Submissions for variant NM_000277.3(PAH):c.1163T>C (p.Val388Ala)

dbSNP: rs281865435

Total submissions: 2

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen PAH Variant Curation Expert Panel	RCV000106341	SCV001146702	likely pathogenic	Phenylketonuria	2019-05-05	reviewed by expert panel	curation	The c.1163T>C (p.Val388Ala) variant in PAH has been previously reported Likely Pathogenic by one clinical laboratory in ClinVar (see variant ID 120260); the collection method is stated as 'literature only' and no further information is provided. With respect to the published literature, it has been previously reported in a French proband classified as having mild PKU (defined by the authors as plasma phenylalanine levels between 600-1200uL/L) (PMID: 26666653); formal testing to exclude BH4 deficiency was not noted (PP4). The proband was said to be heterozygous for the variant and also harbor the known pathogenic (per ClinGen PAH working group classification, see ClinVar ID 92731) c.1208C>T (Ala403Val); however, the manuscript did not specify whether the phase of the variants was confirmed via parental testing. Thus, at this point, PM3 cannot be applied with full confidence. The variant results in the substitution of a moderately conserved Valine residue with Alanine, a physiochemically similar amino acid. However, the amino acid substitution is predicted damaging by multiple lines of computational evidence e.g., Predicted deleterious in SIFT, Polyphen2, Mutation Taster. REVEL= 0.919) (PP3). It is absent from control databases including ethnically matched individuals, including gnomAD/ExAC, 1000 Genomes, and ESP (PM2). Other missense changes at this Valine residue (Val388) have been previously reported Pathogenic or Likely Pathogenic in ClinVar, e.g., p.Val388Met (Pathogenic per internal PAH ClinGen Working Group classification, ClinVar ID 619), as well as p.Val388Leu (PM5). The c.181A>G (p.Asn61Asp) variant in PAH has been reported in 1 individual with mild PKU (BH4 deficiency excluded). (PP4_Moderate; PMID: 12501224). This variant is absent in population databases (PM2). This variant was detected with p.R261Q (Pathogenic/likely pathogenic in ClinVar) (PM3; PMID: 12501224). Computational evidence is conflicting. In summary, this variant meets criteria to be classified as likely pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PP4, PM2, PM5, PP3.
Inserm U 954, Faculté de Médecine de Nancy	RCV000106341	SCV000143840	probable-pathogenic	Phenylketonuria		no assertion criteria provided	not provided	Converted during submission to Likely pathogenic.