Submissions for variant NM_000277.3(PAH):c.311C>A (p.Ala104Asp)

gnomAD frequency: 0.00003  dbSNP: rs62642929

Total submissions: 16

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen PAH Variant Curation Expert Panel	RCV000349567	SCV000852162	pathogenic	Phenylketonuria	2018-08-07	reviewed by expert panel	curation	PAH-specific ACMG/AMP criteria applied: PM2: Extremely low frequency: 0.00009 in gnomAD; PS3: 26% PAH enzyme activity; PM3_Strong: Detected with Y414C, pathogenic in ClinVar and V245L (P/LP) (PMID:9429153; PMID:24368688). In summary this variant meets criteria to be classified as pathogenic for phenylketonuria in an autosomal recessive manner based on the ACMG/AMP criteria applied as specified by the PAH Expert Panel: (PM2, PS3, PM3_Strong).
Eurofins Ntd Llc (ga)	RCV000088896	SCV000330985	pathogenic	not provided	2016-04-07	criteria provided, single submitter	clinical testing
GeneDx	RCV000088896	SCV000617703	pathogenic	not provided	2024-06-26	criteria provided, single submitter	clinical testing	Reported previously in the heterozygous state, in the presence of a second PAH variant, in association with phenylketonuria (PKU) (PMID: 1301187, 9429153, 12655551, 17627389, 24368688); Published functional studies found this variant is associated with reduced protein expression and catalytic activity (PMID: 9191407, 21953985); Not observed at a significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Associated with tetrahydrobiopterin (BH4) responsiveness (PMID: 17935162); This variant is associated with the following publications: (PMID: 11461190, 10384369, 9792411, 22526846, 9429153, 24368688, 17627389, 23357515, 12655551, 30037505, 30648773, 31355225, 22112818, 18299955, 23764561, 26666653, 26542770, 23514811, 34426522, 32668217, 33101986, 32778825, 9191407, 1301187, 17935162, 21953985)
Labcorp Genetics (formerly Invitae), Labcorp	RCV000349567	SCV000830766	pathogenic	Phenylketonuria	2024-12-26	criteria provided, single submitter	clinical testing	This sequence change replaces alanine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 104 of the PAH protein (p.Ala104Asp). This variant is present in population databases (rs62642929, gnomAD 0.009%). This missense change has been observed in individual(s) with phenylketonuria (PMID: 18299955, 22112818, 22526846, 23764561, 26666653). ClinVar contains an entry for this variant (Variation ID: 102650). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt PAH protein function with a negative predictive value of 80%. For these reasons, this variant has been classified as Pathogenic.
Illumina Laboratory Services, Illumina	RCV000349567	SCV000914557	pathogenic	Phenylketonuria	2019-01-11	criteria provided, single submitter	clinical testing	Across a selection of the available literature, the PAH c.311C>A (p.Ala104Asp) missense variant has been identified in at least 12 individuals with phenylalanine hydroxylase deficiency (PAH), including in one in a homozygous state, and in 11 in a compound heterozygous state (Guldberg et al. 1995; Zekanowski et al. 1997; Pronina et al. 2003; Ho et al. 2014; Trunzo et al. 2015). The p.Ala104Asp variant is associated with a mild phenotype with the exception of one compound heterozygous individual who presented with the classical form. Control data are unavailable for this variant, which is reported at a frequency of 0.000089 in the European (non-Finnish) population of the Genome Aggregation Database. Functional studies demonstrated that the p.Ala104Asp PAH retained 26% of its activity but with a significantly reduced half-life of the aggregates compared to wild type PAH. In vitro, wild type PAH was comprised of tetramers and dimers, whereas mutant PAH was primarily dimeric with moderate amounts of aggregates, and significantly reduced amounts of tetramers (Waters et al. 1998). Additionally, hybrid expression models have shown a modest decrease in reporter activity as well as an increase in the rate of degradation in homomeric interactions for the p.Ala104Asp mutant as compared to wildtype (Waters et al. 2001). Based on the collective evidence, the p.Ala104Asp 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000349567	SCV000919919	pathogenic	Phenylketonuria	2018-08-27	criteria provided, single submitter	clinical testing	Variant summary: PAH c.311C>A (p.Ala104Asp) results in a non-conservative amino acid change located in the ACT domain of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 5.3e-05 in 246214 control chromosomes (gnomAD). This frequency is not significantly higher than expected for a pathogenic variant in PAH causing Phenylalanine Hydroxylase Deficiency (Phenylketonuria) (5.3e-05 vs 0.0079), allowing no conclusion about variant significance. c.311C>A has been reported in the literature in multiple individuals affected with mild PKU due to Phenylalanine Hydroxylase Deficiency (mild Phenylketonuria)(Zurfluh_2008, Bayat_2016). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in 10%-<30% of normal activity. Two ClinVar submissions from other clinical diagnostic laboratories (evaluation after 2014) cite the variant as "pathogenic." Based on the evidence outlined above, the variant was classified as pathogenic.
Revvity Omics, Revvity	RCV000349567	SCV002016507	pathogenic	Phenylketonuria	2021-07-15	criteria provided, single submitter	clinical testing
Fulgent Genetics, Fulgent Genetics	RCV000349567	SCV002800918	pathogenic	Phenylketonuria	2022-05-19	criteria provided, single submitter	clinical testing
Baylor Genetics	RCV000349567	SCV004201382	pathogenic	Phenylketonuria	2024-03-28	criteria provided, single submitter	clinical testing
Laboratory of Medical Genetics, National & Kapodistrian University of Athens	RCV000349567	SCV005051913	pathogenic	Phenylketonuria	2024-02-01	criteria provided, single submitter	curation
Mayo Clinic Laboratories, Mayo Clinic	RCV000088896	SCV005414124	pathogenic	not provided	2023-11-01	criteria provided, single submitter	clinical testing	PM2_moderate, PM3_strong, PS3
DeBelle Laboratory for Biochemical Genetics, MUHC/MCH RESEARCH INSTITUTE	RCV000088896	SCV000119494	not provided	not provided		no assertion provided	not provided
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV000088896	SCV001743459	pathogenic	not provided		no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV000088896	SCV001927449	pathogenic	not provided		no assertion criteria provided	clinical testing
Natera, Inc.	RCV000349567	SCV002088669	pathogenic	Phenylketonuria	2017-06-21	no assertion criteria provided	clinical testing
PreventionGenetics, part of Exact Sciences	RCV003915115	SCV004733016	pathogenic	PAH-related disorder	2024-01-02	no assertion criteria provided	clinical testing	The PAH c.311C>A variant is predicted to result in the amino acid substitution p.Ala104Asp. This variant has been reported in the homozygous state or with a second PAH variant in patients with phenylalanine hydroxylase deficiency, ranging from mild hyperphenylalaninemia to classic phenylketonuria (PKU) (e.g., Zekanowski et al. 1997. PubMed ID: 9429153; Bercovich et al. 2008. PubMed ID: 18299955; Jeannesson-Thivisol et al. 2015. PubMed ID: 26666653; Trunzo et al. 2015. PubMed ID: 26210745; Su et al. 2019. PubMed ID: 31355225; Table S3 in Hillert et al. 2020. PubMed ID: 32668217). Based on functional studies, the p.Ala104Asp amino acid change has been reported to result in reduced PAH enzyme activity and has been classified as a BH4-responsive amino acid substitution (Zurflüh et al. 2008. PubMed ID: 17935162; Shi et al. 2012. PubMed ID: 21953985; Himmelreich et al. 2018. PubMed ID: 30037505). This variant is reported in 0.014% of alleles in individuals of European (Finnish) descent in gnomAD. It has been classified as pathogenic by multiple outside laboratories as well as the ClinGen PAH Variant Curation Expert Panel (https://www.ncbi.nlm.nih.gov/clinvar/variation/102650/). Based on these observations, we classify this variant as pathogenic.