsense variant) in a gene where LOF is a known mechanism of disease, leading to premature truncation and NMD (PVS1). It is present at extremely low frequencies in ethnically diverse control databases (gnomAD AF 0.00000399; PAH PM2 cutoff: <0.0002) (PM2). It has been identified in at least 13 PKU probands, at least 5 of whom BH4 deficiency was formally excluded (PP4_Moderate), including in trans with pathogenic or likely pathogenic variants in 9 cases, in trans with VUS in two cases, and homozygous in two cases (PM3_VeryStrong). It was first identified in a Korean patient with classic PKU (as confirmed by blood Phe levels) in trans with the N207D variant (pathogenic per PAH VCEP) (PMID: 9452061; PMID: 15503242); BH4 deficiency was excluded by urinary pterin analysis and DPHR assay. It was also found in another four patients with PKU, BH4 deficiency was excluded by urinary pterin analysis and DPHR assay (PMID: 15503242): one in trans with the known pathogenic (per PAH VCEP and in Clinvar) p.R413P variant (patient's PKU phenotype not specified); one with classic PKU in trans with the known pathogenic (per PAH VCEP) p.V388M variant; one with mild hyperphenylalanemia in trans with the ClinVar pathogenic p.Y204C variant; and one in trans with the known pathogenic (per PAH VCEP) p. R243Q variant (PKU phenotype not specified). It has also been found in a Hispanic patient with classic PKU and BH4 deficiency excluded in trans with the pathogenic (per PAH VCEP) p.R261X variant (PMID: 23430918). It has also been found in 9 Chinese PKU cases (PMID: 26503515; PMID: 30050108), BH4 deficiency does not appear to have been ruled out: 2 homozygotes (classic PKU); one classic PKU case in trans with p.EX6-96A>G variant (pathogenic per PAH VCEP); one classic PKU case in trans with c.843-14_-11delCTTT (no PAH VCEP classification); one mild PKU case in trans with p.A434D (pathogenic per PAH VCEP); one mild hyperphenylalanemia case in trans with p.R241C (ClinVar pathogenic, PAH VCEP pathogenic); one classic PKU case in trans with p.Y206C (Likely pathogenic per PAH VCEP); and one mild hyperphenylalanemia case in trans with p.T418P (VUS per PAH VCEP). It is also listed Pathogenic in ClinVar by two labs (variant ID 102921). Classification: Pathogenic Supporting Criteria: PVS1, PM2; PM3_VeryStrong; PP4_Moderate
Counsyl RCV000410321 SCV000486345 pathogenic Phenylketonuria 2016-05-13 criteria provided, single submitter clinical testing
Invitae RCV000410321 SCV001224687 pathogenic Phenylketonuria 2023-07-25 criteria provided, single submitter clinical testing 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: 102921). This premature translational stop signal has been observed in individual(s) with phenylketonuria (PMID: 9452061, 26503515). This sequence change creates a premature translational stop signal (p.Tyr325*) in the PAH gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PAH are known to be pathogenic (PMID: 1301187, 9634518). This variant is present in population databases (rs62508573, gnomAD 0.006%).
DeBelle Laboratory for Biochemical Genetics, MUHC/MCH RESEARCH INSTITUTE RCV000089187 SCV000119803 not provided not provided no assertion provided not provided

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