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NM_000277.3(PAH):c.1223G>A (p.Arg408Gln) AND Phenylketonuria

Germline classification:
Pathogenic (12 submissions)
Last evaluated:
Aug 5, 2018
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000000643.95

Allele description [Variation Report for NM_000277.3(PAH):c.1223G>A (p.Arg408Gln)]

NM_000277.3(PAH):c.1223G>A (p.Arg408Gln)

Gene:
PAH:phenylalanine hydroxylase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12q23.2
Genomic location:
Preferred name:
NM_000277.3(PAH):c.1223G>A (p.Arg408Gln)
Other names:
NM_000277.1(PAH):c.1223G>A
HGVS:
  • NC_000012.12:g.102840492C>T
  • NG_008690.2:g.122919G>A
  • NM_000277.3:c.1223G>AMANE SELECT
  • NM_001354304.2:c.1223G>A
  • NP_000268.1:p.Arg408Gln
  • NP_001341233.1:p.Arg408Gln
  • NC_000012.11:g.103234270C>T
  • NM_000277.1:c.1223G>A
  • NM_000277.2:c.1223G>A
  • P00439:p.Arg408Gln
  • c.1223G>A (p.Arg408Gln)
Protein change:
R408Q; ARG408GLN
Links:
UniProtKB: P00439#VAR_001034; OMIM: 612349.0038; dbSNP: rs5030859
NCBI 1000 Genomes Browser:
rs5030859
Molecular consequence:
  • NM_000277.3:c.1223G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354304.2:c.1223G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Phenylketonuria (PKU)
Synonyms:
Phenylketonurias; Oligophrenia phenylpyruvica; Folling disease
Identifiers:
MONDO: MONDO:0009861; MedGen: C0031485; Orphanet: 716; OMIM: 261600

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000020793OMIM
no assertion criteria provided
Pathogenic
(Aug 1, 1992)
germlineliterature only

PubMed (2)
[See all records that cite these PMIDs]

SCV000830376Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Jan 20, 2024)
germlineclinical testing

PubMed (8)
[See all records that cite these PMIDs]

SCV000852159ClinGen PAH Variant Curation Expert Panel
reviewed by expert panel

(ClinGen PAH ACMG Specifications v1)
Pathogenic
(Aug 5, 2018)
germlinecuration

PubMed (3)
[See all records that cite these PMIDs]

Citation Link,

SCV000919913Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Pathogenic
(Jan 8, 2018)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link,

SCV001163710Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 26, 2024)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001194182Myriad Genetics, Inc.
criteria provided, single submitter

(Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2019))
Pathogenic
(Dec 19, 2019)
unknownclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Citation Link,

SCV001458998Natera, Inc.
no assertion criteria provided
Pathogenic
(Sep 16, 2020)
germlineclinical testing

SCV002016494Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jul 26, 2021)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002768000Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(May 6, 2021)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

SCV002810394Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Dec 15, 2021)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004035236Cellular and Molecular Medicine Research Institute, Urmia University of Medical Sciences
criteria provided, single submitter

(Zastrow et al. (Hum Mutat. 2018))
Pathogenic
Score: 30311390
(Sep 19, 2023)
inheritedclinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV004800860Neonatal Disease Screening Center, Medical Genetics Center, Huaihua City Maternal and Child Health Care Hospital
no assertion criteria provided

(ACMG Guidelines, 2015)
Pathogenicgermlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, curation
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
Donggermlineyes1not providednot provided1not providedclinical testing
turkishinheritedyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Diverse PAH transcripts in lymphocytes of PKU patients with putative nonsense (G272X, Y356X) and missense (P281L, R408Q) mutations.

Ellingsen S, Knappskog PM, Apold J, Eiken HG.

FEBS Lett. 1999 Sep 3;457(3):505-8.

PubMed [citation]
PMID:
10471838

Haplotype-based Noninvasive Prenatal Diagnosis of Hyperphenylalaninemia through Targeted Sequencing of Maternal Plasma.

Ye J, Chen C, Yuan Y, Han L, Wang Y, Qiu W, Zhang H, Asan, Gu X.

Sci Rep. 2018 Jan 9;8(1):161. doi: 10.1038/s41598-017-18358-y.

PubMed [citation]
PMID:
29317692
PMCID:
PMC5760544
See all PubMed Citations (19)
PMC

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Details of each submission

From OMIM, SCV000020793.66

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

In a Norwegian patient with phenylketonuria (PKU; 261600), Eiken et al. (1992) identified a novel mutation in exon 12 in association with haplotype 12 alleles, by use of SSCP analyses. A patient who was homozygous for the arg408-to-gln (R408Q) mutation exhibited a mild PKU variant. Eiken et al. (1992) mapped the district of origin of the R408Q and phe299-to-cys (F299C; 612349.0039) mutations by determining the birthplaces of the relevant grandparents. In contrast to both the overall distribution of PKU mutations and the general population density in Norway, the ancestors of these 2 mutations appeared to be restricted to the western and northern coastal districts. See 612349.0042.

In Chinese, Lin et al. (1992) found a G-to-A transition in codon 408 as the basis of phenylketonuria. The missense mutation resulted in the substitution of arginine for glutamine and accounted for about 5% of PKU chromosomes among Chinese. The mutation was in linkage disequilibrium with RFLP haplotype 4. The arg408-to-trp mutation (R408W; 612349.0002) is in the same codon.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV000830376.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (8)

Description

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 408 of the PAH protein (p.Arg408Gln). This variant is present in population databases (rs5030859, gnomAD 0.03%). This missense change has been observed in individual(s) with PAH-related disease (PMID: 1312992, 10471838, 24401910, 29317692). 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: 612). 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 with a positive predictive value of 80%. Experimental studies have shown that this missense change affects PAH function (PMID: 12655546). This variant disrupts the p.Arg408 amino acid residue in PAH. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 2014036, 12173030, 24401910). 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From ClinGen PAH Variant Curation Expert Panel, SCV000852159.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (3)

Description

PAH-specific ACMG/AMP criteria applied: PM3_Strong: In trans with R408W, IVS4-1G>A, R241C (ClinGen, P) (PMID:1312992; PMID:14722928); PP3: ; PS3: Mutant enzyme activity of 46% in BioPKU (PMID:9860305); PP4_Moderate: ~830 uml/L w/o BH4 deficiency & 823 umol/L, BH4 status unknown (PMID:9860305; PMID:1312992). 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: (PM3_Strong, PP3, PS3, PP4_Moderate).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000919913.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

Variant summary: The PAH c.1223G>A (p.Arg408Gln) variant located in the Aromatic amino acid hydroxylas, C-terminal domain (InterPro) involves the alteration of a conserved nucleotide and 4/5 in silico tools predict a damaging outcome for this variant. This variant was found in 13/277144 control chromosomes (gnomAD) at a frequency of 0.0000469, which does not exceed the estimated maximal expected allele frequency of a pathogenic PAH variant (0.0079057). Multiple publications have cited the variant in affected compound heterozygous individuals, presenting with a significant decrease in PAH activity. In support of this, there are other variants at the 408 codon that have been reported in patients with PKU (R408L, R408W), suggesting the codon is important for function. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Baylor Genetics, SCV001163710.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Myriad Genetics, Inc., SCV001194182.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

NM_000277.1(PAH):c.1223G>A(R408Q) is classified as pathogenic in the context of phenylalanine hydroxylase deficiency and can be associated with variant or non-PKU HPA. Sources cited for classification include the following: PMID 14722928, 1312992, 1355066, 1301200, and 8533759. Classification of NM_000277.1(PAH):c.1223G>A(R408Q) is based on the following criteria: This is a well-established pathogenic variant in the literature that has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Natera, Inc., SCV001458998.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Revvity Omics, Revvity, SCV002016494.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002768000.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with phenylketonuria (PKU; MIM#261600). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to glutamine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (v2: 14 heterozygotes, 0 homozygotes). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v2) (252 heterozygotes, 0 homozygotes). (I) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated catalytic domain (PMID: 30037505). (I) 0705 - The well-reported pathogenic variant, p.(Arg408Trp), affecting the same residue has previously been reported in association with phenylketonuria (ClinVar), however it is not considered a comparable variant as it has a major Grantham score, whereas this variant has a minor score, therefore cannot be used to inform pathogenicity. (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. It has been reported in multiple individuals with mild PKU, mild hyperphenylalaninemia ( MHP) and non-PKU hyperphenylalaninemia (ClinVar, PMID: 1312992). (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function. Site-directed mutagenesis studies have shown a reduction of 41% in PAH activity compared to wild-type (PMID: 30037505). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Fulgent Genetics, Fulgent Genetics, SCV002810394.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Cellular and Molecular Medicine Research Institute, Urmia University of Medical Sciences, SCV004035236.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1turkishnot providednot providednot providedclinical testing PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedyesnot providednot providednot providednot providednot providednot providednot provided

From Neonatal Disease Screening Center, Medical Genetics Center, Huaihua City Maternal and Child Health Care Hospital, SCV004800860.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Dong1not providednot providedclinical testingnot provided

Description

PS3+PM3_VS+PM5+PP1+PP3+PP4_M

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

Last Updated: Jul 7, 2024