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NM_000277.3(PAH):c.1278T>C (p.Asn426=)

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Interpretation:
Benign​

Review status:
reviewed by expert panel FDA Recognized Database
Submissions:
11 (Most recent: Sep 15, 2021)
Last evaluated:
Aug 10, 2018
Accession:
VCV000092732.7
Variation ID:
92732
Description:
single nucleotide variant
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NM_000277.3(PAH):c.1278T>C (p.Asn426=)

Allele ID
98639
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
12q23.2
Genomic location
12: 102840437 (GRCh38) GRCh38 UCSC
12: 103234215 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000012.11:g.103234215A>G
NC_000012.12:g.102840437A>G
NG_008690.2:g.122974T>C
... more HGVS
Protein change
-
Other names
NM_000277.2(PAH):c.1278T>C
Canonical SPDI
NC_000012.12:102840436:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.04653 (G)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.01362
1000 Genomes Project 0.04653
The Genome Aggregation Database (gnomAD), exomes 0.01102
The Genome Aggregation Database (gnomAD) 0.04053
Trans-Omics for Precision Medicine (TOPMed) 0.04579
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.04652
Links
ClinGen: CA145978
dbSNP: rs59326968
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 4 reviewed by expert panel Aug 10, 2018 RCV000400696.9
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Oct 13, 2016 RCV000078509.6
Benign 4 criteria provided, multiple submitters, no conflicts Mar 1, 2019 RCV000088823.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PAH - - GRCh38
GRCh37
1103 1132

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Aug 10, 2018)
reviewed by expert panel
Method: curation
Phenylketonuria
(Autosomal recessive inheritance)
Allele origin: germline
ClinGen PAH Variant Curation Expert Panel
FDA Recognized Database
Accession: SCV000852128.3
Submitted: (Feb 25, 2019)
Evidence details
Other databases
https://erepo.clinicalgenome.org…
Comment:
PAH-specific ACMG/AMP criteria applied: BA1: MAF=0.16641; BP4: no impact on gene in SIFT, Polyphen2, MutationTaster. In summary this variant meets criteria to be classified as … (more)
Benign
(Oct 13, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV000601709.1
Submitted: (Aug 01, 2017)
Evidence details
Publications
PubMed (1)
Benign
(Jul 31, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000696435.1
Submitted: (Jan 25, 2018)
Evidence details
Publications
PubMed (1)
Comment:
Variant summary: The PAH c.1278T>C (p.Asn426Asn) variant involves the alteration of a non-conserved nucleotide causing a synonymous change and 5/5 splice prediction tools predict no … (more)
Benign
(Oct 13, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV000888342.1
Submitted: (Aug 31, 2018)
Evidence details
Benign
(Dec 05, 2020)
criteria provided, single submitter
Method: clinical testing
Phenylketonuria
Allele origin: germline
Invitae
Accession: SCV000629178.3
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000303442.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Oct 18, 2012)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000110365.8
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Phenylketonuria
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000375559.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Benign
(Mar 01, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001872489.1
Submitted: (Sep 15, 2021)
Evidence details
Benign
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Phenylketonuria
Allele origin: germline
Natera, Inc.
Accession: SCV001458994.1
Submitted: (Dec 28, 2020)
Evidence details
not provided
(-)
no assertion provided
Method: not provided
not provided
Allele origin: not provided
DeBelle Laboratory for Biochemical Genetics, MUHC/MCH RESEARCH INSTITUTE
Accession: SCV000119414.1
Submitted: (Mar 30, 2012)
Evidence details

Functional evidence

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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 this variant

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Title Author Journal Year Link
Mutations of the phenylalanine hydroxylase (PAH) gene in Brazilian patients with phenylketonuria. Acosta A Human mutation 2001 PMID: 11180595
Ten novel mutations in the phenylalanine hydroxylase gene (PAH) observed in Brazilian patients with phenylketonuria. Acosta AX Human mutation 2001 PMID: 11139255
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=PAH - - - -
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/66eeb668-a8a7-49cb-a6cd-26afcc800972 - - - -

Text-mined citations for rs59326968...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 18, 2021