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NM_000277.3(PAH):c.320A>G (p.His107Arg)

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Interpretation:
Pathogenic​

Review status:
reviewed by expert panel FDA Recognized Database
Submissions:
5 (Most recent: Apr 30, 2021)
Last evaluated:
Dec 9, 2020
Accession:
VCV000225134.5
Variation ID:
225134
Description:
single nucleotide variant
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NM_000277.3(PAH):c.320A>G (p.His107Arg)

Allele ID
227029
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
12q23.2
Genomic location
12: 102894767 (GRCh38) GRCh38 UCSC
12: 103288545 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000012.11:g.103288545T>C
NC_000012.12:g.102894767T>C
NM_000277.3:c.320A>G MANE Select NP_000268.1:p.His107Arg missense
... more HGVS
Protein change
H107R
Other names
-
Canonical SPDI
NC_000012.12:102894766:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (C)

Allele frequency
1000 Genomes Project 0.00020
Exome Aggregation Consortium (ExAC) 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00001
The Genome Aggregation Database (gnomAD), exomes 0.00001
Links
ClinGen: CA354151
dbSNP: rs542645236
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 5 reviewed by expert panel Dec 9, 2020 RCV000210807.5
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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
Pathogenic
(Dec 09, 2020)
reviewed by expert panel
Method: curation
Phenylketonuria
(Autosomal recessive inheritance)
Allele origin: germline
ClinGen PAH Variant Curation Expert Panel
FDA Recognized Database
Accession: SCV001572860.1
Submitted: (Apr 30, 2021)
Evidence details
Other databases
https://erepo.clinicalgenome.org…
Comment:
This c.320A>G (p.His107Arg) variant in PAH was reported in 22 patients with PAH deficiency (>120 uMol/L Phe), detected in trans in 16 patients with pathogenic … (more)
Likely pathogenic
(May 13, 2017)
criteria provided, single submitter
Method: clinical testing
Phenylketonuria
Allele origin: unknown
Counsyl
Accession: SCV000791589.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (6)
Pathogenic
(-)
criteria provided, single submitter
Method: clinical testing
Phenylketonuria
Allele origin: germline
Baylor Genetics
Accession: SCV001163352.1
Submitted: (Sep 27, 2019)
Evidence details
Pathogenic
(Aug 25, 2020)
criteria provided, single submitter
Method: clinical testing
Phenylketonuria
Allele origin: germline
Invitae
Accession: SCV001223781.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (5)
Comment:
This sequence change replaces histidine with arginine at codon 107 of the PAH protein (p.His107Arg). The histidine residue is highly conserved and there is a … (more)
Likely pathogenic
(Oct 01, 2013)
no assertion criteria provided
Method: clinical testing
Phenylketonuria
Allele origin: paternal
Department of Prenatal Diagnosis, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital
Accession: SCV000266851.1
Submitted: (Jun 28, 2015)
Comment:
This variant was reported to be a novel likely pathogenic mutation for the first time by us.
Evidence details
Publications
PubMed (1)

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
Analysis of the genotype-phenotype correlation in patients with phenylketonuria in mainland China. Li N Scientific reports 2018 PMID: 30050108
Mutational spectrum of the phenylalanine hydroxylase gene in patients with phenylketonuria in the central region of China. Zhang Z Scandinavian journal of clinical and laboratory investigation 2018 PMID: 29390883
Prenatal diagnosis of Chinese families with phenylketonuria. Liu N Genetics and molecular research : GMR 2015 PMID: 26600521
Molecular characterisation of phenylketonuria in a Chinese mainland population using next-generation sequencing. Li N Scientific reports 2015 PMID: 26503515
Fast clinical molecular diagnosis of hyperphenylalaninemia using next-generation sequencing-based on a custom AmpliSeq™ panel and Ion Torrent PGM sequencing. Cao YY Molecular genetics and metabolism 2014 PMID: 25456745
[Mutational spectrum of phenylalanine hydroxylase gene and identification of novel mutations in patients with hyperphenylalaninemia in Jiangsu province]. Zhang JJ Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics 2013 PMID: 24078561
Variations in genotype-phenotype correlations in phenylalanine hydroxylase deficiency in Chinese Han population. Zhu T Gene 2013 PMID: 23932990
Molecular characterization of phenylketonuria and tetrahydrobiopterin-responsive phenylalanine hydroxylase deficiency in Japan. Okano Y Journal of human genetics 2011 PMID: 21307867
http://www.ncbi.nlm.nih.gov/pubmed/24078561 - - - -
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/43c0e463-29fc-4579-ad14-55bf5d1fab63 - - - -

Text-mined citations for rs542645236...

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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 Aug 07, 2021