rs118092776

chr12-102912801-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 4P and 16B. PM1 PM5 BP4_Strong BP6_Strong BS1 BS2

The NM_000277.3(PAH):c.158G>A(p.Arg53His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00156 in 1,608,812 control chromosomes in the GnomAD database, including 31 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R53C) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: 𝑓 0.0013 (1 hom., cov: 32)
  • Exomes 𝑓: 0.0016 (30 hom.)
• Consequence: PAH NM_000277.3 missense
• Clinical Significance: Uncertain significance reviewed by expert panel U:8 B:5 O:1
• Conservation: PhyloP100: 3.51

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 Benign. Variant got -12 ACMG points.

• PM1: In a hotspot region, there are 10 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 7 uncertain in NM_000277.3
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr12-102912802-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 102600.Status of the report is reviewed_by_expert_panel, 3 stars.
• BP4: Computational evidence support a benign effect (MetaRNN=0.01224637).
• BP6: Variant 12-102912801-C-T is Benign according to our data. Variant chr12-102912801-C-T is described in ClinVar as [Uncertain_significance]. Clinvar id is 102601.Status of the report is reviewed_by_expert_panel, 3 stars. We mark this variant Likely_benign, oryginal submissions are: {Benign=2, Uncertain_significance=7, not_provided=1, Likely_benign=1}. Variant chr12-102912801-C-T is described in Lovd as [Pathogenic]. Variant chr12-102912801-C-T is described in Lovd as [Pathogenic].
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00128 (195/152260) while in subpopulation EAS AF= 0.0201 (104/5182). AF 95% confidence interval is 0.0169. There are 1 homozygotes in gnomad4. There are 120 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAdExome at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PAH	NM_000277.3	c.158G>A	p.Arg53His	missense_variant	2/13	ENST00000553106.6
PAH	NM_001354304.2	c.158G>A	p.Arg53His	missense_variant	3/14
PAH	XM_017019370.2	c.158G>A	p.Arg53His	missense_variant	2/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PAH	ENST00000553106.6	c.158G>A	p.Arg53His	missense_variant	2/13	1	NM_000277.3	P1

Frequencies

GnomAD3 genomes AF: 0.00128 AC: 195 AN: 152142 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00203

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0200

Gnomad SAS AF: 0.00166

Gnomad FIN AF: 0.0000942

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000603

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.00168 AC: 422 AN: 251382 Hom.: 3 AF XY: 0.00164 AC XY: 223 AN XY: 135854

Gnomad AFR exome AF: 0.000185

Gnomad AMR exome AF: 0.000954

Gnomad ASJ exome AF: 0.0000992

Gnomad EAS exome AF: 0.0138

Gnomad SAS exome AF: 0.00147

Gnomad FIN exome AF: 0.0000925

Gnomad NFE exome AF: 0.000677

Gnomad OTH exome AF: 0.00130

GnomAD4 exome AF: 0.00159 AC: 2315 AN: 1456552 Hom.: 30 Cov.: 30 AF XY: 0.00154 AC XY: 1118 AN XY: 725058

Gnomad4 AFR exome AF: 0.000330

Gnomad4 AMR exome AF: 0.000850

Gnomad4 ASJ exome AF: 0.000575

Gnomad4 EAS exome AF: 0.0329

Gnomad4 SAS exome AF: 0.00133

Gnomad4 FIN exome AF: 0.000169

Gnomad4 NFE exome AF: 0.000705

Gnomad4 OTH exome AF: 0.000681

GnomAD4 genome AF: 0.00128 AC: 195 AN: 152260 Hom.: 1 Cov.: 32 AF XY: 0.00161 AC XY: 120 AN XY: 74448

Gnomad4 AFR AF: 0.000241

Gnomad4 AMR AF: 0.00203

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0201

Gnomad4 SAS AF: 0.00166

Gnomad4 FIN AF: 0.0000942

Gnomad4 NFE AF: 0.000603

Gnomad4 OTH AF: 0.00

Alfa AF: 0.00143 Hom.: 3

Bravo AF: 0.00150

TwinsUK AF: 0.000809 AC: 3

ALSPAC AF: 0.00208 AC: 8

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000930 AC: 8

ExAC AF: 0.00175 AC: 212

Asia WGS AF: 0.00549 AC: 19 AN: 3478

EpiCase AF: 0.000545

EpiControl AF: 0.000830

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:8 Benign:5 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

Phenylketonuria Uncertain:6 Benign:4

Uncertain significance, no assertion criteria provided	clinical testing	Neonatal Disease Screening Center, Medical Genetics Center, Huaihua City Maternal and Child Health Care Hospital	-	PM3_VS+PP3+PP4+BS1 -
Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 29, 2024	- -
Likely benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 2017	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Benign, no assertion criteria provided	clinical testing	Natera, Inc.	Jan 06, 2020	- -
Uncertain significance, reviewed by expert panel	curation	ClinGen PAH Variant Curation Expert Panel	Aug 10, 2018	PAH-specific ACMG/AMP criteria applied: BS1: MAF=0.01596 in ExAC (138/8648) and 0.0104 in gnomAD (265/18868 with 3 homozygotes); PP4: Detected in a patient with mild hyperphe (PMID:24401910); PM3: Detected with V388L (LP) (PMID:24401910). In summary this variant meets criteria to be classified as uncertain significance for phenylketonuria in an autosomal recessive manner based on the ACMG/AMP criteria applied as specified by the PAH Expert Panel: (BS1, PP4, PM3). -
Uncertain significance, criteria provided, single submitter	reference population	Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center	Mar 18, 2016	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	May 18, 2021	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Nov 08, 2022	- -
Likely benign, no assertion criteria provided	curation	SingHealth Duke-NUS Institute of Precision Medicine	Jun 07, 2017	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -

not provided Uncertain:1 Other:1

Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Apr 30, 2020	Reported primarily in association with a mild hyperphenylalaninemia (HPA) phenotype (Dateki et al., 2016; Polak et al., 2013; Tao et al., 2015; Zhu et al., 2013); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 30747360, 17924342, 25087612, 27264808, 26666653, 28676969, 20981092, 24082139, 26521805, 27173423, 23764561, 26322415, 9452061, 17935162, 23932990, 29653233, 29499199, 29032371, 30512147, 30459323, 28982351, 29454221, 30050108, 29390883, 29353259, 24401910, 30945278, 31355225, 30275481, 32668217) -
not provided, no classification provided	literature only	DeBelle Laboratory for Biochemical Genetics, MUHC/MCH RESEARCH INSTITUTE	-	- -

PAH-related condition Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Mar 03, 2023

The PAH c.158G>A variant is predicted to result in the amino acid substitution p.Arg53His. This variant has been documented as a common PAH variant in the Chinese population, and has been associated with mild hyperphenylalanemia (mHPA) (Park et al. 1998. PubMed ID: 9452061; Song et al. 2005. PubMed ID: 16256386; Liang et al. 2014 PubMed ID: 24401910; Lin et al. 2019. PubMed ID: 30904546). In a recent study of individuals identified by newborn genetic screening, 16 patients were identified with mildly elevated phenylalanine and the c.158G>A (p.Arg53His) variant on the opposite allele (in trans) from a pathogenic or likely pathogenic PAH variant (Huang et al. 2022. PubMed ID: 35193651). It should be noted that this particular variant has been reported to have an allele frequency of >1% in eastern Asian populations, including 3 homozygous individuals (http://gnomad.broadinstitute.org/variant/12-103306579-C-T) and has been suggested to be a likely benign variant based on higher allele frequencies in East Asian populations (Choi et al. 2017. PubMed ID: 29032371). While these higher allele frequencies would normally be considered too common for a recessive, pathogenic variant, the p.Arg53His amino acid change has been shown to only decrease the activity of the PAH protein to ~80% of wild-type (Liang et al. 2014. PubMed ID: 24401910). Such a modest effect on protein activity and the mild clinical phenotype associated with this variant may be consistent with this somewhat high allele frequency, and it is possible this variant may be causative for MHPA but is less likely to be causative for mild to classic phenylketonuria. This variant is currently interpreted as benign, likely benign, or uncertain in the ClinVar database, with the PAH Variant Curation Expert Panel interpreting it as uncertain (https://www.ncbi.nlm.nih.gov/clinvar/variation/102601/). Based on the collective evidence, we also interpret the clinical significance of this variant as uncertain. -

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

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

Feb 24, 2022

Variant summary: PAH c.158G>A (p.Arg53His) results in a non-conservative amino acid change located in the ACT domain (IPR002912) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0017 in 251382 control chromosomes (gnomAD), predominantly at a frequency of 0.014 within the East Asian subpopulation in the gnomAD database, including 3 homozygotes. Ten homozygotes for c.158G>A have also been reported in individuals from the general Japanese population (Yamaguchi-Kabata_2019). The observed variant frequency within East Asian control individuals in the gnomAD database is approximately 1.8 fold of the estimated maximal expected allele frequency for a pathogenic variant in PAH causing Phenylalanine Hydroxylase Deficiency (Phenylketonuria) phenotype (0.0079), strongly suggesting that the variant is a benign polymorphism found primarily in populations of East Asian origin. c.158G>A has been reported in the literature in (mostly East Asian) individuals affected with Phenylalanine Hydroxylase Deficiency (Phenylketonuria) and hyperphenylalaninemia (HPA) without strong evidence for causality (e.g. Park_1998, Liang_2014, Tao_2015, Zong_2018, Kuznetkova_2019, Lin_2019, Su_2019), with one report showing no clinical symptoms or signs of disease in 6 compound heterozygous patients identified during newborn screening and 1 homozygous parent, all of whom had blood Phe within the normal range while on a normal diet (e.g. Choi_2017). In multiple patients, the variant was reported in cis with another variant cited as pathogenic in ClinVar (e.g. Tao_2015, Odagiri_2021). In addition, the variant has been reported to co-occur with other pathogenic variants in PAH in individuals with PKU or HPA who were genotyped as either homozygotes or compound heterozygotes for other pathogenic variants that would be likely to explain the phenotype (e.g. Su_2019, Odagiri_2021). At least one publication reports experimental evidence evaluating an impact on protein function, where the variant protein had 79% enzymatic activity relative to the wild type control (Liang_2014). Nine ClinVar submitters have assessed the variant since 2014: five have classified the variant as of uncertain significance, two as likely benign, and two as benign. Based on the evidence outlined above, the variant was classified as benign. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.041	T
BayesDel_noAF	Pathogenic	0.21
Cadd	Uncertain	23
Dann	Uncertain	1.0
DEOGEN2	Pathogenic	0.87	D;D;D;D
Eigen	Uncertain	0.51
Eigen_PC	Uncertain	0.54
FATHMM_MKL	Uncertain	0.90	D
LIST_S2	Benign	0.78	T;T;T;T
MetaRNN	Benign	0.012	T;T;T;T
MetaSVM	Uncertain	0.74	D
MutationAssessor	Uncertain	2.2	M;.;.;.
MutationTaster	Benign	1.0	D;D
PrimateAI	Benign	0.46	T
PROVEAN	Benign	-2.2	N;N;D;D
REVEL	Pathogenic	0.79
Sift	Uncertain	0.0070	D;D;T;T
Sift4G	Uncertain	0.0060	D;D;D;.
Polyphen		0.88	P;.;.;.
Vest4		0.55
MVP		0.99
MPC		0.035
ClinPred		0.086	T
GERP RS		5.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.53
gMVP		0.73

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: rs118092776; hg19: chr12-103306579; COSMIC: COSV61020094; COSMIC: COSV61020094;