Submissions for variant NM_000277.3(PAH):c.212G>A (p.Arg71His)

gnomAD frequency: 0.00001  dbSNP: rs62508695

Total submissions: 11

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen PAH Variant Curation Expert Panel	RCV000672919	SCV001146695	likely pathogenic	Phenylketonuria	2019-09-29	reviewed by expert panel	curation	The c.212G>A (p.Arg71His) variant in PAH has been reported in multiple individual with PAH deficiency with BH4 deficiency excluded (PP4_Moderate; PMID: 10495930, 26503515). This variant is absent in population databases (PM2). This variant was detected in trans with known pathogenic variant p.R408W (PM3). Computational evidence supports a deleterious effect. In summary, this variant meets criteria to be classified as likely pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PP4_Moderate, PM2, PM3, PP3.
GeneDx	RCV000088876	SCV000239046	likely pathogenic	not provided	2019-03-04	criteria provided, single submitter	clinical testing	The majority of missense variants in this gene are considered pathogenic (Stenson et al., 2014); Reported as pathogenic in a well-curated database but additional evidence is not available (PAH Consortium Database); This variant is associated with the following publications: (PMID: 30747360, 10495930, 29390883, 31130284, 32668217)
Counsyl	RCV000672919	SCV000798074	uncertain significance	Phenylketonuria	2018-02-21	criteria provided, single submitter	clinical testing
Invitae	RCV000672919	SCV001574359	pathogenic	Phenylketonuria	2023-06-21	criteria provided, single submitter	clinical testing	Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt PAH protein function. For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Arg71 amino acid residue in PAH. Other variant(s) that disrupt this residue have been observed in individuals with PAH-related conditions (PMID: 17627389), which suggests that this may be a clinically significant amino acid residue. ClinVar contains an entry for this variant (Variation ID: 102633). This missense change has been observed in individual(s) with hyperphenylalaninemia (PMID: 10495930, 29390883, 32668217; BIOPKU http://www.biopku.org). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 71 of the PAH protein (p.Arg71His).
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000672919	SCV002547958	likely pathogenic	Phenylketonuria	2024-03-08	criteria provided, single submitter	clinical testing	Variant summary: PAH c.212G>A (p.Arg71His) results in a non-conservative amino acid change located in the ACT domain (IPR002912) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251342 control chromosomes. c.212G>A has been reported in the literature in individuals affected with Phenylalanine Hydroxylase Deficiency (Phenylketonuria) (e.g. Zekanowski_1999, Zhang_2018, Monies_2019, Yan_2020). These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 26503515, 10495930, 29499199, 30747360, 31130284, 32039316, 29390883). ClinVar contains an entry for this variant (Variation ID: 102633). Based on the evidence outlined above, the variant was classified as likely pathogenic.
Fulgent Genetics, Fulgent Genetics	RCV000672919	SCV002806213	likely pathogenic	Phenylketonuria	2022-04-06	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV003407486	SCV004108878	pathogenic	PAH-related disorder	2023-05-17	criteria provided, single submitter	clinical testing	The PAH c.212G>A variant is predicted to result in the amino acid substitution p.Arg71His. This variant has been reported along with a second known pathogenic PAH variant in individuals with hyperphenylalaninemia (Zekanowski et al. 1999. PubMed ID: 10495930, patient IW in Table 1; Li et al. 2015. PubMed ID: 26503515; Hillert et al 2020. PubMed ID: 32668217). The p.Arg71 residue has been moderately conserved during evolution (Alamut Visual v2.10). It is located in a region of the PAH protein where it is thought to be involved in interdomain interactions in the protein monomer, and it is thought that a change in the amino acids in this region could result in a structural disturbance of the protein (Pey et al. 2007. PubMed ID: 17924342). Other variants that disrupt the same amion acid (e.g., p.Arg71Cys, p.Arg71Pro) have been reported in patients with phenylalanine hydroxylase deficiency (Wang et al. 2007. PubMed ID: 17627389; Hillert et al 2020. PubMed ID: 32668217). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. This variant has been interpreted as likely pathogenic or pathogenic by the majority of submitters to ClinVar, including the ClinGen PAH Variant Curation Expert Panel (https://www.ncbi.nlm.nih.gov/clinvar/variation/102633/). Taken together, we classify the c.212G>A (p.Arg71His) variant as pathogenic.
Baylor Genetics	RCV000672919	SCV004209678	likely pathogenic	Phenylketonuria	2024-02-28	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV004525871	SCV005039983	likely pathogenic	Familial multiple polyposis syndrome	2024-03-08	criteria provided, single submitter	clinical testing	Variant summary: APC c.212G>A (p.Arg71His) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 8e-06 in 250788 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.212G>A has been reported in the literature in individuals affected with Familial Adenomatous Polyposis. These report(s) do not provide unequivocal conclusions about association of the variant with Familial Adenomatous Polyposis. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.
DeBelle Laboratory for Biochemical Genetics, MUHC/MCH RESEARCH INSTITUTE	RCV000088876	SCV000119473	not provided	not provided		no assertion provided	not provided
Natera, Inc.	RCV000672919	SCV001455113	likely pathogenic	Phenylketonuria	2020-09-16	no assertion criteria provided	clinical testing