rs148393887

chr12-102894788-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM1 PM2 BP4_Moderate

The NM_000277.3(PAH):c.299A>G(p.His100Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000571 in 1,614,066 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★★).

• Frequency:
  • Genomes: 𝑓 0.00034 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00059 (1 hom.)
• Consequence: PAH NM_000277.3 missense
• Clinical Significance: Uncertain significance reviewed by expert panel U:11
• Conservation: PhyloP100: 1.73

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 Uncertain_significance. Variant got 2 ACMG points.

• PM1: In a hotspot region, there are 9 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 6 uncertain in NM_000277.3
• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.12393728).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PAH	NM_000277.3	c.299A>G	p.His100Arg	missense_variant	3/13	ENST00000553106.6
LOC124902999	XR_007063428.1	n.863-9910T>C		intron_variant, non_coding_transcript_variant
PAH	NM_001354304.2	c.299A>G	p.His100Arg	missense_variant	4/14
PAH	XM_017019370.2	c.299A>G	p.His100Arg	missense_variant	3/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PAH	ENST00000553106.6	c.299A>G	p.His100Arg	missense_variant	3/13	1	NM_000277.3	P1

Frequencies

GnomAD3 genomes AF: 0.000342 AC: 52 AN: 152230 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000482

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000131

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0000942

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000661

Gnomad OTH AF: 0.000956

GnomAD3 exomes AF: 0.000314 AC: 79 AN: 251456 Hom.: 0 AF XY: 0.000361 AC XY: 49 AN XY: 135896

Gnomad AFR exome AF: 0.0000615

Gnomad AMR exome AF: 0.000376

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000462

Gnomad NFE exome AF: 0.000536

Gnomad OTH exome AF: 0.000489

GnomAD4 exome AF: 0.000594 AC: 869 AN: 1461836 Hom.: 1 Cov.: 31 AF XY: 0.000589 AC XY: 428 AN XY: 727224

Gnomad4 AFR exome AF: 0.000119

Gnomad4 AMR exome AF: 0.000358

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.0000562

Gnomad4 NFE exome AF: 0.000723

Gnomad4 OTH exome AF: 0.000679

GnomAD4 genome AF: 0.000342 AC: 52 AN: 152230 Hom.: 0 Cov.: 32 AF XY: 0.000255 AC XY: 19 AN XY: 74378

Gnomad4 AFR AF: 0.0000482

Gnomad4 AMR AF: 0.000131

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.0000942

Gnomad4 NFE AF: 0.000661

Gnomad4 OTH AF: 0.000956

Alfa AF: 0.000487 Hom.: 0

Bravo AF: 0.000378

TwinsUK AF: 0.000270 AC: 1

ALSPAC AF: 0.00 AC: 0

ESP6500AA AF: 0.000454 AC: 2

ESP6500EA AF: 0.000465 AC: 4

ExAC AF: 0.000247 AC: 30

EpiCase AF: 0.000981

EpiControl AF: 0.000533

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:11

Revision: reviewed by expert panel

Submissions by phenotype

Phenylketonuria Uncertain:8

Uncertain significance, no assertion criteria provided	clinical testing	Natera, Inc.	Jan 17, 2020	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Counsyl	May 12, 2017	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 2017	The PAH c.299A>G (p.His100Arg) missense variant has been reported in one individual in a compound heterozygous state with a known pathogenic intronic variant (Mallolas et al. 1999). The individual was described as having non-phenylketonuria hyperphenylalaninemia, which is included in the PAH deficiency spectrum. Control data are unavailable for the p.His100Arg variant, which is reported at a frequency of 0.00047 in the European American population of the Exome Sequencing Project. Based on the limited evidence, the p.His100Arg variant is classified as a variant of unknown significance, but suspicious for pathogenicity for phenylalanine hydroxylase deficiency. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Uncertain significance, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Oct 31, 2018	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Oct 19, 2021	- -
Uncertain significance, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The PAH c.299A>G (p.His100Arg) variant was identified in ClinVar (classified as a VUS by multiple sources) and dbSNP (rs148393887). The PAH c.299A>G (p.His100Arg) missense variant has been reported in one individual in a compound heterozygous state with a known pathogenic intronic variant (Mallolas et al. 1999). The individual was described as having non-phenylketonuria hyperphenylalaninemia, which is included in the PAH deficiency spectrum. The variant was identified in control databases in 83 of 282, 858 chromosomes (0 homozygous) at a frequency of 0.0293%, and was observed at the highest frequency in the European Non-Finnish population in 129,164 of 282, 858 chromosomes (freq: 0.0503%) (Genome Aggregation Database March 6, 2019, v2.1.1). The p. His100Arg residue is conserved in mammals and computational analyses (MUT Assesor, PolyPhen-2, SIFT, MutationTaster, Revel, FATHMM, MetaLR, DANN) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (Splice AI exome) do not predict a deleterious effect on splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.PAH is associated with autosomal recessive Phenylketonuria (PKU) and non-PKU mild hyperphenylalaninemia (Phenotype MIM number: 261600). PKU is an inborn error of metabolism resulting from a deficiency of phenylalanine hydroxylase (PAH), an enzyme that catalyzes the hydroxylation of phenylalanine to tyrosine, the rate-limiting step in phenylalanine catabolism. If undiagnosed and untreated, phenylketonuria can result in impaired postnatal cognitive development resulting from a neurotoxic effect of hyperphenylalaninemia (Zurfluh et al., 2008). -
Uncertain significance, reviewed by expert panel	curation	ClinGen PAH Variant Curation Expert Panel	Aug 10, 2018	PAH-specific ACMG/AMP criteria applied: BP4: In silico overwhelmingly predict benign. REVEL = 0.553; PP4: Detected in a patient with non PKU hyperphe (PMID:11244681); PM3: H100R detected with IVS10 (PMID:11244681). 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: (BP4, PP4, PM3). -
Uncertain significance, criteria provided, single submitter	clinical testing	Invitae	Aug 18, 2022	This sequence change replaces histidine, which is basic and polar, with arginine, which is basic and polar, at codon 100 of the PAH protein (p.His100Arg). This variant is present in population databases (rs148393887, gnomAD 0.05%). This missense change has been observed in individual(s) with hyperphenylalaninemia (PMID: 11244681). ClinVar contains an entry for this variant (Variation ID: 306914). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

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

Jan 11, 2021

Variant summary: PAH c.299A>G (p.His100Arg) results in a non-conservative amino acid change located in the ACT domain (IPR002912) of the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00031 in 251456 control chromosomes (gnomAD). This frequency is not significantly higher than expected for a pathogenic variant in PAH causing Phenylalanine Hydroxylase Deficiency (Phenylketonuria) (0.00031 vs 0.0079), allowing no conclusion about variant significance. c.299A>G has been reported in the literature in at least an individual affected with non PKU HPA (Mallolas_1999). This report however, does not provide unequivocal conclusions about association of the variant with Phenylalanine Hydroxylase Deficiency (Phenylketonuria). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Five ClinVar submitters (evaluation after 2014) including an expert panel (ClinGen PAH Variant Curation Expert Panel) cite the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance. -

Inborn genetic diseases Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 08, 2022

The c.299A>G (p.H100R) alteration is located in exon 3 (coding exon 3) of the PAH gene. This alteration results from a A to G substitution at nucleotide position 299, causing the histidine (H) at amino acid position 100 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

not provided Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

GeneDx

Jan 28, 2022

In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 25087612, 30311390, 11244681, 32668217, 10598814) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.062
BayesDel_addAF	Benign	-0.027	T
BayesDel_noAF	Uncertain	0.070
Cadd	Benign	13
Dann	Benign	0.93
DEOGEN2	Benign	0.25	T;T;T;T
Eigen	Benign	-0.40
Eigen_PC	Benign	-0.23
FATHMM_MKL	Benign	0.51	D
LIST_S2	Benign	0.77	T;T;T;T
M_CAP	Benign	0.078	D
MetaRNN	Benign	0.12	T;T;T;T
MetaSVM	Uncertain	0.043	D
MutationAssessor	Benign	0.090	N;.;.;.
MutationTaster	Benign	1.0	N;N
PrimateAI	Benign	0.43	T
PROVEAN	Benign	0.23	N;N;N;N
REVEL	Uncertain	0.55
Sift	Benign	0.44	T;T;T;T
Sift4G	Benign	0.55	T;T;T;.
Polyphen		0.0	B;.;.;.
Vest4		0.73
MVP		0.97
MPC		0.034
ClinPred		0.022	T
GERP RS		5.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.23
gMVP		0.55

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: rs148393887; hg19: chr12-103288566;