rs62517167

chr12-102894794-A-G

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.293T>C(p.Leu98Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000929 in 1,614,014 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 Likely pathogenic (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L98V) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0000096 (0 hom.)
• Consequence: PAH NM_000277.3 missense
• Clinical Significance: Likely pathogenic reviewed by expert panel P:6 U:3 O:1
• Conservation: PhyloP100: 8.30

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 18 ACMG points.

• PM1: In a hotspot region, there are 8 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 7 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 chr12-102894795-A-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 805817.Status of the report is reviewed_by_expert_panel, 3 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.979
• PP5: Variant 12-102894794-A-G is Pathogenic according to our data. Variant chr12-102894794-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 627.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr12-102894794-A-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PAH	NM_000277.3	c.293T>C	p.Leu98Ser	missense_variant	3/13	ENST00000553106.6
LOC124902999	XR_007063428.1	n.863-9904A>G		intron_variant, non_coding_transcript_variant
PAH	NM_001354304.2	c.293T>C	p.Leu98Ser	missense_variant	4/14
PAH	XM_017019370.2	c.293T>C	p.Leu98Ser	missense_variant	3/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PAH	ENST00000553106.6	c.293T>C	p.Leu98Ser	missense_variant	3/13	1	NM_000277.3	P1

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152168 Hom.: 0 Cov.: 32

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: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000159 AC: 4 AN: 251448 Hom.: 0 AF XY: 0.0000221 AC XY: 3 AN XY: 135896

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: 0.000131

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000958 AC: 14 AN: 1461846 Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9 AN XY: 727216

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: 0.000162

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152168 Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1 AN XY: 74346

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ExAC AF: 0.00000824 AC: 1

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:6 Uncertain:3 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

Phenylketonuria Pathogenic:4 Uncertain:1

Likely pathogenic, reviewed by expert panel	curation	ClinGen PAH Variant Curation Expert Panel	Jan 14, 2022	The c.293T>C (p.Leu98Ser) variant in PAH has been reported as homozygous in a Pakistani patient with mild PKU (BH4 deficiency excluded) (PMID: 8364546, 9634518, 26542770) This variant has an extremely low frequency in gnomAD v2.1.1 (MAF=0.0001307). A deleterious effect is predicted in SIFT, Polyphen-2, MutationTaster, and REVEL=0.846. In summary, this variant meets criteria to be classified as likely pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PP4_Moderate, PM2, PM3_supporting, PP3. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jun 30, 2021	For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Leu98 amino acid residue in PAH. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 26322415). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. 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 expected to disrupt PAH protein function. This variant has been observed in individual(s) with hyperphenylalaninemia (PMID: 26542770). ClinVar contains an entry for this variant (Variation ID: 627). This sequence change replaces leucine with serine at codon 98 of the PAH protein (p.Leu98Ser). The leucine residue is highly conserved and there is a large physicochemical difference between leucine and serine. This variant is present in population databases (rs62517167, ExAC 0.006%). -
Likely pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Feb 06, 2023	The p.Leu98Ser variant in PAH has been reported in at least 4 individuals with phenylalanine hydroxylase deficiency (mild non-PKU hyperphenylalaninemia, mild PKU) who were either homozygous or compound heterozygous with another pathogenic variant (Guldberg 1993 PMID: 8364546, Bayat 2016 PMID: 26542770, Hillert 2020 PMID: 32668217). It has also been identified in 0.02% (1/4822) of South Asian chromosomes by gnomAD (http://gnomad.broadinstitute.org). This variant has been reported 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 ClinVar database (Variation ID 627). Computational prediction tools and conservation analyses suggest the variant may impact the protein this codon (p.Leu98Val) have been identified in individuals with phenylalanine hydroxylase deficiency and is classified as pathogenic by the ClinGen PAH Variant Curation Expert Panel. In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely pathogenic autosomal recessive phenylalanine hydroxylase deficiency. ACMG/AMP Criteria applied: PM3, PM2_Supporting, PP3, PP4_Moderate, PM5. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Mar 11, 2023	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Counsyl	Jul 27, 2017	- -

not provided Pathogenic:1 Other:1

not provided, no classification provided	literature only	DeBelle Laboratory for Biochemical Genetics, MUHC/MCH RESEARCH INSTITUTE	-	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Sep 10, 2020	Not observed at a significant frequency in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 26542770, 8364546, 9634518, 10527663) -

Mild non-PKU hyperphenylalanemia Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jul 01, 1993

- -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

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

Jul 18, 2023

Variant summary: PAH c.293T>C (p.Leu98Ser) 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 1.6e-05 in 251448 control chromosomes (gnomAD). c.293T>C has been reported in the literature in the homozygous state in an individual affected with Hyperphenylalaninemia who has subsequently been cited by others (Guldberg_1993, Bayat_2016, Hillert_2020). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. However, another variant affecting the same amino acid (L98V) has been observed in at least one affected individual and has been classified as likely pathogenic, suggesting Leu98 may be important for protein function. The following publications have been ascertained in the context of this evaluation (PMID: 26542770, 8364546, 32668217). Four submitters, including the ClinGen PAH Variant Curation Expert Panel, have cited clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as pathogenic (n=1)/likely pathogenic (n=2) and VUS (n=1). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic until further clinical and/or functional information becomes available. -

PAH-related condition Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 13, 2024

The PAH c.293T>C variant is predicted to result in the amino acid substitution p.Leu98Ser. This variant has been reported in the homozygous state in at least one patient with hyperphenylalaninemia (Guldberg et al. 1993. PubMed ID: 8364546; Bayat et al. 2016. PubMed ID: 26542770; Table S3, Hillert et al. 2020. PubMed ID: 32668217). It has also been listed in an unclassified variant in a large study of patients with hyperphenylalaninemia, although no additional evidence that could help determine the pathogenicity of this variant was provided (Guldberg et al. 1998. PubMed ID: 9634518). A different substitution of the same amino acid (p.Leu98Val) has been reported, in the compound heterozygous state with the common p.Arg408Trp pathogenic variant, in a patient with mild phenylketonuria (Tao et al. 2015. PubMed ID: 26322415). Although we suspect that the c.293T>C (p.Leu98Ser) variant could possibly be pathogenic, at this time its clinical significance is uncertain due to the absence of conclusive functional and genetic evidence. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.97
BayesDel_addAF	Pathogenic	0.39	D
BayesDel_noAF	Pathogenic	0.58
Cadd	Pathogenic	27
Dann	Uncertain	1.0
DEOGEN2	Uncertain	0.66	D;T;T;T
Eigen	Pathogenic	0.89
Eigen_PC	Pathogenic	0.86
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Benign	0.86	D;D;D;D
M_CAP	Pathogenic	0.65	D
MetaRNN	Pathogenic	0.98	D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.7	H;.;.;.
MutationTaster	Benign	1.0	A;A
PrimateAI	Uncertain	0.68	T
PROVEAN	Benign	-1.6	N;N;N;N
REVEL	Pathogenic	0.85
Sift	Benign	0.047	D;D;D;D
Sift4G	Uncertain	0.032	D;D;T;.
Polyphen		1.0	D;.;.;.
Vest4		0.94
MutPred		0.89		Loss of stability (P = 0.0088);.;Loss of stability (P = 0.0088);Loss of stability (P = 0.0088);
MVP		0.99
MPC		0.25
ClinPred		0.90	D
GERP RS		6.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.86
gMVP		0.94

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: rs62517167; hg19: chr12-103288572;