12-102866599-C-T

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM1 PM2 PM5 PP5_Very_Strong

The NM_000277.3(PAH):c.506G>A(p.Arg169His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000201 in 1,612,298 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely pathogenic (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R169C) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: 𝑓 0.00020 (1 hom., cov: 32)
  • Exomes 𝑓: 0.00020 (0 hom.)
• Consequence: PAH NM_000277.3 missense
• Clinical Significance: Likely pathogenic reviewed by expert panel P:18 U:3 O:1
• Conservation: PhyloP100: 2.06

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]

LOC124902999 (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 14 ACMG points.

• PM1: In a hotspot region, there are 12 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 6 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 chr12-102866600-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 125436.Status of the report is reviewed_by_expert_panel, 3 stars.
• PP5: Variant 12-102866599-C-T is Pathogenic according to our data. Variant chr12-102866599-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 102706.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr12-102866599-C-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PAH	NM_000277.3	c.506G>A	p.Arg169His	missense_variant	5/13	ENST00000553106.6
LOC124902999	XR_007063428.1	n.807+1372C>T		intron_variant, non_coding_transcript_variant
PAH	NM_001354304.2	c.506G>A	p.Arg169His	missense_variant	6/14
PAH	XM_017019370.2	c.506G>A	p.Arg169His	missense_variant	5/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PAH	ENST00000553106.6	c.506G>A	p.Arg169His	missense_variant	5/13	1	NM_000277.3	P1
PAH	ENST00000549111.5	n.602G>A		non_coding_transcript_exon_variant	5/6	1
PAH	ENST00000307000.7	c.491G>A	p.Arg164His	missense_variant	6/14	5
PAH	ENST00000551988.5	n.530+10863G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.000204 AC: 31 AN: 152092 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000197

Gnomad ASJ AF: 0.00547

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000103

Gnomad OTH AF: 0.000957

GnomAD3 exomes AF: 0.000299 AC: 75 AN: 250586 Hom.: 0 AF XY: 0.000251 AC XY: 34 AN XY: 135546

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00597

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000327

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000882

Gnomad OTH exome AF: 0.000655

GnomAD4 exome AF: 0.000201 AC: 293 AN: 1460206 Hom.: 0 Cov.: 30 AF XY: 0.000198 AC XY: 144 AN XY: 726554

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00498

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000464

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000111

Gnomad4 OTH exome AF: 0.000514

GnomAD4 genome AF: 0.000204 AC: 31 AN: 152092 Hom.: 1 Cov.: 32 AF XY: 0.000162 AC XY: 12 AN XY: 74298

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.000197

Gnomad4 ASJ AF: 0.00547

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000103

Gnomad4 OTH AF: 0.000957

Alfa AF: 0.000422 Hom.: 1

Bravo AF: 0.000178

ExAC AF: 0.000255 AC: 31

Asia WGS AF: 0.000289 AC: 1 AN: 3478

EpiCase AF: 0.000273

EpiControl AF: 0.000237

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:18 Uncertain:3 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

Phenylketonuria Pathogenic:13

Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	Oct 12, 2018	A heterozygous missense variant, NM_000277.1(PAH):c.506G>A, has been identified in exon 5 of 13 of the PAH gene. The variant is predicted to result in a minor amino acid change from an arginine to a histidine at position 169 of the protein, NP_000268.1(PAH):p.(Arg169His). The arginine residue at this position has moderate conservation (100 vertebrates, UCSC), and is located within the Biopterin domain. In silico predictions of pathogenicity for this variant are conflicting (Polyphen, SIFT, CADD, Mutation Taster). The variant is present in the gnomAD database at a frequency of 0.029% (78 heterozygotes, 1 homozygote). The variant has previously been described as pathogenic or VUS in multiple patients with mild phenylalanine hydroxylase deficiency (ClinVar). Different variants in the same codon resulting in a change to proline and cysteine, p.(Arg169Pro) and p.(Arg169Cys) have been reported in patients with phenylketonuria (ClinVar). Analysis of parental samples indicated this variant was paternally inherited and to be present in cis with the second reported PAH variant. Based on the information available at the time of curation, this variant has been classified as PATHOGENIC. <br /> -
Likely pathogenic, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Jul 18, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Aug 07, 2023	- -
Likely pathogenic, reviewed by expert panel	curation	ClinGen PAH Variant Curation Expert Panel	Aug 10, 2018	PAH-specific ACMG/AMP criteria applied: PP4_Moderate: This variant has been reported in multiple mild hyperphenylalaninaemia (MHP) patients, with BH4 defects excluded. Upgraded per ClinGen Metabolic workgroup. (PMID:10234516); PM3_Strong: Detected with P281L and A403V, both pathogenic variants (PMID:10234516). 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_Strong). -
Likely pathogenic, no assertion criteria provided	clinical testing	Counsyl	Jan 11, 2019	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Jan 04, 2022	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	May 04, 2018	The PAH c.506G>A (p.Arg169His) missense variant has been reported in five studies in which it is found in a total of six patients with phenylalanine hydroxylase (PAH) deficiency including in two in a compound heterozygous state with another missense variant, two in heterozygous state with a mild form of phenylalanine hydroxylase deficiency, and two with unknown zygosity (Desviat et al. 1999; Aulehla-Scholz et al. 2003; Bercovich et al. 2008a; Bercovich et al. 2008b; Réblová et al. 2013). The p.Arg169His variant was absent from at least 200 controls and is reported at a frequency of 0.00046 in the European (non-Finnish) population of the Exome Aggregation Consortium. Based on the evidence, the p.Arg169His variant is classified as likely 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	Invitae	Jan 27, 2024	This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 169 of the PAH protein (p.Arg169His). This variant is present in population databases (rs199475679, gnomAD 0.7%), including at least one homozygous and/or hemizygous individual. This missense change has been observed in individual(s) with hyperphenylalaninemia (PMID: 10234516, 18299955, 21147011, 26666653, 28982351). ClinVar contains an entry for this variant (Variation ID: 102706). 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%. This variant disrupts the p.Arg169 amino acid residue in PAH. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 26503515, 29499199, 30050108). 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. -
Likely pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jun 30, 2022	The p.Arg169His variant in PAH has been reported in 18 individuals with phenylalanine hydroxylase deficiency including 16 compound heterozygotes and one homozygote (Desviat 1999 PMID: 10234516, Wang 2018 PMID: 29499199, Su 2019 PMID: 31355225, Hillert 2020 PMID: 32668217), many of whom presented with classical phenylketo It has also been identified 0.55% (19/3472) 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 102706). Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. Three additional variants involving this codon (p.Arg169Ser, p.Arg169Gly, and p.Arg169Cys) have been identified in individuals with phenylalanine hydroxylase deficiency and are classified as likely pathogenic or 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: PP4_Moderate, PM5, BS1_Supporting, PM3_VeryStrong. -
Pathogenic, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	Mar 23, 2024	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Nov 03, 2021	- -

not provided Pathogenic:2 Uncertain:3 Other:1

Uncertain significance, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Sep 07, 2023	Reported as likely pathogenic by the ClinGen PAH Variant Curation Expert Panel FDA Recognized Database (ClinVar SCV000852129.3; Landrum et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 29789446, 29316886, 23357515, 26982749, 21147011, 12655553, 18294361, 11385716, 19015950, 33677757, 30311390, 29499199, 31355225, 34426522, 33101986, 18299955, 17924342, 31980526, 32668217, 26666653, 10234516, 35405047, 35355500) -
Likely pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Apr 01, 2019	- -
Uncertain significance, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jan 02, 2018	- -
not provided, no classification provided	literature only	DeBelle Laboratory for Biochemical Genetics, MUHC/MCH RESEARCH INSTITUTE	-	- -

Inborn genetic diseases Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 01, 2022

The c.506G>A (p.R169H) alteration is located in exon 5 (coding exon 5) of the PAH gene. This alteration results from a G to A substitution at nucleotide position 506, causing the arginine (R) at amino acid position 169 to be replaced by a histidine (H). Based on data from gnomAD, the A allele has an overall frequency of 0.03% (77/281982) total alleles studied. The highest observed frequency was 0.59% (61/10348) of Ashkenazi Jewish alleles. This alteration has been reported in the compound heterozygous state with a second PAH alteration in multiple patients with hyperphenylalaninemia (Desviat, 1999; Dobrowolski, 2011; Jeannesson-Thivisol, 2015; Liu, 2017; Rajabi, 2019). This amino acid position is highly conserved in available vertebrate species. Based on internal structural analysis, R169H is deleterious. The variant is mildly destabilizing to the local structure. The in silico prediction for this alteration is inconclusive. Based on the available evidence, this alteration is classified as likely pathogenic. -

Pulmonary hypertension, primary, 1 Pathogenic:1

Pathogenic, criteria provided, single submitter

research

Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center

Mar 17, 2024

- -

6-Pyruvoyl-tetrahydrobiopterin synthase deficiency Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Jun 28, 2021

Variant summary: PAH c.506G>A (p.Arg169His) results in a non-conservative amino acid change located in the Aromatic amino acid hydroxylase, C-terminal domain (IPR019774) 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 0.00026 in 395274 control chromosomes in the gnomAD database (v2.1 and v3.1 datasets), including 1 homozygote. This frequency is not higher than the maximum expected for a pathogenic variant in PAH causing Hyperphenylalaninemia (0.00026 vs 0.0079), allowing no conclusion about variant significance. c.506G>A, has been reported in the literature in multiple mild hyperphenylalaninaemia (MHP) patients with another pathogenic variant on the other allele (e.g. Desviat_1999, Bercovich_2008, Jeannesson-Thivisol_2015, Liu_2017, Garbade_2019, Rajabi_2019, Ngiwsara_2021). In addition, a recent meta-analysis reported the variant in several compound heterozygous patients and in one homozygote, in association with MHP, and an allelic phenotype value of 10 (Hillert_2020). At least one publication reported experimental evidence evaluating an impact on protein function, and demonstrated that the variant had a residual activity of 52% of the wild type enzyme (Ngiwsara_2021). Nine other submitters, including one expert panel (ClinGen), have provided clinical-significance assessments for this variant in ClinVar after 2014 and classified the variant as likely pathogenic (n=6; including the expert panel), pathogenic (n=1) and VUS (n=2). Based on the evidence outlined above, the variant was classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Pathogenic	0.21	D
BayesDel_noAF	Pathogenic	0.25
Cadd	Uncertain	24
Dann	Uncertain	1.0
DEOGEN2	Pathogenic	0.98	D;D
Eigen	Uncertain	0.29
Eigen_PC	Uncertain	0.34
FATHMM_MKL	Uncertain	0.90	D
LIST_S2	Uncertain	0.97	D;D
M_CAP	Pathogenic	0.56	D
MetaRNN	Uncertain	0.54	D;D
MetaSVM	Pathogenic	1.0	D
MutationAssessor	Pathogenic	2.9	M;.
MutationTaster	Benign	1.0	D;D
PrimateAI	Uncertain	0.51	T
PROVEAN	Uncertain	-3.5	D;D
REVEL	Pathogenic	0.74
Sift	Uncertain	0.011	D;D
Sift4G	Uncertain	0.012	D;D
Polyphen		0.74	P;.
Vest4		0.79
MutPred		0.91		Loss of MoRF binding (P = 0.0185);.;
MVP		0.96
MPC		0.037
ClinPred		0.22	T
GERP RS		5.2
RBP_binding_hub_radar		0.92
RBP_regulation_power_radar		2.0
Varity_R		0.37
gMVP		0.87

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: rs199475679; hg19: chr12-103260377; COSMIC: COSV61016255;