rs62516152

Positions:

• chr12-102855154-C-T

Variant summary

Our verdict is Likely pathogenic. Variant got 4 ACMG points: 4P and 0B. PM3 PP4_Moderate

This summary comes from the ClinGen Evidence Repository: PAH-specific ACMG/AMP criteria applied: PP4_Moderate: V2301 seen in 1 patient with PAH deficiency. BH4 deficiency ruled out. Upgraded per ClinGen Metabolism WG. (PMID:8268925); PM3_VeryStrong: Detected in trans with IVS 10-11G>A, L48S, R408W, E390G). Upgraded per ClinGen SVI Workgroup. (PMID:15943553; PMID:21147011). 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: (PP4_Moderate, PM3_VeryStrong). LINK:https://erepo.genome.network/evrepo/ui/classification/CA286506/MONDO:0009861/006

• Frequency:
  • Genomes: 𝑓 0.00032 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00031 (1 hom.)
• Consequence: PAH NM_000277.3 missense
• Clinical Significance: Likely pathogenic reviewed by expert panel P:23 U:1 O:1
• Conservation: PhyloP100: 1.65

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 Likely_pathogenic. Variant got 4 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PAH	NM_000277.3	c.688G>A	p.Val230Ile	missense_variant	6/13	ENST00000553106.6
PAH	NM_001354304.2	c.688G>A	p.Val230Ile	missense_variant	7/14
PAH	XM_017019370.2	c.688G>A	p.Val230Ile	missense_variant	6/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PAH	ENST00000553106.6	c.688G>A	p.Val230Ile	missense_variant	6/13	1	NM_000277.3	P1
PAH	ENST00000549111.5	n.784G>A		non_coding_transcript_exon_variant	6/6	1
PAH	ENST00000307000.7	c.673G>A	p.Val225Ile	missense_variant	7/14	5

Frequencies

GnomAD3 genomes AF: 0.000322 AC: 49 AN: 152172 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000966

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000589

Gnomad ASJ AF: 0.000864

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.000660

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000265

Gnomad OTH AF: 0.00191

GnomAD3 exomes AF: 0.000541 AC: 136 AN: 251314 Hom.: 0 AF XY: 0.000552 AC XY: 75 AN XY: 135810

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000492

Gnomad ASJ exome AF: 0.00278

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00150

Gnomad FIN exome AF: 0.000693

Gnomad NFE exome AF: 0.000238

Gnomad OTH exome AF: 0.000489

GnomAD4 exome AF: 0.000315 AC: 460 AN: 1461696 Hom.: 1 Cov.: 34 AF XY: 0.000366 AC XY: 266 AN XY: 727174

Gnomad4 AFR exome AF: 0.0000299

Gnomad4 AMR exome AF: 0.000380

Gnomad4 ASJ exome AF: 0.00279

Gnomad4 EAS exome AF: 0.000101

Gnomad4 SAS exome AF: 0.00144

Gnomad4 FIN exome AF: 0.000786

Gnomad4 NFE exome AF: 0.000125

Gnomad4 OTH exome AF: 0.000778

GnomAD4 genome AF: 0.000322 AC: 49 AN: 152290 Hom.: 0 Cov.: 33 AF XY: 0.000349 AC XY: 26 AN XY: 74468

Gnomad4 AFR AF: 0.0000963

Gnomad4 AMR AF: 0.000588

Gnomad4 ASJ AF: 0.000864

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.000414

Gnomad4 FIN AF: 0.000660

Gnomad4 NFE AF: 0.000265

Gnomad4 OTH AF: 0.00189

Alfa AF: 0.000423 Hom.: 0

Bravo AF: 0.000408

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000349 AC: 3

ExAC AF: 0.000420 AC: 51

Asia WGS AF: 0.000289 AC: 1 AN: 3478

EpiCase AF: 0.0000545

EpiControl AF: 0.000415

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:23 Uncertain:1 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

Phenylketonuria Pathogenic:19

Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Mar 30, 2024	- -
Pathogenic, criteria provided, single submitter	clinical testing	Johns Hopkins Genomics, Johns Hopkins University	Feb 17, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	Oct 08, 2014	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jun 10, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Mar 03, 2022	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Genomic Research Center, Shahid Beheshti University of Medical Sciences	Dec 03, 2017	- -
Likely pathogenic, reviewed by expert panel	curation	ClinGen PAH Variant Curation Expert Panel	Aug 12, 2018	PAH-specific ACMG/AMP criteria applied: PP4_Moderate: V2301 seen in 1 patient with PAH deficiency. BH4 deficiency ruled out. Upgraded per ClinGen Metabolism WG. (PMID:8268925); PM3_VeryStrong: Detected in trans with IVS 10-11G>A, L48S, R408W, E390G). Upgraded per ClinGen SVI Workgroup. (PMID:15943553; PMID:21147011). 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: (PP4_Moderate, PM3_VeryStrong). -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Mar 03, 2016	Variant summary: The c.688G>A in PAH gene is a missense variant that involves a conserved nucleotide and 3/5 in silico tools predict benign outcome. The variant is present in the broad control population dataset of ExAC at a low frequency (0.042%), which does not exceed the maximum frequency for a pathogenic variant in PAH gene (0.79%). The variant has been reported in multiple pts presented with mild hyperphenylalaninemia or mild PKU with the remaining enzymatic activity being about 63% of normal. In general, patients with mild hyperphenylalaninemia do not require restrictive diet or supplementary treatment unless Phe concentrations reach the clinical threshold. Taken together, the variant was classified as Pathogenic for Mild Hyperphenylalaninemia. -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jun 30, 2022	The p.Val230Ile variant in PAH has been reported in at least 10 individuals with phenylalanine hydroxylase deficiency including several individuals who were compound heterozygotes with a pathogenic variant or were homozygous (Guldberg 1993 PMID: 8268925, Zaffanello 2005 PMID: 15943553, Zurflüh 2008 PMID: 17935162, Couce 2013 PMID: 23500595, Yan 2019 PMID: 30747360, Su 2019 PMID: 31355225). It has also been identified in 0.0866% (3/3472) of Ashkenazi Jewish chromosomes by gnomAD (http://gnomad.broadinstitute.org). This variant has been reported in ClinVar as likely pathogenic by the ClinGen PAH Variant Curation Expert Panel using the . ACMG-AMP criteria specific for phenylalanine hydroxylase variants (Zastrow 2018 PMID: 30311390) and is curated in the FDA-recognized human genetic variant database (Variation ID 102784). Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. Another variant involving this codon (p.V230A) have been identified in individuals with phenylalanine hydroxylase deficiency and is classified as pathogenic by the ClinGen PAH Variant Curation Expert Panel. In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive phenylalanine hydroxylase deficiency. ACMG/AMP Criteria applied: PM3_VeryStrong, PP4_Moderate, PM5_Supporting. -
Pathogenic, criteria provided, single submitter	clinical testing	Molecular Genetics, Royal Melbourne Hospital	Nov 30, 2020	This sequence change is predicted to replace valine with isoleucine at codon 230 of the PAH protein (p.Val230Ile). The valine residue is not conserved (100 vertebrates, UCSC), and is located in the catalytic Biopterin H domain. There is a small physicochemical difference between valine and isoleucine. The variant is present in a large population cohort at a frequency of 0.05% (rs62516152, 141/282,716 alleles, 0 homozygotes in gnomAD v2.1.1). It has consistently been identified in cases with mild hyperphenylalaninemia or mild phenylketonuria in the homozygous state or compound heterozygote with a second pathogenic allele (PMID: 18299955, 21871829, 23764561, 24048906 - PM3_VeryStrong). Cases have PAH deficiency with acquired hyperphenylalaninemia ruled out (PMID: 8268925 - PP4_Moderate). The average residual mutant enzyme activity is 63% (PMID: 11161839). Multiple lines of computational evidence have conflicting predictions for the missense substitution (3/7 algorithms). Additionally, a different missense change at the same residue (p.Val230Ala), determined to be likely pathogenic has been seen previously (PM5_Supporting). Based on the classification scheme RMH ACMG Guidelines v1.1.1 and disease-specific specifications from the PAH VCEP, this variant is classified as PATHOGENIC. Following criteria are met: PM3_VeryStrong, PP4_Moderate, PM5_Supporting. -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	Jan 18, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	Jul 17, 2023	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 (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 valine to isoleucine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (v2: 141 heterozygotes, 0 homozygotes). (SP) 0600 - Variant is located in the annotated biopterin_H domain (DECIPHER). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. It has been classified as likely pathogenic by an expert panel in 2018 (ClinVar). (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	Revvity Omics, Revvity	Jun 15, 2023	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Centogene AG - the Rare Disease Company	Mar 29, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 19, 2024	This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 230 of the PAH protein (p.Val230Ile). This variant is present in population databases (rs62516152, gnomAD 0.3%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with hyperphenylalaninemia (HPA) or mild phenylketonuria (PKU) (PMID: 8268925, 10598814, 17096675, 17935162, 18299955, 23500595, 23792259, 24048906, 25087612; 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: 102784). 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 with a negative predictive value of 80%. Experimental studies have shown that this missense change affects PAH function (PMID: 11161839). 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	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Dec 26, 2019	NM_000277.1(PAH):c.688G>A(V230I) is classified as likely 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 11161839, 21147011, 17924342, 23764561, 9012412, 17096675, 21871829, 11678552, 10679941, 16198137, 10598814, 10693064, 10234516, 12655553, 24048906, 18299955, 23500595, 23792259, 8088845, 8268925 and 10679941. Classification of NM_000277.1(PAH):c.688G>A(V230I) is based on the following criteria: This variant 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	research	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	Mar 17, 2024	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Mar 17, 2022	- -

not provided Pathogenic:3 Uncertain:1 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Feb 01, 2024	PAH: PM3:Very Strong, PP4:Moderate, PS3:Moderate, PM2:Supporting -
Pathogenic, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
not provided, no classification provided	literature only	DeBelle Laboratory for Biochemical Genetics, MUHC/MCH RESEARCH INSTITUTE	-	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Sep 08, 2023	Described as responsive to tetrahydrobiopterin (BH4) therapy (Zurfluh et al., 2008); This variant is associated with the following publications: (PMID: 31998365, 23792259, 23500595, 32039316, 33101986, 32893076, 25087612, 21228398, 26990548, 11161839, 8088845, 24048906, 8268925, 31355225, 30747360, 31980526, 30275481, 33465300, 23764561, 31589614, 32668217, 32778825, z[case report], 34828281, 33564846, 31947737, 34405919, 18299955, 28182360, 35193651, 35405047, 17935162, 34426522, 36537053) -
Uncertain significance, criteria provided, single submitter	clinical testing	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	Nov 03, 2021	- -

PAH-related disorder Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 14, 2024

The PAH c.688G>A variant is predicted to result in the amino acid substitution p.Val230Ile. This variant has been documented to be causative for hyperphenylalaninemia (for example, see Guldberg et al. 1993. PubMed ID: 8268925; Aulehla-Scholz et al. 2003. PubMed ID: 12655553; Bercovich et al. 2008. PubMed ID: 18299955; Supplemental Data for Hillert et al. 2020. PubMed ID: 32668217). Moreover, this variant has been reported to reduce the activity of the PAH protein to approximately 63% of wild-type (Bercovich et al. 2008. PubMed ID: 18299955; Couce et al. 2013. PubMed ID: 23500595) and the p.Val230Ile amino acid substitution has been reported to lead to a PAH protein that is responsive to tetrahydrobiopterin (BH4) (Zurflüh et al. 2008. PubMed ID: 17935162). The ClinGen PAH Variant Curation Expert Panel classifies this variant as likely pathogenic, and other laboratories have listed it in the ClinVar database as likely pathogenic or pathogenic (https://www.ncbi.nlm.nih.gov/clinvar/variation/102784/). Based on the available evidence, we classify the c.688G>A (p.Val230Ile) variant as likely pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.087
BayesDel_addAF	Benign	-0.054	T
BayesDel_noAF	Uncertain	0.12
CADD	Benign	19
DANN	Uncertain	0.98
DEOGEN2	Uncertain	0.65	D;T
Eigen	Benign	-0.17
Eigen_PC	Benign	-0.012
FATHMM_MKL	Uncertain	0.88	D
LIST_S2	Uncertain	0.97	D;D
M_CAP	Uncertain	0.24	D
MetaRNN	Benign	0.071	T;T
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Benign	0.18	N;.
MutationTaster	Benign	1.0	D;D
PrimateAI	Uncertain	0.54	T
PROVEAN	Benign	-0.16	N;N
REVEL	Uncertain	0.51
Sift	Benign	0.24	T;T
Sift4G	Benign	0.36	T;T
Polyphen		0.090	B;.
Vest4		0.37
MVP		0.86
MPC		0.031
ClinPred		0.028	T
GERP RS		5.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.40
gMVP		0.84

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs62516152; hg19: chr12-103248932;