ClinVar Miner

Submissions for variant NM_000277.3(PAH):c.169-13T>G

gnomAD frequency: 0.00001  dbSNP: rs62507341
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen PAH Variant Curation Expert Panel RCV000778351 SCV002032195 likely pathogenic Phenylketonuria 2020-08-17 reviewed by expert panel curation The c.169-13T>G variant in PAH has been reported in multiple individuals with PAH deficiency (BH4 deficiency excluded, PMID: 9521426, PMID: 21147011). This variant has extremely low frequency in gnomAD (MAF=0.00001). This variant was detected with pathogenic variants: IVS10-11G>A (PMID: 21147011); p.L213P (PMID: 9521426); p.R158Q (PMID: 12640344); p.Y356X (c.1068C > G in 1 patient and c.1068C > A in 1 patient, PMID: 30389586). Computational evidence support a deleterious effect on splicing. In summary, this variant meets criteria to be classified as likely pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PP4_Moderate, PM2, PM3_strong, PP3.
GeneDx RCV000088853 SCV000617704 likely pathogenic not provided 2022-09-23 criteria provided, single submitter clinical testing In silico analysis supports a deleterious effect on splicing; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 9521426, 12655550, 34426522, 10394930, 32668217)
Illumina Laboratory Services, Illumina RCV000778351 SCV000914559 pathogenic Phenylketonuria 2018-12-06 criteria provided, single submitter clinical testing The PAH c.169-13T>G intron variant has been reported in five studies and is found in a total of seven individuals with phenylalanine hydroxylase deficiency including in six in a compound heterozygous state and in one in a heterozygous state where the second variant could not be identified (Bosco et al. 1998; Kasnauskiene et al. 2003; Kasnauskiene et al. 2008; Zurflüh et al. 2008; Esfahani et al. 2018). Control data are unavailable for this variant which is reported at a frequency of 0.000009 in the European (non-Finnish) population of the Genome Aggregation Database. This is based on one allele only in a region with good coverage, suggesting that this is a rare variant. Authors predict this variant may activate a cryptic splice site, but no supporting evidence is provided (Bosco et al. 1998). Based on the clinical evidence, the c.169-13T>G variant is classified as pathogenic for phenylalanine hydroxylase deficiency. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Invitae RCV000778351 SCV001590611 pathogenic Phenylketonuria 2023-06-02 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: 102611). This variant is also known as IVS2-13T>G. This variant has been observed in individual(s) with phenylketonuria (PMID: 9521426, 30389586). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is present in population databases (rs62507341, gnomAD 0.0009%). This sequence change falls in intron 2 of the PAH gene. It does not directly change the encoded amino acid sequence of the PAH protein.
DeBelle Laboratory for Biochemical Genetics, MUHC/MCH RESEARCH INSTITUTE RCV000088853 SCV000119448 not provided not provided no assertion provided not provided
Natera, Inc. RCV000778351 SCV002088673 pathogenic Phenylketonuria 2017-09-20 no assertion criteria provided clinical testing

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