rs62516092

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1PM2PM5PP3_StrongPP5_Very_Strong

The NM_000277.3(PAH):c.1042C>G(p.Leu348Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00021 in 1,613,198 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. L348P) has been classified as Likely pathogenic.

Frequency

Genomes: 𝑓 0.00012 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00022 ( 0 hom. )

Consequence

PAH
NM_000277.3 missense

Scores

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:17O:1

Conservation

PhyloP100: 2.07

Variant links:

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]

PAH links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 18 ACMG points.

PM1

In a hotspot region, there are 11 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 7 uncertain in NM_000277.3

PM2

Very rare variant in population databases, with high coverage;

PM5

Other missense variant is known to change same aminoacid residue: Variant chr12-102844358-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 932253.Status of the report is reviewed_by_expert_panel, 3 stars.

PP3

MetaRNN computational evidence supports a deleterious effect, 0.957

PP5

Variant 12-102844359-G-C is Pathogenic according to our data. Variant chr12-102844359-G-C is described in ClinVar as [Pathogenic]. Clinvar id is 92727.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-102844359-G-C is described in Lovd as [Pathogenic]. Variant chr12-102844359-G-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PAH	NM_000277.3 linkuse as main transcript	c.1042C>G	p.Leu348Val	missense_variant	10/13	ENST00000553106.6
PAH	NM_001354304.2 linkuse as main transcript	c.1042C>G	p.Leu348Val	missense_variant	11/14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PAH	ENST00000553106.6 linkuse as main transcript	c.1042C>G	p.Leu348Val	missense_variant	10/13	1	NM_000277.3	P1

Frequencies

GnomAD3 genomes

AF:

0.000125

AC:

AN:

152202

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000196

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000235

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000103

AC:

AN:

251212

Hom.:

AF XY:

0.000103

AC XY:

AN XY:

135768

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000579

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000211

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000218

AC:

319

AN:

1460996

Hom.:

Cov.:

AF XY:

0.000210

AC XY:

153

AN XY:

726864

show subpopulations

Gnomad4 AFR exome

AF:

0.0000598

Gnomad4 AMR exome

AF:

0.0000447

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000274

Gnomad4 OTH exome

AF:

0.000166

GnomAD4 genome

AF:

0.000125

AC:

AN:

152202

Hom.:

Cov.:

AF XY:

0.000121

AC XY:

AN XY:

74350

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.000196

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000235

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000201

Hom.:

Bravo

AF:

0.000113

TwinsUK

AF:

0.000270

AC:

ALSPAC

AF:

0.000259

AC:

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000116

AC:

ExAC

AF:

0.0000494

AC:

EpiCase

AF:

0.000164

EpiControl

AF:

0.000296

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:17Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Phenylketonuria

Pathogenic:8

Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Oct 28, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center	May 04, 2022	PS3_Moderate, PM2, PM3_Very Strong, PP3 -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jul 24, 2018	Variant summary: PAH c.1042C>G (p.Leu348Val) results in a conservative amino acid change located in the in the catalytic domain (Sarkissian 2011) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00011 in 276972 control chromosomes (gnomAD). This frequency is not significantly higher than expected for a pathogenic variant in PAH causing Phenylalanine Hydroxylase Deficiency (Phenylketonuria) (0.00011 vs 0.0079), allowing no conclusion about variant significance. c.1042C>G has been reported in the literature in multiple individuals affected with the classic and mild form of Phenylalanine Hydroxylase Deficiency (i.e. Phenylketonuria) (e.g. Quirk 2012, Sarkissian 2011, Jeannesson-Thivisol 2015). These data indicate that the variant is very likely to be associated with disease. Publications also reported experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in 20%-40% of normal activity (see e.g. Benit 1999, Zurfluh 2008), with variable Bh4 responsivity, depending on the genotype (Sarkissian 2011, Jeannesson-Thivisol 2015). Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 26, 2024	This sequence change replaces leucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 348 of the PAH protein (p.Leu348Val). This variant is present in population databases (rs62516092, gnomAD 0.02%). This missense change has been observed in individuals with classic and mild phenylketonuria (PKU) (PMID: 1301187, 8632937, 18937047, 20082265). ClinVar contains an entry for this variant (Variation ID: 92727). 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: 10479481, 17935162, 23500595, 25596310). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Sep 03, 2021	- -
Pathogenic, no assertion criteria provided	clinical testing	Counsyl	Jan 22, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Mar 21, 2022	- -
Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -

not provided

Pathogenic:6Other:1

Pathogenic, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jan 01, 2024	PAH: PM3:Very Strong, PS3, PM2, PP4:Moderate, PP3 -
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	GeneDx	Feb 10, 2020	Functional studies report the in vitro phenylalanine hydroxylase activity associated with L348V as 25-44% of wild type (Couce et al., 2013; Zurfluh et al., 2008; Pey et al., 2007), and that the mutant enzyme showed a substantial reduction in binding affinity for BH4, but stabilization by BH4 was similar to wild type (Dobrowolski et al., 2009); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Responsiveness to BH4 therapy is not clear (Zurflh et al., 2008; Dobrowolski et al., 2009; Aldmiz-Echevarra et al., 2016).; This variant is associated with the following publications: (PMID: 25750018, 10479481, 25087612, 18937047, 25596310, 21953985, 17924342, 17935162, 23500595, 28850634, 29102225, 30037505, 30648773, 31355225, 1301187, 27121329, 31589614, 32668217) -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Jul 13, 2023	The PAH c.1042C>G (p.Leu348Val) variant has been reported in the published literature in multiple individuals affected with classical phenylketonuria or mild hyperphenylalaninemia (PMIDs: 8632937 (1996), 9012412 (1997), 18937047 (2009), 26666653 (2015), 31355225 (2019), 33375644 (2020), 34828281 (2021)). Functional studies show that this variant is destabilizing, though improvement was observed with tetrahydrobiopterin (BH4) treatment (PMID: 30648773 (2019)). The variant was also reported to have lower BH4 binding affinity (PMID: 18937047 (2009)). In addition, the variant had a PAH activity range of 8-41% of the wild-type in vitro (PMIDs: 10479481 (1999), 17935162 (2008), 25596310 (2015), 30037505 (2018)). The frequency of this variant in the general population, 0.00043 (22/50764 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is consistent with pathogenicity. Based on the available information, this variant is classified as pathogenic. -
not provided, no classification provided	literature only	DeBelle Laboratory for Biochemical Genetics, MUHC/MCH RESEARCH INSTITUTE	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	May 20, 2014	- -

PAH-related disorder

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 16, 2023

The PAH c.1042C>G variant is predicted to result in the amino acid substitution p.Leu348Val. This variant has been reported in the homozygous state or heterozygous state with a second PAH variant in individuals with hyperphenylalaninemia (e.g., Eisensmith et al. 1992. PubMed ID: 1301187; Jeannesson-Thivisol et al. 2015. PubMed ID: 26666653; Himmelreich et al. 2018. PubMed ID: 30037505, Table S3 in Hillert et al. 2020. PubMed ID: 32668217). It has been associated with mild or classic phenylketonuria (PKU) (Réblová et al. 2015. PubMed ID: 25750018; Himmelreich et al. 2018. PubMed ID: 30037505). The p.Leu348 amino acid is located in the enzyme active site crevice (Dobrowolski et al. 2009. PubMed ID: 18937047) and the p.Leu348Val substitution has been reported to moderately reduce enzyme activity (Couce et al. 2013. PubMed ID: 23500595; Himmelreich et al. 2018. PubMed ID: 30037505). The p.Leu348Val 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). This variant has been interpreted as pathogenic by multiple outside laboratories (https://www.ncbi.nlm.nih.gov/clinvar/variation/92727/). Taken together, we interpret this variant as pathogenic. -

Inborn genetic diseases

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 26, 2022

The c.1042C>G (p.L348V) alteration is located in exon 10 (coding exon 10) of the PAH gene. This alteration results from a C to G substitution at nucleotide position 1042, causing the leucine (L) at amino acid position 348 to be replaced by a valine (V). Based on data from gnomAD, the G allele has an overall frequency of 0.011% (31/282614) total alleles studied. The highest observed frequency was 0.022% (28/129064) of European (non-Finnish) alleles. This variant has been detected in the homozygous state or in conjunction with a second PAH variant in multiple individuals with phenylalanine hydroxylase (PAH) deficiency (Bik_multanowski, 2013; Rajabi, 2019; Su, 2019; Jeannesson, 2015; Quirk, 2012). This amino acid position is highly conserved in available vertebrate species. Functional studies indicate this alteration impairs phenylalanine hydroxylase activity (Dobrowolski, 2009; Danecka, 2015; Himmelreich, 2018). This 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

Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein

Jan 07, 2022

ACMG classification criteria: PM2, PM3, PP3, PP4 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.61

BayesDel_addAF

Pathogenic

0.29

BayesDel_noAF

Pathogenic

0.47

Cadd

Benign

Dann

Uncertain

1.0

DEOGEN2

Pathogenic

0.98

D;D

Eigen

Uncertain

0.41

Eigen_PC

Uncertain

0.30

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Pathogenic

0.98

D;D

M_CAP

Pathogenic

0.59

MetaRNN

Pathogenic

0.96

D;D

MetaSVM

Pathogenic

1.1

MutationAssessor

Pathogenic

3.0

M;.

MutationTaster

Benign

1.0

D;D

PrimateAI

Uncertain

0.77

PROVEAN

Uncertain

-2.7

D;D

REVEL

Pathogenic

0.87

Sift

Uncertain

0.012

D;D

Sift4G

Uncertain

0.0020

D;D

Polyphen

1.0

D;.

Vest4

0.97

MVP

0.93

MPC

0.21

ClinPred

0.69

GERP RS

0.33

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.91

gMVP

0.94

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over