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NM_000277.3(PAH):c.157C>T (p.Arg53Cys) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 12, 2022
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV002281929.1

Allele description [Variation Report for NM_000277.3(PAH):c.157C>T (p.Arg53Cys)]

NM_000277.3(PAH):c.157C>T (p.Arg53Cys)

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.157C>T (p.Arg53Cys)
HGVS:
  • NC_000012.12:g.102912802G>A
  • NG_008690.2:g.50609C>T
  • NM_000277.3:c.157C>TMANE SELECT
  • NM_001354304.2:c.157C>T
  • NP_000268.1:p.Arg53Cys
  • NP_001341233.1:p.Arg53Cys
  • NC_000012.11:g.103306580G>A
  • NC_000012.11:g.103306580G>A
  • NM_000277.1:c.157C>T
  • NM_000277.3(PAH):c.157C>TMANE SELECT
  • p.Arg53Cys
Protein change:
R53C
Links:
dbSNP: rs199475619
NCBI 1000 Genomes Browser:
rs199475619
Molecular consequence:
  • NM_000277.3:c.157C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354304.2:c.157C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002571984Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Uncertain significance
(Aug 12, 2022) 		germlineclinical testing

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

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Spectrum of PAH gene variants among a population of Han Chinese patients with phenylketonuria from northern China.

Liu N, Huang Q, Li Q, Zhao D, Li X, Cui L, Bai Y, Feng Y, Kong X.

BMC Med Genet. 2017 Oct 5;18(1):108. doi: 10.1186/s12881-017-0467-7. Erratum in: BMC Med Genet. 2018 Jan 9;19(1):6. doi: 10.1186/s12881-017-0516-2.

PubMed [citation]
PMID:
28982351
PMCID:
PMC5629770

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002571984.1

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

Description

Variant summary: PAH c.157C>T (p.Arg53Cys) results in a non-conservative amino acid change located in the ACT domain (IPR002912) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 3.2e-05 in 251390 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.157C>T has been reported in the literature in at least one individual affected with Phenylalanine Hydroxylase Deficiency (Phenylketonuria, Liu_2017). These data do not allow any conclusion about variant significance. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Three ClinVar submitters, including one expert panel, have assessed the variant since 2014: one classified the variant as of uncertain significance, and two (including the expert panel) classified the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as uncertain significance.

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

Last Updated: Oct 13, 2024