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

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Oct 11, 2023
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:: RCV000088841.2

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:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000119434	DeBelle Laboratory for Biochemical Genetics, MUHC/MCH RESEARCH INSTITUTE	no classification provided	not provided	not provided	not provided
SCV005326122	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Oct 11, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000119434

DeBelle Laboratory for Biochemical Genetics, MUHC/MCH RESEARCH INSTITUTE

no classification provided

not provided

SCV005326122

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Oct 11, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	not provided	not provided	not provided	not provided	not provided	1	not provided	literature only

Details of each submission

From DeBelle Laboratory for Biochemical Genetics, MUHC/MCH RESEARCH INSTITUTE, SCV000119434.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	not provided	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	not provided	not provided	1	not provided	not provided		not provided	not provided	not provided	not provided

From GeneDx, SCV005326122.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Reported in a child with mild hyperphenylalaninemia (Liu et al., 2017); This variant is associated with the following publications: (PMID: 29316886, 28982351, 17924342)

#	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		not provided	not provided	not provided	not provided

Last Updated: Oct 13, 2024

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