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NM_000277.3(PAH):c.814G>T (p.Gly272Ter) AND Phenylketonuria

Germline classification:
Pathogenic (10 submissions)
Last evaluated:
Aug 10, 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:
RCV000000627.96

Allele description [Variation Report for NM_000277.3(PAH):c.814G>T (p.Gly272Ter)]

NM_000277.3(PAH):c.814G>T (p.Gly272Ter)

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.814G>T (p.Gly272Ter)
Other names:
p.G272*:GGA>TGA; NM_000277.1(PAH):c.814G>T; p.Gly272*
HGVS:
  • NC_000012.12:g.102852843C>A
  • NG_008690.2:g.110568G>T
  • NM_000277.3:c.814G>TMANE SELECT
  • NM_001354304.2:c.814G>T
  • NP_000268.1:p.Gly272Ter
  • NP_001341233.1:p.Gly272Ter
  • NC_000012.11:g.103246621C>A
  • NM_000277.1:c.814G>T
  • NM_000277.2:c.814G>T
  • c.814G>T (p.Gly272*)
Protein change:
G272*; GLY272TER
Links:
OMIM: 612349.0020; dbSNP: rs62514952
NCBI 1000 Genomes Browser:
rs62514952
Molecular consequence:
  • NM_000277.3:c.814G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354304.2:c.814G>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV000020777OMIM
no assertion criteria provided
Pathogenic
(Sep 1, 1993)
germlineliterature only

PubMed (4)
[See all records that cite these PMIDs]

SCV000754076Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Dec 25, 2023)
germlineclinical testing

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

SCV000852120ClinGen PAH Variant Curation Expert Panel
reviewed by expert panel

(ClinGen PAH ACMG Specifications v1)
Pathogenic
(Aug 10, 2018)
germlinecuration

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

Citation Link,

SCV000919920Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Pathogenic
(Aug 31, 2018)
germlineclinical testing

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

Citation Link,

SCV001194050Myriad Genetics, Inc.
criteria provided, single submitter

(Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2019))
Pathogenic
(Dec 9, 2019)
unknownclinical testing

PubMed (6)
[See all records that cite these PMIDs]

Citation Link,

SCV001251473UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill - NSIGHT-NC NEXUS
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicgermlineresearch

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

SCV001453102Natera, Inc.
no assertion criteria provided
Pathogenic
(Sep 16, 2020)
germlineclinical testing

SCV002016483Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jan 28, 2021)
germlineclinical testing

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

SCV004209581Baylor Genetics
criteria provided, single submitter

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

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

SCV005051911Laboratory of Medical Genetics, National & Kapodistrian University of Athens
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Feb 1, 2024)
germlinecuration

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineyes1not providednot providednot providednot providedresearch
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, curation
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenonot providednot providednot providednot providednot providedcuration

Citations

PubMed

A European multicenter study of phenylalanine hydroxylase deficiency: classification of 105 mutations and a general system for genotype-based prediction of metabolic phenotype.

Guldberg P, Rey F, Zschocke J, Romano V, François B, Michiels L, Ullrich K, Hoffmann GF, Burgard P, Schmidt H, Meli C, Riva E, Dianzani I, Ponzone A, Rey J, Güttler F.

Am J Hum Genet. 1998 Jul;63(1):71-9. Erratum in: Am J Hum Genet 1998 Oct;63(4):1252-3.

PubMed [citation]
PMID:
9634518
PMCID:
PMC1377241
See all PubMed Citations (14)

Details of each submission

From OMIM, SCV000020777.67

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (4)

Description

In a patient with classic phenylketonuria (PKU; 261600), Svensson et al. (1990) identified compound heterozygosity for a G-to-T transversion in the PAH gene, resulting in a gly272-to-ter (G272X) substitution, and a deletion of CTT leucine codon 364 (612349.0021).

In 47 Norwegian nuclear families with at least 1 child with PKU, Apold et al. (1990) found haplotype 7, which is relatively rare in other populations, in 20% of all mutant haplotypes. In 14 of the 17 mutant haplotypes 7, a deletion of the BamHI restriction site in exon 7 of the PAH gene was found. The abrogation of the site was shown to be due to a G-to-T transversion, changing glycine-272 to a stop codon in exon 7. The families with this mutation were clustered along the southeastern coast of Norway, suggesting a founder effect. Melle et al. (1991) found the same mutation on the background of RFLP haplotype 7 in patients from northeastern France or Belgium.

Apold et al. (1993) compiled data on the frequency of the G272X mutation in European populations. The mutation occurs north of the Alps and has a particularly high frequency in the Oslo Fjord region of Norway with the adjacent Bohuslan region of Sweden. An intermediate frequency was noted in the eastern part of Germany with the adjacent western part of Czechoslovakia. Genealogic studies revealed no common source for this mutation, but there was some geographic convergence to the Bohuslan region. The findings suggested a single origin for this mutation, with at least one founding population in southeastern Norway/adjacent Sweden.

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000754076.8

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

Description

This sequence change creates a premature translational stop signal (p.Gly272*) in the PAH gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PAH are known to be pathogenic (PMID: 1301187, 9634518). This variant is present in population databases (rs62514952, gnomAD 0.009%). This premature translational stop signal has been observed in individual(s) with PKU (PMID: 1975559, 10471838). ClinVar contains an entry for this variant (Variation ID: 596). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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, SCV000852120.4

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

Description

PAH-specific ACMG/AMP criteria applied: PM2: Absent from 1000G, ESP. Extrememly low frequency in ExAC, gnomAD (MAF= 0.00006, 0.0003093); PVS1: Nonsense variant. Predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay.; PP4: G272X found on one allele of a patient with classic PKU (PMID:1975559). 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, PVS1, PP4).

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

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000919920.1

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

Description

Variant summary: PAH c.814G>T (p.Gly272X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant allele was found at a frequency of 5.1e-05 in 277088 control chromosomes (gnomAD). This frequency is not higher than expected for a pathogenic variant in PAH causing Phenylalanine Hydroxylase Deficiency (Phenylketonuria) (5.1e-05 vs 0.0079), allowing no conclusion about variant significance. c.814G>T has been reported in the literature in multiple individuals affected with Phenylalanine Hydroxylase Deficiency (Phenylketonuria)(Jeannesson-Thivisol_2015, Aldamiz-Echevarria_2016). These data indicate that the variant is very likely to be associated with disease. The variant was found to cause a loss of enzyme activity via functional studies (Aldamiz-Echevarria_2016). Three ClinVar submissions from other clinical diagnostic laboratories (evaluation after 2014) cite the variant as "pathogenic." Based on the evidence outlined above, the variant was classified as pathogenic.

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

From Myriad Genetics, Inc., SCV001194050.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

NM_000277.1(PAH):c.814G>T(G272*) is classified as pathogenic in the context of phenylalanine hydroxylase deficiency and is associated with the classic form of disease. Sources cited for classification include the following: PMID 1671881, 24350308, 1978553, 10471838, 1975559 and 12655550. Classification of NM_000277.1(PAH):c.814G>T(G272*) is based on the following criteria: The variant causes a premature termination codon that is expected to be targeted by nonsense-mediated mRNA decay and is reported in individuals with the relevant phenotype. 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 UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill - NSIGHT-NC NEXUS, SCV001251473.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedresearch PubMed (8)

Description

The PAH c.814G>T (p.G272*) nonsense variant is predicted to result in premature termination of the PAH protein and/or nonsense-mediated decay. This variant has been previously reported as pathogenic in individuals with phenylketonuria (PMID: 8370573; 1975559; 1978553; 17935162; 10471838; 12655550).

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

From Natera, Inc., SCV001453102.1

#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, SCV002016483.3

#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 Baylor Genetics, SCV004209581.2

#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 Laboratory of Medical Genetics, National & Kapodistrian University of Athens, SCV005051911.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenonot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 24, 2024