rs199475602

chr12-102855313-C-Gchr12-102855313-C-T

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1 PM2 PM5 PP3_Moderate PP5_Very_Strong

The NM_000277.3(PAH):c.529G>C(p.Val177Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000929 in 1,613,972 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. V177M) has been classified as Pathogenic.

• Frequency:
  • Genomes: 𝑓 0.000020 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0000082 (0 hom.)
• Consequence: PAH NM_000277.3 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:10 O:1
• Conservation: PhyloP100: 3.39

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 16 ACMG points.

• PM1: In a hotspot region, there are 12 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 8 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 chr12-102855313-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 102726.Status of the report is reviewed_by_expert_panel, 3 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.937
• PP5: Variant 12-102855313-C-G is Pathogenic according to our data. Variant chr12-102855313-C-G is described in ClinVar as [Pathogenic]. Clinvar id is 102727.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr12-102855313-C-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PAH	NM_000277.3	c.529G>C	p.Val177Leu	missense_variant	6/13	ENST00000553106.6
PAH	NM_001354304.2	c.529G>C	p.Val177Leu	missense_variant	7/14
PAH	XM_017019370.2	c.529G>C	p.Val177Leu	missense_variant	6/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PAH	ENST00000553106.6	c.529G>C	p.Val177Leu	missense_variant	6/13	1	NM_000277.3	P1
PAH	ENST00000549111.5	n.625G>C		non_coding_transcript_exon_variant	6/6	1
PAH	ENST00000307000.7	c.514G>C	p.Val172Leu	missense_variant	7/14	5
PAH	ENST00000551988.5	n.550G>C		non_coding_transcript_exon_variant	5/5	3

Frequencies

GnomAD3 genomes AF: 0.0000197 AC: 3 AN: 152142 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

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: 0.0000441

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000199 AC: 5 AN: 251188 Hom.: 0 AF XY: 0.0000221 AC XY: 3 AN XY: 135756

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

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: 0.0000440

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000821 AC: 12 AN: 1461830 Hom.: 0 Cov.: 34 AF XY: 0.00000963 AC XY: 7 AN XY: 727224

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

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: 0.0000108

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0000197 AC: 3 AN: 152142 Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1 AN XY: 74316

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000441

Gnomad4 OTH AF: 0.00

Bravo AF: 0.0000113

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000116 AC: 1

ExAC AF: 0.0000412 AC: 5

EpiCase AF: 0.0000545

EpiControl AF: 0.000119

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:10 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

Phenylketonuria Pathogenic:7

Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Apr 30, 2023	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Molecular Diagnostics Laboratory, M Health Fairview: University of Minnesota	Oct 25, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	May 14, 2018	Variant summary: PAH c.529G>C (p.Val177Leu) results in a conservative amino acid change located in the catalytic domain of the encoded protein sequence (Jeannesson-Thivisol 2015). 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 2.9e-05 in 276898 control chromosomes. This frequency is not higher than expected for a pathogenic variant in PAH causing Phenylalanine Hydroxylase Deficiency (Phenylketonuria) (2.9e-05 vs 0.0079), allowing no conclusion about variant significance. The variant, c.529G>C has been reported in the literature in multiple individuals affected with mild Phenylalanine Hydroxylase Deficiency (Phenylketonuria) and also found in individuals with Hyperphenylalaninemia (e.g. Djordjevic 2012, Sterl 2013, Reblova 2013, Anjema 2013, Jeannesson-Thivisol2015). These data indicate that the variant is very likely to be associated with disease. Tetrahydrobiopterin (BH4) responsiveness was reported to be inconsistent in patients, probably influenced by the other variant found in trans (Djordjevic 2012, Anjema 2013). In a recent study a compound heterozygous patient carrying this mutation with a null mutation, was found to be BH4-responsive (Jeannesson-Thivisol 2015). One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, and classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Aug 12, 2020	- -
Pathogenic, no assertion criteria provided	clinical testing	Counsyl	Oct 02, 2017	- -
Pathogenic, reviewed by expert panel	curation	ClinGen PAH Variant Curation Expert Panel	Sep 22, 2019	The c.529G>C (p.Val177Leu) variant in PAH has been reported in multiple individuals with PAH deficiency (BH4 deficiency excluded). (PP4_Moderate). This variant has an extremely low allele frequency (Pop Max MAF=0.00005 ENF) in gnomAD (PM2). This variant was detected with pathogenic variants: F39L, L48S, F39del, R408W, R261Q, F55fs, R158Q, Trp187*. Parental testing not reported. PMID: 8659548, PMID: 16879198, PMID: 19609714, PMID: 23430918, PMID: 22391997, PMID: 22513348, PMID: 26666653 (PM3_very-strong. Computational prediction tools and conservation analysis do not agree. In summary, this variant meets criteria to be classified as pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PP4_Moderate, PM3_very-strong, PM2. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 16, 2024	This sequence change replaces valine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 177 of the PAH protein (p.Val177Leu). This variant is present in population databases (rs199475602, gnomAD 0.006%). This missense change has been observed in individual(s) with PAH-related conditions (PMID: 8659548, 8807331, 22513348, 23430547, 24789341, 25087612, 26666653). ClinVar contains an entry for this variant (Variation ID: 102727). 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.Val177 amino acid residue in PAH. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 12501224, 17096675, 23430547, 23500595, 23764561, 27121329). 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. -

not provided Pathogenic:2 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Oct 01, 2019	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	May 31, 2018	The V177L variant in the PAH gene has been reported as a pathogenic variant in the PAH Consortium database. The V177L variant has previously been reported in association with mild phenylketonuria (PKU) and hyperphenylalaninemia (Eiken et al., 1996; Réblová et al.,2013; Jeannesson-Thivisol et al., 2015). Tetrahydrobiopterin (BH4) responsiveness is inconsistent in patients with V177L (Zurfluh et al., 2008; Sarkissian et al., 2012; Anjema et al., 2013). Therefore, we interpret V177L in PAH as a pathogenic variant. -
not provided, no classification provided	literature only	DeBelle Laboratory for Biochemical Genetics, MUHC/MCH RESEARCH INSTITUTE	-	- -

PAH-related disorder Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 10, 2022

The PAH c.529G>C variant is predicted to result in the amino acid substitution p.Val177Leu. This patient is also heterozygous in the PAH gene for a sequence variant designated c.529G>C, which is predicted to result in the amino acid substitution p.Val177Leu. This variant has been reported, along with a second pathogenic PAH variant, in several individuals that presented with either mild hyperphenylalaninemia (MHP) or mild phenylketonuria (mPKU) (Guldberg et al. 1996. PubMed ID: 8659548; Langenbeck et al. 2009. PubMed ID: 19609714; Feillet et al. 2014. PubMed ID: 24789341; Djordjevic et al. 2013. PubMed ID: 23430547). Different substitutions of the same codon (p.Val177Met, p.Val177Ala) have also been reported in association with phenylalanine hydroxylase deficiency (Muntau et al. 2002. PubMed ID: 12501224; Jennings et al. 2000. PubMed ID: 10980574). Internally, we have observed the c.529G>C (p.Val177Leu) variant along with a second pathogenic PAH variant in affected individuals. This variant is also documented in the PAH variant database (http://www.biopku.org/home/home.asp) and is classified as a MHP variant. Additionally, it is interpreted as pathogenic by the ClinGen PAH Variant Curation Expert Panel and as pathogenic or likely pathogenic by other outside laboratories (https://www.ncbi.nlm.nih.gov/clinvar/variation/102727/). Based on the collective evidence, this variant is interpreted as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.40
BayesDel_addAF	Pathogenic	0.24	D
BayesDel_noAF	Pathogenic	0.28
Cadd	Uncertain	24
Dann	Uncertain	0.99
DEOGEN2	Pathogenic	0.96	D;D
Eigen	Uncertain	0.42
Eigen_PC	Uncertain	0.46
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.93	D;D
M_CAP	Pathogenic	0.45	D
MetaRNN	Pathogenic	0.94	D;D
MetaSVM	Pathogenic	1.0	D
MutationAssessor	Pathogenic	3.2	M;.
MutationTaster	Benign	1.0	D;D
PrimateAI	Uncertain	0.58	T
PROVEAN	Uncertain	-2.4	N;N
REVEL	Pathogenic	0.78
Sift	Uncertain	0.0050	D;D
Sift4G	Uncertain	0.021	D;D
Polyphen		0.048	B;.
Vest4		0.88
MutPred		0.95		Loss of sheet (P = 0.1158);.;
MVP		0.97
MPC		0.045
ClinPred		0.70	D
GERP RS		4.8
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.86
gMVP		0.91

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: rs199475602; hg19: chr12-103249091;