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NM_000277.3(PAH):c.353-2059_353-1160del AND Phenylketonuria

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 25, 2020
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
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:
RCV002260491.2

Allele description [Variation Report for NM_000277.3(PAH):c.353-2059_353-1160del]

NM_000277.3(PAH):c.353-2059_353-1160del

Gene:
PAH:phenylalanine hydroxylase [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
12q23.2
Genomic location:
Preferred name:
NM_000277.3(PAH):c.353-2059_353-1160del
Other names:
NM_001354304.2:c.353-2059_353-1160del
HGVS:
  • NC_000012.12:g.102878710_102879609del
  • NG_008690.2:g.83802_84701del
  • NM_000277.3:c.353-2059_353-1160delMANE SELECT
  • NM_001354304.2:c.353-2059_353-1160del
  • NC_000012.11:g.103272488_103273387del
Links:
dbSNP: rs2136680756
NCBI 1000 Genomes Browser:
rs2136680756
Molecular consequence:
  • NM_000277.3:c.353-2059_353-1160del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354304.2:c.353-2059_353-1160del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Phenylketonuria (PKU)
Synonyms:
FOLLING DISEASE; OLIGOPHRENIA PHENYLPYRUVICA; Phenylketonurias
Identifiers:
MONDO: MONDO:0009861; MedGen: C0031485; Orphanet: 716; OMIM: 261600

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002540132ClinGen PAH Variant Curation Expert Panel
reviewed by expert panel

(ClinGen PAH ACMG Specifications v1)		Uncertain significance
(Dec 25, 2020) 		germlinecuration

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Details of each submission

From ClinGen PAH Variant Curation Expert Panel, SCV002540132.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The p.Intron3del899 (g.103272488_103273387del) variant is an 899bp deletion in Intron 3 of PAH. It has been previously reported as a variant of “uncertain clinical significance” in patient with PKU (plasma Phe levels not provided in paper; BH4 deficiency excluded by sequencing of the genes in the BH4 cofactor metabolism pathway) (PP4_Moderate), who also harbored a deletion in exon 5 (g.103272488_103273386del, leading to a frameshift at His170) and the c.994G>A (p.G322R) missense variant (unclassified/VUS) (PMID: 23942198). It is absent from ethnically diverse control databases, including gnomAD (structural variant version, gnomAD SVs v2.1) (PM2). Classification: VUS Supporting criteria: PM2; PP4_Moderate

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

Last Updated: Jan 13, 2025