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 starsreviewed by expert panel
- Somatic classification
of clinical impact: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Somatic classification
of oncogenicity: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno 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*)
This HGVS expression did not pass validation- 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)
Assertion and evidence details
Submission Accession | Submitter | Review Status (Assertion method) | Clinical Significance (Last evaluated) | Origin | Method | Citations |
---|---|---|---|---|---|---|
SCV000020777 | OMIM | no assertion criteria provided | Pathogenic (Sep 1, 1993) | germline | literature only | |
SCV000754076 | Labcorp Genetics (formerly Invitae), Labcorp | criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) | Pathogenic (Dec 25, 2023) | germline | clinical testing | |
SCV000852120 | ClinGen PAH Variant Curation Expert Panel | reviewed by expert panel (ClinGen PAH ACMG Specifications v1) | Pathogenic (Aug 10, 2018) | germline | curation | |
SCV000919920 | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015) | Pathogenic (Aug 31, 2018) | germline | clinical testing | |
SCV001194050 | Myriad Genetics, Inc. | criteria provided, single submitter (Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2019)) | Pathogenic (Dec 9, 2019) | unknown | clinical testing | |
SCV001251473 | UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill - NSIGHT-NC NEXUS | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic | germline | research | |
SCV001453102 | Natera, Inc. | no assertion criteria provided | Pathogenic (Sep 16, 2020) | germline | clinical testing | |
SCV002016483 | Revvity Omics, Revvity | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Jan 28, 2021) | germline | clinical testing | |
SCV004209581 | Baylor Genetics | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Mar 26, 2024) | unknown | clinical testing | |
SCV005051911 | Laboratory of Medical Genetics, National & Kapodistrian University of Athens | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Feb 1, 2024) | germline | curation |
Summary from all submissions
Ethnicity | Origin | Affected | Individuals | Families | Chromosomes tested | Number Tested | Family history | Method |
---|---|---|---|---|---|---|---|---|
not provided | germline | not provided | not provided | not provided | not provided | not provided | not provided | literature only |
not provided | germline | yes | 1 | not provided | not provided | not provided | not provided | research |
not provided | germline | unknown | not provided | not provided | not provided | not provided | not provided | clinical testing, curation |
not provided | unknown | unknown | not provided | not provided | not provided | not provided | not provided | clinical testing |
not provided | germline | no | not provided | not provided | not provided | not provided | not provided | curation |
Citations
PubMed
Eisensmith RC, Woo SL.
Hum Mutat. 1992;1(1):13-23. Review.
- PMID:
- 1301187
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.
- PMID:
- 9634518
- PMCID:
- PMC1377241
Details of each submission
From OMIM, SCV000020777.67
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | literature 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.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | not provided | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Labcorp Genetics (formerly Invitae), Labcorp, SCV000754076.8
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical 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.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From ClinGen PAH Variant Curation Expert Panel, SCV000852120.4
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | curation | 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).
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000919920.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical 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.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Myriad Genetics, Inc., SCV001194050.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical 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.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill - NSIGHT-NC NEXUS, SCV001251473.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 1 | not provided | not provided | research | 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).
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | 1 | not provided | not provided | not provided |
From Natera, Inc., SCV001453102.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Revvity Omics, Revvity, SCV002016483.3
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Baylor Genetics, SCV004209581.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Laboratory of Medical Genetics, National & Kapodistrian University of Athens, SCV005051911.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | curation | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | no | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
Last Updated: Nov 24, 2024