ClinVar Genomic variation as it relates to human health
NM_000277.3(PAH):c.926C>T (p.Ala309Val)
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_000277.3(PAH):c.926C>T (p.Ala309Val)
Variation ID: 92753 Accession: VCV000092753.21
- Type and length
-
single nucleotide variant, 1 bp
- Location
-
Cytogenetic: 12q23.2 12: 102846938 (GRCh38) [ NCBI UCSC ] 12: 103240716 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Mar 19, 2014 Oct 8, 2024 Aug 10, 2018 - HGVS
-
Nucleotide Protein Molecular
consequenceNM_000277.3:c.926C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000268.1:p.Ala309Val missense NM_001354304.1:c.926C>T NM_001354304.2:c.926C>T NP_001341233.1:p.Ala309Val missense NC_000012.12:g.102846938G>A NC_000012.11:g.103240716G>A NG_008690.2:g.116473C>T P00439:p.Ala309Val - Protein change
- A309V
- Other names
-
NM_000277.1(PAH):c.926C>T
- Canonical SPDI
- NC_000012.12:102846937:G:A
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
- -
-
Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
- -
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
-
Exome Aggregation Consortium (ExAC) 0.00001
The Genome Aggregation Database (gnomAD) 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00001
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
---|---|---|---|---|---|---|
HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
|||
PAH | - | - |
GRCh38 GRCh37 |
1506 | 1629 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
---|---|---|---|---|
Pathogenic (3) |
criteria provided, multiple submitters, no conflicts
|
Oct 5, 2023 | RCV000078538.17 | |
Pathogenic (6) |
reviewed by expert panel
|
Aug 10, 2018 | RCV000150082.28 | |
PAH-related disorder
|
Pathogenic (1) |
no assertion criteria provided
|
Sep 29, 2024 | RCV004739343.1 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
|
---|---|---|---|---|---|
Pathogenic
(Aug 10, 2018)
|
reviewed by expert panel
Method: curation
|
Phenylketonuria
(Autosomal recessive inheritance)
Affected status: unknown
Allele origin:
germline
|
ClinGen PAH Variant Curation Expert Panel
FDA Recognized Database
Accession: SCV000852158.4 First in ClinVar: Oct 10, 2018 Last updated: Dec 11, 2022 |
Comment:
PAH-specific ACMG/AMP criteria applied: PM2: Low frequency. 1.0e-5; PP3: All databases agree on damaging effect. REVEL=0.921; PS3: Enzyme activity = 30% (Ho, 2008) (PMID:18590700); PM3: … (more)
PAH-specific ACMG/AMP criteria applied: PM2: Low frequency. 1.0e-5; PP3: All databases agree on damaging effect. REVEL=0.921; PS3: Enzyme activity = 30% (Ho, 2008) (PMID:18590700); PM3: Single patient with classic PKU, c.842C>T (pathogenic in ClinVar) / c.926C>T (PMID:26666653); PP4: Single patient with classic PKU (>1200umol/L), BH4 defect not excluded (PMID:26666653). 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, PP3, PS3, PM3, PP4). (less)
|
|
Pathogenic
(Aug 07, 2012)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
germline
|
Eurofins Ntd Llc (ga)
Accession: SCV000110394.8
First in ClinVar: Jan 17, 2014 Last updated: Dec 15, 2018 |
Number of individuals with the variant: 2
Sex: mixed
|
|
Pathogenic
(Jul 19, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Phenylketonuria
Affected status: unknown
Allele origin:
germline
|
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001774587.1
First in ClinVar: Aug 07, 2021 Last updated: Aug 07, 2021 |
Comment:
Variant summary: PAH c.926C>T (p.Ala309Val) results in a non-conservative amino acid change located in the Aromatic amino acid hydroxylase, C-terminal domain (IPR019774) of the encoded … (more)
Variant summary: PAH c.926C>T (p.Ala309Val) results in a non-conservative amino acid change located in the Aromatic amino acid hydroxylase, C-terminal domain (IPR019774) 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 251284 control chromosomes. c.926C>T has been reported in the literature in multiple individuals affected with Phenylalanine Hydroxylase Deficiency (Phenylketonuria) (example, Hennermann_2000, Ley_2003, Dobrowolski_2007, Rivera_2011, Aldamiz-Echevarria_2016). These data indicate that the variant is very likely to be associated with disease. Multiple publications report experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in reduced enzyme activity, folding defect causing reduced stability and accelarated degradation (example, Ley_2003, Aldamiz-Echevarria_2016). Multiple clinical diagnostic laboratories and an expert panel (ClinGen PAH Variant Curation Expert Panel) have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All submitters classified the variant as pathogenic (n=4)/likely pathogenic (n=1). Based on the evidence outlined above, the variant was classified as pathogenic. (less)
|
|
Pathogenic
(Oct 05, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Not Provided
Affected status: yes
Allele origin:
germline
|
GeneDx
Accession: SCV000581842.3
First in ClinVar: Feb 02, 2015 Last updated: Nov 25, 2023 |
Comment:
Not observed at a significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein … (more)
Not observed at a significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Classified as responsive to tetrahydrobiopterin (BH4) therapy (Zurflh et al., 2008; Aldmiz- Echevarra et al., 2016); This variant is associated with the following publications: (PMID: 23559577, 16051511, 8830172, 16091306, 10679941, 15459954, 8533759, 25087612, 21953985, 8268925, 16504182, 15464430, 10234516, 26990548, 32668217, 31589614, 32778825, 12655546, 17935162, 33465300, 30037505, 27121329) (less)
|
|
Pathogenic
(Dec 01, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Phenylketonuria
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000629226.8
First in ClinVar: Dec 26, 2017 Last updated: Feb 20, 2024 |
Comment:
This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 309 of the PAH protein (p.Ala309Val). … (more)
This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 309 of the PAH protein (p.Ala309Val). This variant is present in population databases (rs62642935, gnomAD 0.003%). This missense change has been observed in individual(s) with PKU (PMID: 12655546, 21871829, 26666653, 27121329). ClinVar contains an entry for this variant (Variation ID: 92753). 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 not expected to disrupt PAH protein function with a negative predictive value of 80%. Experimental studies have shown that this missense change affects PAH function (PMID: 12655546, 15459954, 16504182). For these reasons, this variant has been classified as Pathogenic. (less)
|
|
Pathogenic
(Mar 27, 2024)
|
criteria provided, single submitter
Method: clinical testing
|
Phenylketonuria
Affected status: unknown
Allele origin:
unknown
|
Baylor Genetics
Accession: SCV004201378.2
First in ClinVar: Dec 30, 2023 Last updated: Jun 17, 2024 |
|
|
Pathogenic
(Sep 16, 2020)
|
no assertion criteria provided
Method: clinical testing
|
Phenylketonuria
Affected status: unknown
Allele origin:
germline
|
Natera, Inc.
Accession: SCV001463130.1
First in ClinVar: Jan 02, 2021 Last updated: Jan 02, 2021 |
|
|
Likely pathogenic
(Oct 20, 2016)
|
no assertion criteria provided
Method: clinical testing
|
Phenylketonuria
Affected status: unknown
Allele origin:
unknown
|
Counsyl
Accession: SCV000487182.2
First in ClinVar: Jun 28, 2015 Last updated: Apr 22, 2019 |
|
|
Pathogenic
(Sep 29, 2024)
|
no assertion criteria provided
Method: clinical testing
|
PAH-related condition
Affected status: unknown
Allele origin:
germline
|
PreventionGenetics, part of Exact Sciences
Accession: SCV005360388.1
First in ClinVar: Oct 08, 2024 Last updated: Oct 08, 2024 |
Comment:
The PAH c.926C>T variant is predicted to result in the amino acid substitution p.Ala309Val. This variant has been reported as causative for phenylalanine hydroxylase deficiency … (more)
The PAH c.926C>T variant is predicted to result in the amino acid substitution p.Ala309Val. This variant has been reported as causative for phenylalanine hydroxylase deficiency (Guldberg et al. 1993. PubMed ID: 8268925; Romano et al. 1996. PubMed ID: 8830172; Zschocke et al. 1995. PubMed ID: 8533759; Jeannesson-Thivisol et al. 2015. PubMed ID: 26666653). This variant has been reported to reduce PAH enzyme activity to less than 50% of that of the wild-type protein (Ho et al. 2008. PubMed ID: 18590700; Zurflüh et al. 2008. PubMed ID: 17935162). Several other laboratories as well as the ClinGen PAH Variant Curation Expert Panel classify this variant as pathogenic (https://www.ncbi.nlm.nih.gov/clinvar/variation/92753/). This variant is interpreted as pathogenic. (less)
|
|
not provided
(-)
|
no classification provided
Method: not provided
|
not provided
Affected status: not provided
Allele origin:
not provided
|
DeBelle Laboratory for Biochemical Genetics, MUHC/MCH RESEARCH INSTITUTE
Accession: SCV000119775.1
First in ClinVar: Mar 19, 2014 Last updated: Mar 19, 2014 |
|
Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
---|---|---|---|---|
Molecular genetics of a cohort of 635 cases of phenylketonuria in a consanguineous population. | Shirzadeh T | Journal of inherited metabolic disease | 2018 | PMID: 30159852 |
Molecular epidemiology, genotype-phenotype correlation and BH4 responsiveness in Spanish patients with phenylketonuria. | Aldámiz-Echevarría L | Journal of human genetics | 2016 | PMID: 27121329 |
Genotype-phenotype associations in French patients with phenylketonuria and importance of genotype for full assessment of tetrahydrobiopterin responsiveness. | Jeannesson-Thivisol E | Orphanet journal of rare diseases | 2015 | PMID: 26666653 |
Molecular genetics of PKU in Poland and potential impact of mutations on BH4 responsiveness. | Bik-Multanowski M | Acta biochimica Polonica | 2013 | PMID: 24350308 |
Chaperone-like therapy with tetrahydrobiopterin in clinical trials for phenylketonuria: is genotype a predictor of response? | Sarkissian CN | JIMD reports | 2012 | PMID: 23430918 |
Protein stability and in vivo concentration of missense mutations in phenylalanine hydroxylase. | Shi Z | Proteins | 2012 | PMID: 21953985 |
Phenylalanine hydroxylase deficiency: molecular epidemiology and predictable BH4-responsiveness in South Portugal PKU patients. | Rivera I | Molecular genetics and metabolism | 2011 | PMID: 21871829 |
Simultaneous assessment of the effects of exonic mutations on RNA splicing and protein functions. | Ho PY | Biochemical and biophysical research communications | 2008 | PMID: 18590700 |
Predicted effects of missense mutations on native-state stability account for phenotypic outcome in phenylketonuria, a paradigm of misfolding diseases. | Pey AL | American journal of human genetics | 2007 | PMID: 17924342 |
Mutations in the phenylalanine hydroxylase gene identified in 95 patients with phenylketonuria using novel systems of mutation scanning and specific genotyping based upon thermal melt profiles. | Dobrowolski SF | Molecular genetics and metabolism | 2007 | PMID: 17502162 |
Analysis of the effect of tetrahydrobiopterin on PAH gene expression in hepatoma cells. | Aguado C | FEBS letters | 2006 | PMID: 16504182 |
Mechanisms underlying responsiveness to tetrahydrobiopterin in mild phenylketonuria mutations. | Pey AL | Human mutation | 2004 | PMID: 15459954 |
Phenylketonuria: genotype-phenotype correlations based on expression analysis of structural and functional mutations in PAH. | Pey AL | Human mutation | 2003 | PMID: 12655546 |
Phenylketonuria and hyperphenylalaninemia in eastern Germany: a characteristic molecular profile and 15 novel mutations. | Hennermann JB | Human mutation | 2000 | PMID: 10679941 |
Phenylketonuria mutation analysis in Northern Ireland: a rapid stepwise approach. | Zschocke J | American journal of human genetics | 1995 | PMID: 8533759 |
Mutational spectrum of phenylalanine hydroxylase deficiency in Sicily: implications for diagnosis of hyperphenylalaninemia in southern Europe. | Guldberg P | Human molecular genetics | 1993 | PMID: 8268925 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=PAH | - | - | - | - |
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/db2881e3-3790-4e61-95e9-4ee16b4291d4 | - | - | - | - |
click to load more click to collapse |
Text-mined citations for rs62642935 ...
HelpRecord last updated Nov 19, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.