Submissions for variant NM_000277.3(PAH):c.842C>T (p.Pro281Leu)

gnomAD frequency: 0.00010  dbSNP: rs5030851

Total submissions: 24

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen PAH Variant Curation Expert Panel	RCV000000620	SCV000852092	likely pathogenic	Phenylketonuria	2018-08-27	reviewed by expert panel	curation	PAH-specific ACMG/AMP criteria applied: PP3: ; PS3: 2% activity in bioPKU (PAH0309) (PMID:25596310; PMID:17935162); PP4_Moderate: 2 patients with moderate or classical PKU; patients with severe PKU. BH4 deficiency ruled out. (PMID:15503242; PMID:12655553); PM3: IVS4-1G>A (P/LP) (PMID:15503242). In summary this variant meets criteria to be classified as likely pathogenic for phenylketonuria in an autosomal recessive manner based on the ACMG/AMP criteria applied as specified by the PAH Expert Panel: (PP3, PS3, PP4_Moderate, PM3).
Eurofins Ntd Llc (ga)	RCV000078534	SCV000110390	pathogenic	not provided	2017-01-26	criteria provided, single submitter	clinical testing
GeneDx	RCV000078534	SCV000329448	pathogenic	not provided	2020-05-18	criteria provided, single submitter	clinical testing	Associated with very low (0-1%) residual phenylalanine hydroxylase enzyme activity and is considered a severe PAH variant as individuals homozygous for this variant have been reported with classic phenylketonuria (Okano et al., 1991; Rivera et al., 2011; Shi et al., 2012; Danecka et al., 2015); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Reported to not be responsive to tetrahydrobiopterin (BH4) therapy (Zurflh et al., 2008); This variant is associated with the following publications: (PMID: 33101986, 31589614, 32853555, 30275481, 30747360, 31355225, 30648773, 30963030, 30159272, 12501224, 24296287, 21871829, 29288420, 1672294, 29499199, 2014036, 28676969, 19194782, 22513348, 8889590, 1672290, 25750018, 17935162, 1481864, 21953985, 25596310, 25087612, 22975760, 21228398, 10471838)
Invitae	RCV000000620	SCV000629222	pathogenic	Phenylketonuria	2024-01-25	criteria provided, single submitter	clinical testing	This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 281 of the PAH protein (p.Pro281Leu). This variant is present in population databases (rs5030851, gnomAD 0.02%). This missense change has been observed in individual(s) with PAH-related conditions (PMID: 1672294, 21871829, 25596310; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 589). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects PAH function (PMID: 1672294, 17935162, 21953985). For these reasons, this variant has been classified as Pathogenic.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000000620	SCV000696468	pathogenic	Phenylketonuria	2017-01-19	criteria provided, single submitter	clinical testing	Variant summary: The PAH c.842C>T (p.Pro281Leu) variant involves the alteration of a conserved nucleotide. 5/5 in silico tools predict a damaging outcome for this variant, which was confirmed by at least one in vitro study showing the activity of PAH p.P281L was <1% of wild-type PAH activity (Kayaalp_1997). This variant was found in 12/121404 control chromosomes at a frequency of 0.0000988, which does not exceed the estimated maximal expected allele frequency of a pathogenic PAH variant (0.0079057). This variant has been reported in numerous patients with classic PKU. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic.
Fulgent Genetics, Fulgent Genetics	RCV000000620	SCV000893941	pathogenic	Phenylketonuria	2018-10-31	criteria provided, single submitter	clinical testing
Baylor Genetics	RCV000000620	SCV001163718	pathogenic	Phenylketonuria		criteria provided, single submitter	clinical testing
Myriad Genetics, Inc.	RCV000000620	SCV001193964	pathogenic	Phenylketonuria	2019-12-04	criteria provided, single submitter	clinical testing	NM_000277.1(PAH):c.842C>T(P281L) is classified as pathogenic in the context of phenylalanine hydroxylase deficiency. Sources cited for classification include the following: PMID 22513348, 22526846, 19394257, 15503242, 20920871, 20187763, 22763404, 18299955, 17935162 and 10471838. Classification of NM_000277.1(PAH):c.842C>T(P281L) is based on the following criteria: This is a well-established pathogenic variant in the literature that has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening.
CeGaT Center for Human Genetics Tuebingen	RCV000078534	SCV001249178	pathogenic	not provided	2022-06-01	criteria provided, single submitter	clinical testing	PAH: PM3:Very Strong, PM1, PM2, PM5, PP3, PS3:Supporting
UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill	RCV000000620	SCV001251474	pathogenic	Phenylketonuria		criteria provided, single submitter	research	The PAH c.842C>T (p.P281L) variant is located at an intron/exon boundary, and this variant has been reported as pathogenic in individuals with phenylketonuria. This variant was also shown to abolish the function of the phenylalanine hydroxylase enzyme in vitro (PMID: 1672290; 9634518; 10234516; 17935162).
Institute of Human Genetics, University of Leipzig Medical Center	RCV000000620	SCV001440177	pathogenic	Phenylketonuria	2019-01-01	criteria provided, single submitter	clinical testing	This variant was identified as compound heterozygous.
Ambry Genetics	RCV001265833	SCV001444005	pathogenic	Inborn genetic diseases	2021-05-21	criteria provided, single submitter	clinical testing	The c.842C>T (p.P281L) alteration is located in exon 7 (coding exon 7) of the PAH gene. This alteration results from a C to T substitution at nucleotide position 842, causing the proline (P) at amino acid position 281 to be replaced by a leucine (L). Based on data from the Genome Aggregation Database (gnomAD) database, the PAH c.842C>T alteration was observed in 0.01% (29/282652) of total alleles studied, with a frequency of 0.02% (26/128978) in the European (non-Finnish) subpopulation. This mutation has been identified in numerous individuals with phenylalanine hydroxylase (PAH) deficiency (Okano, 1991; Shi, 2012; Gundorova, 2019) Activity and protein levels were approximately 1% when this variant was expressed n COS cells (Shi, 2012) The p.P281L alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic.
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000078534	SCV001470579	pathogenic	not provided	2019-11-04	criteria provided, single submitter	clinical testing	In the literature, this variant has been reported as homozygous or compound heterozygous with other pathogenic PAH variants in many individuals with PAH-related diseases (PMIDs: 30747360 (2019), 29749107 (2018), 25596310 (2015), 21871829 (2011), 20082265 (2010), 18294361 (2008), and 1672294 (1991)). An in vitro study indicated that the homozygous c.842C>T (p.Pro281Leu) variant could generate a full length splicing product and a shorter splicing product without exon 8. The full length product has minimal enzyme activity and the shorter product causes the premature termination of the PAH protein (PMID 10471838 (1999)). Multiple other experimental studies have also confirmed that this variant results in diminished enzyme activity and protein expression (PMID: 25596310 (2015), 21953985 (2012), 17935162 (2008), 11161839 (2001), and 1672294 (1991)). This pathogenic variant is located in the catalytic domain of the PAH protein and is associated with classic PKU (PMID 20082265 (2010)).
Genome-Nilou Lab	RCV000000620	SCV001810543	pathogenic	Phenylketonuria	2021-07-22	criteria provided, single submitter	clinical testing
3billion	RCV000000620	SCV002058848	likely pathogenic	Phenylketonuria	2022-01-03	criteria provided, single submitter	clinical testing	Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000000589, PMID:1672294, PS1_S). A different missense change at the same codon has been reported to be associated with PAH related disorder (ClinVar ID: VCV000092749, PMID:12409276,10598814,15171997, PM5_P). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.983, 3CNET: 0.998, PP3_P). A missense variant is a common mechanism associated with Classic phenylketonuria (PP2_P). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000103, PM2_M). Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline.
Centogene AG - the Rare Disease Company	RCV000000620	SCV002059760	pathogenic	Phenylketonuria	2017-11-03	criteria provided, single submitter	clinical testing
Revvity Omics, Revvity	RCV000000620	SCV003826584	pathogenic	Phenylketonuria	2021-11-15	criteria provided, single submitter	clinical testing
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center	RCV000000620	SCV004244480	pathogenic	Phenylketonuria	2023-11-10	criteria provided, single submitter	clinical testing	PS3, PM3_Strong, PP3
PreventionGenetics, part of Exact Sciences	RCV003914790	SCV004735001	pathogenic	PAH-related condition	2024-01-02	criteria provided, single submitter	clinical testing	The PAH c.842C>T variant is predicted to result in the amino acid substitution p.Pro281Leu. This variant is a recurrent variant that has been documented as causative for phenylalanine hydroxylase deficiency and has been associated with classical phenylketonuria (PKU) (e.g., Okano et al. 1991. PubMed ID: 2014036; Ellingsen et al. 1999, PubMed ID: 10471838; Trunzo et al. 2014, PubMed ID: 24296287; Hillert et al. 2020. PubMed ID: 32668217). The p.Pro281 amino acid resides in the cofactor binding site (CBR) region of the PAH enzyme, and the p.Pro281Leu substitution has been reported to reduce enzyme activity to ~1% of control and result in a mutant PAH protein that is non-responsive to BH4 (Zurflüh et al. 2008. PubMed ID: 17935162). This variant is classified as pathogenic or likely pathogenic by multiple outside laboratories, as well as the ClinGen PAH Variant Curation Expert Panel (https://www.ncbi.nlm.nih.gov/clinvar/variation/589/). This variant is interpreted as pathogenic.
OMIM	RCV000000620	SCV000020770	pathogenic	Phenylketonuria	1994-01-01	no assertion criteria provided	literature only
DeBelle Laboratory for Biochemical Genetics, MUHC/MCH RESEARCH INSTITUTE	RCV000078534	SCV000119744	not provided	not provided		no assertion provided	not provided
GeneReviews	RCV000000620	SCV000324889	not provided	Phenylketonuria		no assertion provided	literature only
Natera, Inc.	RCV000000620	SCV001453099	pathogenic	Phenylketonuria	2020-09-16	no assertion criteria provided	clinical testing
Payam Genetics Center, General Welfare Department of North Khorasan Province	RCV000000620	SCV003842177	pathogenic	Phenylketonuria	2023-03-01	no assertion criteria provided	clinical testing