Submissions for variant NM_000277.3(PAH):c.169-2A>G

gnomAD frequency: 0.00001  dbSNP: rs1226613045

Total submissions: 7

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen PAH Variant Curation Expert Panel	RCV000670987	SCV001370795	pathogenic	Phenylketonuria	2019-08-26	reviewed by expert panel	curation	The c.169-2A>G variant has been identified in at least 1 proband with classic PKU (PMID: 24368688). It has been detected in the homozygous form (PMID: 20188615) as well as in trans with the pathogenic variant Gly272Ter (PMID: 24368688). This variant is present at very low allele frequencies; 0.000007993 overall in gnomAD with a MAF of 0.00003267 (1/30612) in the South Asian population. Computational analysis predicts an alteration of the WT acceptor site, most probably affecting splicing, generating a frameshift, and leading to nonsense mediated decay. In summary, this variant meets criteria to be classified as pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PVS1, PM3, PM2, PP1_Moderate, PP4.
Counsyl	RCV000670987	SCV000795919	pathogenic	Phenylketonuria	2017-11-29	criteria provided, single submitter	clinical testing
Fulgent Genetics, Fulgent Genetics	RCV000670987	SCV000893955	pathogenic	Phenylketonuria	2018-10-31	criteria provided, single submitter	clinical testing
Revvity Omics, Revvity	RCV000670987	SCV002016503	pathogenic	Phenylketonuria	2020-12-04	criteria provided, single submitter	clinical testing
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	RCV000670987	SCV002767866	pathogenic	Phenylketonuria	2020-10-19	criteria provided, single submitter	clinical testing	Based on the classification scheme VCGS_Germline_v1.3.3, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with phenylketonuria (PKU) (MIM#261600). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0201 - Variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein (premature termination codon is located at least 54 nucleotides upstream of the final exon-exon junction). (SP) 0210 - Splice site variant proven to affect splicing of the transcript with a known effect on protein sequence (p.(Glu57Valfs*13)). Analysis of patient cells concludes this variant introduces the use of an upstream cryptic acceptor splice site in intron two, resulting in retention of intronic sequence, a frameshift and a premature termination codon (PMID: 20188615). (SP) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD v2 <0.01 for a recessive condition (2 heterozygotes,0 homozygotes). (SP) 0703 - Another splice variant comparable to the one identified in this case has moderate previous evidence for pathogenicity. A splice variant at the same intron junction (c.169-13T>G) has been reported several times as pathogenic in patients with PKU (ClinVar). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported multiple times as pathogenic (ClinVar), and has been observed in a homozygous family, and a compound heterozygous patient with PKU (ClinVar, PMID: 20188615, PMID: 24368688). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign
Labcorp Genetics (formerly Invitae), Labcorp	RCV000670987	SCV003441013	pathogenic	Phenylketonuria	2022-08-11	criteria provided, single submitter	clinical testing	For these reasons, this variant has been classified as Pathogenic. Studies have shown that disruption of this splice site results in activation of a cryptic splice site and introduces a premature termination codon (PMID: 20188615). The resulting mRNA is expected to undergo nonsense-mediated decay. Studies have shown that disruption of this splice site alters PAH gene expression (PMID: 20188615). ClinVar contains an entry for this variant (Variation ID: 555212). This variant is also known as c.168-2A>G. Disruption of this splice site has been observed in individual(s) with hyperphenylalaninemia (PMID: 20188615, 29499199, 32668217). It has also been observed to segregate with disease in related individuals. This variant is present in population databases (no rsID available, gnomAD 0.006%). This sequence change affects an acceptor splice site in intron 2 of the PAH gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or disrupted protein product.
Neuberg Centre For Genomic Medicine, NCGM	RCV000670987	SCV004047580	pathogenic	Phenylketonuria		criteria provided, single submitter	clinical testing	This invariant splice site c.169-2A>G has been detected in the homozygous form in proband with classic Phenylketonuria (PKU) (Ho G et al). This variant has allele frequency of 0.00080% in the gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. This variant has been reported to the ClinVar database as Pathogenic. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Pathogenic.