12-102846924-G-T

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1 PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_000277.3(PAH):c.940C>A(p.Pro314Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000411 in 1,461,478 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. P314H) has been classified as Pathogenic.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000041 (0 hom.)
• Consequence: PAH NM_000277.3 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:5 O:1
• Conservation: PhyloP100: 5.49

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 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, 10 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 chr12-102846923-G-T is described in ClinVar as [Pathogenic]. Clinvar id is 102907.Status of the report is reviewed_by_expert_panel, 3 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.985
• PP5: Variant 12-102846924-G-T is Pathogenic according to our data. Variant chr12-102846924-G-T is described in ClinVar as [Pathogenic]. Clinvar id is 102904.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr12-102846924-G-T is described in Lovd as [Likely_pathogenic]. Variant chr12-102846924-G-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PAH	NM_000277.3	c.940C>A	p.Pro314Thr	missense_variant	9/13	ENST00000553106.6
PAH	NM_001354304.2	c.940C>A	p.Pro314Thr	missense_variant	10/14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PAH	ENST00000553106.6	c.940C>A	p.Pro314Thr	missense_variant	9/13	1	NM_000277.3	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000796 AC: 2 AN: 251290 Hom.: 0 AF XY: 0.00000736 AC XY: 1 AN XY: 135800

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000109

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000411 AC: 6 AN: 1461478 Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3 AN XY: 727078

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000151

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:5 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

Phenylketonuria Pathogenic:5

Pathogenic, reviewed by expert panel	curation	ClinGen PAH Variant Curation Expert Panel	Dec 30, 2023	The NM_000277.1(PAH):c.940C>A (p.Pro314Thr) variant is a missense variant in exon 9/13 of PAH. It has been found to result in 25% of wild-type PAH enzyme activity in a standard cDNA system and 19% of wild-type PAH enzyme activity in an Intinc system (PMID: 18590700) (PS3_supporting). It has been reported in at least five PKU patients, including those with BH4 deficiency excluded and in trans with Pathogenic variants (PM3_VeryStrong (4.25 points); PP4_Moderate). It has been previously reported in a Taiwanese proband in trans with p.V399V (Pathogenic in ClinVar and per ClinGen PAH VCEP) with mild hyperphenylalanemia and BH4 deficiency excluded by urinary pterins, dihydropteridine reductase activity in erythrocytes, and sequencing of the genes in the BH4 cofactor metabolism pathway (PMID: 14722928). It has also been found in trans with p.V399V (Pathogenic in ClinVar and per ClinGen PAH VCEP) in a Chinese patient with classic PKU (plasma Phe 1230 umol/L) and BH4 deficiency excluded (PMID: 28982351). It has been noted in a Chinese patient with plasma Phe 184 umol/L and BH4 deficiency excluded in trans with a deletion of exons 1-3 (unclassified) (PMID: 29499199). It has been also noted in a Chinese patient with mild hyperphenylalanemia (plasma Phe 148 umol/L) in trans with the p.S70del (Pathogenic in ClinVar and per ClinGen PAH VCEP) variant and in trans with the p.R243Q (Pathogenic in ClinVar and per ClinGen PAH VCEP) variant in a patient with classic PKU (plasma Phe 1561 umol/L); BH4 deficiency was excluded in both cases (PMID: 30459323). Another missense variant at the same site, c.941C>A (p.P314H) is classified as Pathogenic/Likely Pathogenic in ClinVar (ID 102907) (PM5). Two heterozygotes and zero homozygotes for the variant are present in gnomAD, corresponding to a global frequency of 0.00000796 and a maximum population frequency of 0.000109 (South Asian), under the 0.0002 frequency cutoff for use of PM2 (PM2_supporting). The variant is predicted damaging by multiple in-silico predictors, including REVEL (REVEL score 0.867), but tolerated by SIFT; thus, PP3 is not met. Classification: Pathogenic Supporting Criteria: PS3_supporting; PM3_VeryStrong; PM2_supporting; PP4_Moderate -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Sep 12, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jul 17, 2023	Variant summary: PAH c.940C>A (p.Pro314Thr) results in a non-conservative amino acid change located in the Eukaryotic phenylalanine-4-hydroxylase, catalytic domain (IPR041912) 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 8e-06 in 251290 control chromosomes. c.940C>A has been reported in the literature in the compound heterozygous state in multiple individuals affected with mild hyperphenylalaninemia (MHP) or Phenylalanine Hydroxylase Deficiency (Phenylketonuria) (e.g. Chien_2004, Li_2018, Chen_2018, Wang_2018). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function, suggesting reduced enzyme activity of 19-25% compared to wild-type; however, the difference is described as not significant, which does not allow convincing conclusions about the variant effect (Ho_2008). A different variant at the same amino acid position (p.P314H) has also been previously classified by our laboratory as pathogenic. The following publications have been ascertained in the context of this evaluation (PMID: 30459323, 14722928, 18590700, 30050108, 29499199). Two submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Aug 07, 2023	This missense change has been observed in individual(s) with hyperphenylalaninemia (PMID: 24401910, 28982351, 29390883). For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Pro314 amino acid residue in PAH. Other variant(s) that disrupt this residue have been observed in individuals with PAH-related conditions (PMID: 8807319, 12501224), which suggests that this may be a clinically significant amino acid residue. Experimental studies have shown that this missense change does not substantially affect PAH function (PMID: 18590700). 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. ClinVar contains an entry for this variant (Variation ID: 102904). This variant is present in population databases (rs199475650, gnomAD 0.01%). This sequence change replaces proline, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 314 of the PAH protein (p.Pro314Thr). -
Likely pathogenic, criteria provided, single submitter	clinical testing	Counsyl	Feb 08, 2018	- -

not provided Other:1

not provided, no classification provided

literature only

DeBelle Laboratory for Biochemical Genetics, MUHC/MCH RESEARCH INSTITUTE

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.28
BayesDel_addAF	Pathogenic	0.33	D
BayesDel_noAF	Pathogenic	0.46
Cadd	Pathogenic	27
Dann	Benign	0.95
DEOGEN2	Pathogenic	0.94	D;D
Eigen	Uncertain	0.55
Eigen_PC	Uncertain	0.51
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.87	D;D
M_CAP	Pathogenic	0.56	D
MetaRNN	Pathogenic	0.99	D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Benign	1.8	L;.
MutationTaster	Benign	1.0	D;D
PrimateAI	Uncertain	0.75	T
PROVEAN	Pathogenic	-5.2	D;D
REVEL	Pathogenic	0.87
Sift	Benign	0.099	T;T
Sift4G	Benign	0.10	T;T
Polyphen		1.0	D;.
Vest4		0.93
MutPred		0.89		Gain of catalytic residue at P314 (P = 0.0362);.;
MVP		0.98
MPC		0.24
ClinPred		0.83	D
GERP RS		5.4
Varity_R		0.79
gMVP		0.90

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs199475650; hg19: chr12-103240702;