rs5030858

Positions:

• chr12-102840493-G-A

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PS3 PM3_Strong PP4_Moderate PP3

This summary comes from the ClinGen Evidence Repository: PAH-specific ACMG/AMP criteria applied: PP3: ; PS3: PMID 17935162: Table 1: p.Arg408Trp 1.85% WT activity PMID 25596310: 1.3% activity of WT (Table S4) (PMID:25596310; PMID:17935162); PP4_Moderate: most common PAH mutation in cohort; exclude BH4 deficiency. (PMID:25596310; PMID:9634518); PM3_Strong: Detected with IVS12+1G>A, M1V (Pathogenic/LP) (PMID:9634518; PMID:1971147; PMID:1609797). 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: (PP3, PS3, PP4_Moderate, PM3_Strong). LINK:https://erepo.genome.network/evrepo/ui/classification/CA251523/MONDO:0009861/006

• Frequency:
  • Genomes: 𝑓 0.00086 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0014 (0 hom.)
• Consequence: PAH ENST00000553106.6 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:35 O:3
• Conservation: PhyloP100: 4.59

Genes affected

PAH (HGNC:8582): (phenylalanine hydroxylase) This gene encodes a member of the biopterin-dependent aromatic amino acid hydroxylase protein family. The encoded phenylalanine hydroxylase enzyme hydroxylates phenylalanine to tyrosine and is the rate-limiting step in phenylalanine catabolism. Deficiency of this enzyme activity results in the autosomal recessive disorder phenylketonuria. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Pathogenic. Variant got 11 ACMG points.

• PS3: For more information check the summary or visit ClinGen Evidence Repository.
• PM3: For more information check the summary or visit ClinGen Evidence Repository.
• PP3: For more information check the summary or visit ClinGen Evidence Repository.
• PP4: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PAH	NM_000277.3	c.1222C>T	p.Arg408Trp	missense_variant	12/13	ENST00000553106.6	NP_000268.1
PAH	NM_001354304.2	c.1222C>T	p.Arg408Trp	missense_variant	13/14		NP_001341233.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PAH	ENST00000553106.6	c.1222C>T	p.Arg408Trp	missense_variant	12/13	1	NM_000277.3	ENSP00000448059	P1

Frequencies

GnomAD3 genomes AF: 0.000861 AC: 131 AN: 152118 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000193

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000131

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000377

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00166

Gnomad OTH AF: 0.000955

GnomAD3 exomes AF: 0.000760 AC: 191 AN: 251438 Hom.: 0 AF XY: 0.000824 AC XY: 112 AN XY: 135886

Gnomad AFR exome AF: 0.000246

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.000397

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.000554

Gnomad NFE exome AF: 0.00148

Gnomad OTH exome AF: 0.000489

GnomAD4 exome AF: 0.00137 AC: 2005 AN: 1461420 Hom.: 0 Cov.: 31 AF XY: 0.00135 AC XY: 978 AN XY: 727044

Gnomad4 AFR exome AF: 0.000179

Gnomad4 AMR exome AF: 0.0000224

Gnomad4 ASJ exome AF: 0.000230

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.000580

Gnomad4 NFE exome AF: 0.00166

Gnomad4 OTH exome AF: 0.00185

GnomAD4 genome AF: 0.000861 AC: 131 AN: 152236 Hom.: 0 Cov.: 32 AF XY: 0.000833 AC XY: 62 AN XY: 74438

Gnomad4 AFR AF: 0.000193

Gnomad4 AMR AF: 0.000131

Gnomad4 ASJ AF: 0.000576

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000377

Gnomad4 NFE AF: 0.00166

Gnomad4 OTH AF: 0.000945

Alfa AF: 0.00153 Hom.: 0

Bravo AF: 0.000767

TwinsUK AF: 0.00216 AC: 8

ALSPAC AF: 0.000259 AC: 1

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.00174 AC: 15

ExAC AF: 0.000659 AC: 80

EpiCase AF: 0.00169

EpiControl AF: 0.000948

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:35 Other:3

Revision: reviewed by expert panel

Submissions by phenotype

Phenylketonuria Pathogenic:25 Other:2

Pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	May 11, 2022	- -
Pathogenic, reviewed by expert panel	curation	ClinGen PAH Variant Curation Expert Panel	Aug 06, 2018	PAH-specific ACMG/AMP criteria applied: PP3: ; PS3: PMID 17935162: Table 1: p.Arg408Trp 1.85% WT activity PMID 25596310: 1.3% activity of WT (Table S4) (PMID:25596310; PMID:17935162); PP4_Moderate: most common PAH mutation in cohort; exclude BH4 deficiency. (PMID:25596310; PMID:9634518); PM3_Strong: Detected with IVS12+1G>A, M1V (Pathogenic/LP) (PMID:9634518; PMID:1971147; PMID:1609797). 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: (PP3, PS3, PP4_Moderate, PM3_Strong). -
Pathogenic, no assertion criteria provided	literature only	OMIM	Jul 01, 2008	- -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Dec 28, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Jul 19, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Dec 07, 2016	Variant summary: The c.1222C>T (p.Arg408Trp) in PAH gene is a missense change that involves a non-conserved nucleotide and 5/5 in silico tools predict deleterious outcome. The variant of interest is located within the catalytic domain and mutations were proven to lead to severe aggregation and complete disruption of structural integrity, and, as a result, complete abolishment of all residual enzyme activity. The variant is present in the large control population dataset of ExAC at a frequency 0.00066 (80/121328 chrs tested), predominantly in individuals of European descent (0.0011; 74/66718) which does not exceed the maximal expected frequency of a pathogenic allele (0.0079) in this gene. The variant has been identified homozygously or in the compound heterozygous state in numerous affected individuals with severe presentation. It is listed as the most common missense pathogenic variant in European population. Lastly, multiple reputable databases/diagnostic centers classified the variant of interest as Pathogenic. Taken together, the variant was classified as Pathogenic. -
Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	Equipe Genetique des Anomalies du Developpement, Université de Bourgogne	Aug 16, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	Jun 24, 2022	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 tryptophan. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (252 heterozygotes, 0 homozygotes). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v2) (14 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) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. It is one of the most common variants reported in individuals with classic PKU (ClinVar, PMIDs: 26481238, 25596310, 30037505, 30668579). (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function. Site-directed mutagenesis studies have shown a reduction to 2% 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	Baylor Genetics	Mar 30, 2024	- -
not provided, no classification provided	phenotyping only	GenomeConnect, ClinGen	-	GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -
Pathogenic, criteria provided, single submitter	clinical testing	3billion	Jan 03, 2022	Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000000577, PMID:2884570, PS1_S). Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID: 25596310, 17935162, PS3_S). The variant has been reported to be in trans with a pathogenic variant as either compound heterozygous or homozygous in at least 2 similarly affected unrelated individuals(PMID: 1609797, 9634518, 1971147, PM3_S). A different missense change at the same codon has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000000612, PMID:28540274,1312992, PM5_M). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.887, 3CNET: 0.996, PP3_P). A missense variant is a common mechanism associated with Phenylketonuria; PKU (PP2_P). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000891, PM2_M). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. -
Pathogenic, criteria provided, single submitter	research	UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill	-	The PAH c.1222C>T (p.R408W) missense variant has been reported in multiple individuals with phenylketonuria and results in an amino acid change in the catalytic domain of the encoded protein (PMID: 7833927; 1312992; 8659548; 18538294). -
Pathogenic, criteria provided, single submitter	clinical testing	Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center	Oct 30, 2023	PS3, PM3_Strong, PM5, PP3 -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Mar 22, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 2017	The PAH c.1222C>T (p.Arg408Trp) variant is a well-documented missense variant that has been identified in many patients with phenylalanine hydroxylase deficiency (DiLella et al. 1987; Zurflüh et al. 2008). Across a selection of the available literature, the p.Arg408Trp variant has been identified in a homozygous state in 24 patients and in a compound heterozygous state in at least 106 patients (Karacić et al. 2009; Utz et al. 2012; Sterl et al. 2013). Control data are not available from thse studies for this variant, which is reported at a frequency of 0.00174 in the European-American population of the Exome Sequencing Project. Functional studies in E coli with p.Arg408Trp-PAH or wild type PAH demonstrated that the p.Arg408Trp-PAH formed high molecular weight aggregates, suggesting a severe folding defect (Gersting et al. 2008). Based on the collective evidence, the p.Arg408Trp 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. -
Pathogenic, criteria provided, single submitter	clinical testing	Juno Genomics, Hangzhou Juno Genomics, Inc	-	PP3+PS3+PP4_Moderate+PM3_VeryStrong -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	May 04, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genetics and Molecular Pathology, SA Pathology	Jan 13, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Oct 18, 2019	NM_000277.1(PAH):c.1222C>T(R408W) is classified as pathogenic in the context of phenylalanine hydroxylase deficiency and is associated with classic PKU. Sources cited for classification include the following: PMIDs: 17935162, 16879198, 22513348, 18538294, 1671768, 2884570, 8889590. Classification of NM_000277.1(PAH):c.1222C>T(R408W) 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	Genome Diagnostics Laboratory, University Medical Center Utrecht	Oct 08, 2014	- -
Pathogenic, criteria provided, single submitter	clinical testing	Knight Diagnostic Laboratories, Oregon Health and Sciences University	Aug 13, 2015	The c.1222C>T (p. Arg408Trp) missense variant in the PAH gene has been shown to segregate with PKU in a family, wherein the affected individual was found to be homozygous [DiLella AG et al., (1987)]. This variant is predominantly found in the Eastern European population who were diagnosed with PKU [Zschocke J, (2003)]. The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls [Zurflüh MR et al., (2008)]. Furthermore, protein-expression studies in E.coli, using human cDNA containing this variant, showed 100% protein aggregation, which suggests a severe folding defect and loss of function [Gersting SW et al., (2008)]. The frequency of this variant in the population databases (1000Genome, Exome Sequencing Project and ExAC) is lower than the disease-allele frequency and there are no homozygotes present. Several computational algorithms predict a deleterious effect of this variant on the protein. Finally, a reputable source has also classified this variant as Pathogenic. Therefore, the collective evidence supports a classification of the c.1222C>T (p. Arg408Trp) variant in the PAH gene as Pathogenic. We have confirmed this finding in our laboratory using Sanger sequencing. -
not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Centogene AG - the Rare Disease Company	Sep 06, 2019	- -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 408 of the PAH protein (p.Arg408Trp). This variant is present in population databases (rs5030858, gnomAD 0.2%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with phenylketonuria (PKU) and is the most prevalent and widely distributed PKU-causing allele in the European population (PMID: 2014036, 8097262, 12173030, 23430547, 25596310). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 577). 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: 2014036, 12655546, 17935162, 18538294, 18937047, 19036622, 21953985). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	curation	Laboratory of Medical Genetics, National & Kapodistrian University of Athens	Feb 01, 2024	- -
Pathogenic, no assertion criteria provided	clinical testing	Zotz-Klimas Genetics Lab, MVZ Zotz Klimas	Oct 30, 2023	- -

not provided Pathogenic:7 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Nov 01, 2024	PAH: PM3:Very Strong, PS3, PM5, PP4:Moderate, PM2:Supporting -
Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Sep 03, 2024	PP3, PP4_moderate, PM3_strong, PS3 -
Pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	May 03, 2017	- -
not provided, no classification provided	literature only	DeBelle Laboratory for Biochemical Genetics, MUHC/MCH RESEARCH INSTITUTE	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	Dec 23, 2015	- -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Mar 19, 2021	The PAH c.1222C>T (p.Arg408Trp) variant has been associated with null to very low PAH activity and classical PKU (PMIDs: 18937047 (2009), 23500595 (2013), 30037505 (2018), 30747360 (2019), and 31355225 (2019)). Therefore, the variant is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jul 04, 2024	In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Classified as not responsive to tetrahydrobiopterin (BH4) therapy (PMID: 17935162); This variant is associated with the following publications: (PMID: 12655546, 18538294, 19036622, 18937047, 21953985, 25087612, 20981092, 26210745, 24939588, 26919687, 12542580, 9452062, 12501224, 23792259, 22513348, 8825928, 30667134, 30963030, 1609797, 25596310, 9634518, 2014036, 17935162, 34900593, 29413232, 23559577, 23500595, 24401910, 22975760, 25750018, 26542770, 26803807, 2884570, 8889590, 27786189, 24741310, 29102225, 16338627, 19194782, 29499199, 1971147, 30037505, 29030855, 1355066, 31355225, 30747360, 34426522, 31589614, 33101986, 8188310, 32853555, 1677425, 32778825, 33465300, 33375644, 35405047, 37421234, 37924808, 36046396, 36646061, 37189584, 35270292, 36537053, 37443404, 36246604, 38105685) -

PAH-related disorder Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

May 16, 2024

The PAH c.1222C>T variant is predicted to result in the amino acid substitution p.Arg408Trp. This variant is one of the most commonly reported pathogenic PAH variants and has been associated with classical phenylketonuria (PKU) (DiLella et al. 1987. PubMed ID: 2884570; Guldberg et al. 1994. PubMed ID: 8088845; Danecka et al. 2015. PubMed ID: 25596310). The p.Arg408Trp amino acid change has been reported to reduce the activity of the PAH protein to <2% of wild-type, and is reported to result in a PAH protein that is non-responsive to tetrahydrobiopterin (BH4) (Zurflüh et al. 2008. PubMed ID: 17935162). The c.1222C>T variant is interpreted as pathogenic by the ClinGen PAH Variant Curation Expert Panel and other outside laboratories (https://www.ncbi.nlm.nih.gov/clinvar/variation/577/). We also interpret this variant as pathogenic. -

Inborn genetic diseases Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 08, 2021

The c.1222C>T (p.R408W) alteration is located in exon 12 (coding exon 12) of the PAH gene. This alteration results from a C to T substitution at nucleotide position 1222, causing the arginine (R) at amino acid position 408 to be replaced by a tryptophan (W). This common mutation has been reported in multiple homozygous and compound heterozygous individuals with phenylalanine hydroxylase (PAH) deficiency (DiLella, 1987; Guldberg, 1995; Guldberg, 1998; Gundorova, 2019; Lilleväli, 2019; Su, 2019; Tresbach, 2020). This alteration is located in the catalytic domain at the center of the protein structure and leads to severe aggregation with complete disruption of structural integrity and loss of enzyme function (Dobrowolski, 2009; Gersting, 2008). The p.R408W alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic. -

See cases Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Institute of Human Genetics, University Hospital Muenster

Dec 20, 2021

ACMG categories: PS1,PM2,PM7,PP3,PP4,PP5,BP1 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.92
BayesDel_addAF	Pathogenic	0.21	D
BayesDel_noAF	Pathogenic	0.53
CADD	Pathogenic	28
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.99	D;D
Eigen	Uncertain	0.47
Eigen_PC	Uncertain	0.27
FATHMM_MKL	Uncertain	0.83	D
LIST_S2	Pathogenic	1.0	D;D
M_CAP	Pathogenic	0.64	D
MetaRNN	Pathogenic	0.82	D;D
MetaSVM	Pathogenic	1.0	D
MutationAssessor	Pathogenic	4.2	H;.
MutationTaster	Benign	1.0	A;A
PrimateAI	Uncertain	0.62	T
PROVEAN	Pathogenic	-6.8	D;D
REVEL	Pathogenic	0.89
Sift	Pathogenic	0.0	D;D
Sift4G	Pathogenic	0.0	D;D
Polyphen		1.0	D;.
Vest4		0.89
MVP		0.98
MPC		0.24
ClinPred		0.45	T
GERP RS		1.4
Varity_R		0.88
gMVP		0.94

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs5030858; hg19: chr12-103234271; COSMIC: COSV61018595; COSMIC: COSV61018595;