rs5030859
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1PM2PM5PP3_StrongPP5_Very_Strong
The NM_000277.3(PAH):c.1223G>A(p.Arg408Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000083 in 1,613,636 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R408W) has been classified as Pathogenic.
Frequency
Consequence
NM_000277.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PAH | NM_000277.3 | c.1223G>A | p.Arg408Gln | missense_variant | 12/13 | ENST00000553106.6 | |
PAH | NM_001354304.2 | c.1223G>A | p.Arg408Gln | missense_variant | 13/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAH | ENST00000553106.6 | c.1223G>A | p.Arg408Gln | missense_variant | 12/13 | 1 | NM_000277.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 151990Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251438Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135886
GnomAD4 exome AF: 0.0000876 AC: 128AN: 1461530Hom.: 0 Cov.: 31 AF XY: 0.0000715 AC XY: 52AN XY: 727108
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74356
ClinVar
Submissions by phenotype
Phenylketonuria Pathogenic:12
Pathogenic, criteria provided, single submitter | clinical testing | Myriad Genetics, Inc. | Dec 19, 2019 | NM_000277.1(PAH):c.1223G>A(R408Q) is classified as pathogenic in the context of phenylalanine hydroxylase deficiency and can be associated with variant or non-PKU HPA. Sources cited for classification include the following: PMID 14722928, 1312992, 1355066, 1301200, and 8533759. Classification of NM_000277.1(PAH):c.1223G>A(R408Q) 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. - |
Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | - | - - |
Pathogenic, no assertion criteria provided | clinical testing | Neonatal Disease Screening Center, Medical Genetics Center, Huaihua City Maternal and Child Health Care Hospital | - | PS3+PM3_VS+PM5+PP1+PP3+PP4_M - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 01, 1992 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Dec 15, 2021 | - - |
Pathogenic, reviewed by expert panel | curation | ClinGen PAH Variant Curation Expert Panel | Aug 05, 2018 | PAH-specific ACMG/AMP criteria applied: PM3_Strong: In trans with R408W, IVS4-1G>A, R241C (ClinGen, P) (PMID:1312992; PMID:14722928); PP3: ; PS3: Mutant enzyme activity of 46% in BioPKU (PMID:9860305); PP4_Moderate: ~830 uml/L w/o BH4 deficiency & 823 umol/L, BH4 status unknown (PMID:9860305; PMID:1312992). 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: (PM3_Strong, PP3, PS3, PP4_Moderate). - |
Pathogenic, criteria provided, single submitter | clinical testing | Victorian Clinical Genetics Services, Murdoch Childrens Research Institute | May 06, 2021 | Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with phenylketonuria (PKU; MIM#261600). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to glutamine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (v2: 14 heterozygotes, 0 homozygotes). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v2) (252 heterozygotes, 0 homozygotes). (I) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated catalytic domain (PMID: 30037505). (I) 0705 - The well-reported pathogenic variant, p.(Arg408Trp), affecting the same residue has previously been reported in association with phenylketonuria (ClinVar), however it is not considered a comparable variant as it has a major Grantham score, whereas this variant has a minor score, therefore cannot be used to inform pathogenicity. (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. It has been reported in multiple individuals with mild PKU, mild hyperphenylalaninemia ( MHP) and non-PKU hyperphenylalaninemia (ClinVar, PMID: 1312992). (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function. Site-directed mutagenesis studies have shown a reduction of 41% in PAH activity compared to wild-type (PMID: 30037505). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign - |
Pathogenic, criteria provided, single submitter | clinical testing | Cellular and Molecular Medicine Research Institute, Urmia University of Medical Sciences | Sep 19, 2023 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jan 08, 2018 | Variant summary: The PAH c.1223G>A (p.Arg408Gln) variant located in the Aromatic amino acid hydroxylas, C-terminal domain (InterPro) involves the alteration of a conserved nucleotide and 4/5 in silico tools predict a damaging outcome for this variant. This variant was found in 13/277144 control chromosomes (gnomAD) at a frequency of 0.0000469, which does not exceed the estimated maximal expected allele frequency of a pathogenic PAH variant (0.0079057). Multiple publications have cited the variant in affected compound heterozygous individuals, presenting with a significant decrease in PAH activity. In support of this, there are other variants at the 408 codon that have been reported in patients with PKU (R408L, R408W), suggesting the codon is important for function. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic. - |
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Jan 20, 2024 | This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 408 of the PAH protein (p.Arg408Gln). This variant is present in population databases (rs5030859, gnomAD 0.03%). This missense change has been observed in individual(s) with PAH-related disease (PMID: 1312992, 10471838, 24401910, 29317692). 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: 612). 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 expected to disrupt PAH protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects PAH function (PMID: 12655546). This variant disrupts the p.Arg408 amino acid residue in PAH. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 2014036, 12173030, 24401910). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. - |
Pathogenic, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jul 26, 2021 | - - |
not provided Pathogenic:2Other:1
Pathogenic, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 29, 2017 | - - |
not provided, no classification provided | literature only | DeBelle Laboratory for Biochemical Genetics, MUHC/MCH RESEARCH INSTITUTE | - | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Al Jalila Children's Genomics Center, Al Jalila Childrens Speciality Hospital | Dec 17, 2022 | - - |
PAH-related condition Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 16, 2024 | The PAH c.1223G>A variant is predicted to result in the amino acid substitution p.Arg408Gln. This variant has been reported in the homozygous state or with a second pathogenic PAH variant in many patients with phenylalanine hydroxylase deficiency (e.g., Zschocke et al. 1995. PubMed ID: 8533759; Eiken et al. 1996. PubMed ID: 8875186; Table S3, Hillert et al. 2020. PubMed ID: 32668217). The p.Arg408Gln amino acid substitution has been reported to reduce PAH enzyme activity to ~50% of wild-type (Zurflüh et al. 2008. PubMed ID: 17935162) and is generally considered a mild PAH variant (Liang et al. 2014. PubMed ID: 24401910). This variant has been classified as pathogenic by the ClinGen PAH Variant Curation Expert Panel as well as several other outside laboratories (https://www.ncbi.nlm.nih.gov/clinvar/variation/612/). Over twenty patients homozygous for the c.1223G>A (p.Arg408Gln) variant have been reported in the BioPKU database; the majority of these patients presented with mild hyperphenylalaninemia or mild PKU (http://www.biopku.org). In summary, we classify the c.1223G>A variant as pathogenic. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at