chr12-102855309-T-C

Position:

• chr12-102855309-T-C

Variant summary

Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PS3 PM3_Strong PP4_Moderate PM2 PP3

This summary comes from the ClinGen Evidence Repository: PAH-specific ACMG/AMP criteria applied: PM2: Absent from 1000G, ESP. ExAC MAF=0.00017; PP3: Deleterious effect predicted in SIFT, Polyphen2, MutationTaster. REVEL=0.841; PS3: 39% residual phenylalanine hydroxylase activity (PMID:17935162); PP4_Moderate: Detected in 6 PKU patients. BH4 deficiency excluded. Upgraded per ClinGen PAHEP. (PMID:18294361; PMID:9634518); PM3_Strong: In trans with 3 pathogenic variants (PMID:18294361). In summary this variant meets criteria to be classified as pathogenic for phenylketonuria in an autosomal recessive manner based on the ACMG/AMP criteria applied as specified by the PAH Expert Panel: (PM2, PP3, PS3, PP4_Moderate, PM3_Strong). LINK:https://erepo.genome.network/evrepo/ui/classification/CA273110/MONDO:0009861/006

• Frequency:
  • Genomes: 𝑓 0.000092 (0 hom., cov: 33)
  • Exomes 𝑓: 0.000034 (0 hom.)
• Consequence: PAH ENST00000553106.6 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:15 O:1
• Conservation: PhyloP100: 5.25

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 13 ACMG points.

• PS3: For more information check the summary or visit ClinGen Evidence Repository.
• PM2: For more information check the summary or visit ClinGen Evidence Repository.
• PM3: For more information check the summary or visit ClinGen Evidence Repository.
• PP3: For more information check the summary or visit ClinGen Evidence Repository.
• PP4: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PAH	NM_000277.3	c.533A>G	p.Glu178Gly	missense_variant	6/13	ENST00000553106.6	NP_000268.1
PAH	NM_001354304.2	c.533A>G	p.Glu178Gly	missense_variant	7/14		NP_001341233.1
PAH	XM_017019370.2	c.533A>G	p.Glu178Gly	missense_variant	6/7		XP_016874859.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PAH	ENST00000553106.6	c.533A>G	p.Glu178Gly	missense_variant	6/13	1	NM_000277.3	ENSP00000448059	P1
PAH	ENST00000549111.5	n.629A>G		non_coding_transcript_exon_variant	6/6	1
PAH	ENST00000307000.7	c.518A>G	p.Glu173Gly	missense_variant	7/14	5		ENSP00000303500
PAH	ENST00000551988.5	n.554A>G		non_coding_transcript_exon_variant	5/5	3

Frequencies

GnomAD3 genomes AF: 0.0000920 AC: 14 AN: 152148 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000724

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: 0.000162

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000716 AC: 18 AN: 251232 Hom.: 0 AF XY: 0.0000663 AC XY: 9 AN XY: 135778

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000868

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: 0.000123

Gnomad OTH exome AF: 0.000163

GnomAD4 exome AF: 0.0000342 AC: 50 AN: 1461844 Hom.: 0 Cov.: 34 AF XY: 0.0000316 AC XY: 23 AN XY: 727226

Gnomad4 AFR exome AF: 0.0000299

Gnomad4 AMR exome AF: 0.0000671

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: 0.0000387

Gnomad4 OTH exome AF: 0.0000497

GnomAD4 genome AF: 0.0000920 AC: 14 AN: 152148 Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5 AN XY: 74322

Gnomad4 AFR AF: 0.0000724

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: 0.000162

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000121 Hom.: 0

Bravo AF: 0.0000378

ExAC AF: 0.0000494 AC: 6

EpiCase AF: 0.00

EpiControl AF: 0.000237

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:15 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

Phenylketonuria Pathogenic:7

Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Mar 26, 2024	- -
Pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Nov 08, 2021	- -
Pathogenic, no assertion criteria provided	clinical testing	Counsyl	Jan 22, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Dec 04, 2017	Variant summary: The PAH c.533A>G (p.Glu178Gly) variant involves the alteration of a conserved nucleotide. 4/5 in silico tools predict a damaging outcome for this variant. In vitro functional studies reported that the variant protein has a 2040% residual activity when in hemizygous/homozygous form (Benit 1999, Shen 2016), however when it was co-expressed e.g. with the variant Q232E (that had 41% activity in homozygous form), the overall phenylalanine hydroxylase activity was 55%, demonstrating a positive interallelic complementation effect (Shen 2016). This variant was found in 22/276946 control chromosomes at a frequency of 0.0000794, which does not exceed the estimated maximal expected allele frequency of a pathogenic PAH variant (0.0079057). The variant has been reported in the literature with a range of phenotypes depending on the genetic background, i.e. several individuals presenting with mild hyperphenylalaninemia were described (Benit 1999, Rivera 2011, Reblova 2013, Aldamiz-Echevarria 2016), but the variant was also found in numerous patients with mild, moderate or classic PKU phenotype (Bercovich 2008, Reblova 2013). At least two studies reported the variant of interest as a tetrahydrobiopterin (BH4)-responsive (Zurfluh 2008, Rivera 2011), suggesting that this variant represent a mild mutation. In general, patients with mild hyperphenylalaninemia do not require restrictive diet or supplementary treatment unless Phe concentrations reach the clinical threshold. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 03, 2024	This sequence change replaces glutamic acid, which is acidic and polar, with glycine, which is neutral and non-polar, at codon 178 of the PAH protein (p.Glu178Gly). This variant is present in population databases (rs77958223, gnomAD 0.02%). This missense change has been observed in individual(s) with hyperphenylalaninemia and phenylketonuria (PMID: 7707686, 8632937, 10479481, 16198137, 18299955, 19948162, 22330942, 22513348, 23357515). 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: 92746). 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: 10479481, 26803807). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, reviewed by expert panel	curation	ClinGen PAH Variant Curation Expert Panel	Aug 10, 2018	PAH-specific ACMG/AMP criteria applied: PM2: Absent from 1000G, ESP. ExAC MAF=0.00017; PP3: Deleterious effect predicted in SIFT, Polyphen2, MutationTaster. REVEL=0.841; PS3: 39% residual phenylalanine hydroxylase activity (PMID:17935162); PP4_Moderate: Detected in 6 PKU patients. BH4 deficiency excluded. Upgraded per ClinGen PAHEP. (PMID:18294361; PMID:9634518); PM3_Strong: In trans with 3 pathogenic variants (PMID:18294361). In summary this variant meets criteria to be classified as pathogenic for phenylketonuria in an autosomal recessive manner based on the ACMG/AMP criteria applied as specified by the PAH Expert Panel: (PM2, PP3, PS3, PP4_Moderate, PM3_Strong). -

not provided Pathogenic:6 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	May 17, 2017	- -
Pathogenic, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
not provided, no classification provided	literature only	DeBelle Laboratory for Biochemical Genetics, MUHC/MCH RESEARCH INSTITUTE	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	AiLife Diagnostics, AiLife Diagnostics	Jan 25, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Mar 01, 2023	PAH: PM3:Very Strong, PM2, PP1:Moderate, PP4:Moderate, PS3:Moderate -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Sep 03, 2021	PP3, PP4_moderate, PM2, PM3_strong, PS3 -

PAH-related disorder Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Apr 11, 2024

The PAH c.533A>G variant is predicted to result in the amino acid substitution p.Glu178Gly. This is one of the most common pathogenic PAH variants in the Chinese population, and in the homozygous state this variant has been associated with classical phenylketonuria (e.g., Lee et al. 2004. PubMed ID: 15503242; Song et al. 2005. PubMed ID: 16256386; Liang et al. 2014. PubMed ID: 24401910). It has also been observed in studies of non-Chinese patients with phenylalanine hydroxylase deficiency (e.g., Couce et al. 2013. PubMed ID: 23500595). In functional studies, the p.Arg243Gln substitution has been reported to reduce enzyme activity to ~10-20% of control (Shi et al. 2012. PubMed ID: 21953985; Couce et al. 2013. PubMed ID: 23500595; Liang et al. 2014. PubMed ID: 24401910). This variant is classified as pathogenic in the ClinVar database by multiple outside laboratories (https://www.ncbi.nlm.nih.gov/clinvar/variation/591/). Taken together, we classify this variant as pathogenic. -

Inborn genetic diseases Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 29, 2020

The alteration results in an amino acid change:_x000D_ _x000D_ The c.533A>G (p.E178G) alteration is located in coding exon 6 of the PAH gene. This alteration results from an A to G substitution at nucleotide position 533, causing the glutamic acid (E) at amino acid position 178 to be replaced by a glycine (G). The alteration is rare in population databases:_x000D_ _x000D_ Based on data from the Genome Aggregation Database (gnomAD) database, the PAH c.533A>G alteration was observed in 0.008% (24/282,622) of total alleles studied, with a frequency of 0.01% (19/129,000) in the European (non-Finnish) subpopulation. The alteration has been observed in affected individuals:_x000D_ _x000D_ This alteration has been reported in trans with another mutation in PAH in multiple unrelated patients with phenylalanine hydroxylase (PAH) deficiency (Popescu, 1998; Effat, 1999). The altered amino acid is conserved throughout evolution:_x000D_ _x000D_ The p.E178 amino acid is conserved in available mammalian species. Functional analysis reveals a damaging effect of the amino acid alteration: _x000D_ _x000D_ In vitro expression of the E178G allele showed a decrease of PAH activity to 20-40% compared to wild-type (Bénit,1999; Zurflüh, 2008; Shen, 2016). The alteration is predicted inconclusive by in silico modeling:_x000D_ _x000D_ The in silico prediction for the p.E178G alteration is inconclusive. Based on the available evidence, this alteration is classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Uncertain	0.16	D
BayesDel_noAF	Pathogenic	0.30
CADD	Pathogenic	29
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.98	D;D
Eigen	Uncertain	0.56
Eigen_PC	Uncertain	0.58
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Uncertain	0.96	D;D
M_CAP	Pathogenic	0.72	D
MetaRNN	Pathogenic	0.98	D;D
MetaSVM	Pathogenic	1.0	D
MutationAssessor	Pathogenic	3.2	M;.
MutationTaster	Benign	1.0	D;D
PrimateAI	Benign	0.38	T
PROVEAN	Pathogenic	-4.5	D;D
REVEL	Pathogenic	0.84
Sift	Uncertain	0.019	D;D
Sift4G	Uncertain	0.0070	D;D
Polyphen		0.64	P;.
Vest4		0.58
MutPred		0.88		Loss of catalytic residue at E178 (P = 0.0599);.;
MVP		0.98
MPC		0.073
ClinPred		0.64	D
GERP RS		5.7
Varity_R		0.68
gMVP		0.86

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs77958223; hg19: chr12-103249087;