Submissions for variant NM_000277.3(PAH):c.441+2T>A

dbSNP: rs1876618843

Total submissions: 3

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen PAH Variant Curation Expert Panel	RCV001269054	SCV001448249	pathogenic	Phenylketonuria	2020-10-23	reviewed by expert panel	curation	This c.441+2T>A (aka IVS4+2T>A) variant in PAH has been observed in at least two patients with PAH deficiency (PMID: 26503515, 23932990, and 19915519). The variant was observed with pathogenic variant p.Y356X; phase unknown. This variant is absent from controls in population databases. This variant in the +2 splice donor site of intron 4 results in exon skipping or use of a cryptic splice site. The variant disrupts the reading frame and is predicted to undergo nonsense mediated decay. This variant breaks the splice site in intron 4 according to computational models. In summary, this variant meets criteria to be classified as pathogenic in PAH. PAH-specific ACMG/AMP criteria applied: PVS1, PM2, PM3_supporting and PP4_moderate.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV001269054	SCV002819308	pathogenic	Phenylketonuria	2022-12-07	criteria provided, single submitter	clinical testing	Variant summary: PAH c.441+2T>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Four of four computational tools predict a significant impact on normal splicing, predicting the variant abolishes the canonical 5' splicing donor site. However, these predictions have yet to be confirmed by functional studies. The variant was absent in 251482 control chromosomes (gnomAD). c.441+2T>A has been reported in the literature as a compound heterozygous genotype in multiple individuals affected with Phenylalanine Hydroxylase Deficiency (Phenylketonuria), displaying the classic phenotype of the disease (e.g. Zhu_2013, Wang_2018, Hillert_2020). These data indicate that the variant is very likely to be associated with Phenylketonuria. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. One submitter, the ClinGen PAH Variant Curation Expert Panel, has provided an assessment for this variant to ClinVar after 2014 and classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp	RCV001269054	SCV005836114	likely pathogenic	Phenylketonuria	2024-10-27	criteria provided, single submitter	clinical testing	This sequence change affects a donor splice site in intron 4 of the PAH gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in PAH are known to be pathogenic (PMID: 1301187, 9634518). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with clinical features of PAH-related conditions (PMID: 19915519, 30275481, 32668217). ClinVar contains an entry for this variant (Variation ID: 987760). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.