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Please note this is a beta version of the ClinGen Evidence Repository. This resource is intended to provide access to variant level evidence used and applied by ClinGen Variant Curation Expert Panels in the classification of variants. In this beta version, the evidence is limited to curation notes and referenced literature (PMIDs).

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NM_000277.2(PAH):c.169G>A (p.Glu57Lys)

CA220578

92737 (ClinVar)

Gene: PAH
Condition: phenylketonuria
Inheritance Mode: Autosomal recessive inheritance

HGVS expressions

NM_000277.2:c.169G>A
NM_000277.1:c.169G>A (p.Glu57Lys)
NM_001354304.1:c.169G>A (p.Glu57Lys)
NM_000277.3:c.169G>A (p.Glu57Lys)
ENST00000307000.7:c.154G>A (p.Glu52Lys)
ENST00000546844.1:c.169G>A (p.Glu57Lys)
ENST00000548677.2:n.256G>A
ENST00000548928.1:n.91G>A
ENST00000549111.5:n.265G>A
ENST00000550978.6:n.153G>A
ENST00000551337.5:c.169G>A (p.Glu57Lys)
ENST00000551988.5:n.258G>A
ENST00000553106.5:c.169G>A (p.Glu57Lys)
ENST00000635500.1:n.137G>A
NC_000012.12:g.102894918C>T
CM000674.2:g.102894918C>T
NC_000012.11:g.103288696C>T
CM000674.1:g.103288696C>T
NC_000012.10:g.101812826C>T
NG_008690.1:g.27685G>A
NG_008690.2:g.68493G>A

Likely Pathogenic

Met criteria codes 3
PM3 PM2 PP4_Moderate
Unmet criteria codes 1
PP3

Expert Panel

Evidence Links 1

Evidence submitted by expert panel
PAH VCEP
PAH-specific ACMG/AMP criteria applied: PM2: Extremely low frequency. ESP MAF=0.00012.; PP4_Moderate: Detected in a patient with mild HPA. Assessment of the PAH, PTS, and QDPR genes was performed. (PMID:21147011); PM3: Detected with V388M, pathogenic in ClinVar (PMID:21147011). In summary this variant meets criteria to be classified as likely pathogenic for phenylketonuria in an autosomal recessive manner based on the ACMG/AMP criteria applied as specified by the PAH Expert Panel: (PM2, PP4_Moderate, PM3).
Met criteria codes
PM3
Detected with V388M, pathogenic in ClinVar

PM2
Extremely low frequency. ESP MAF=0.00012.
PP4_Moderate
Detected in a patient with mild HPA. Assessment of the PAH, PTS, and QDPR genes was performed.

Unmet criteria codes
PP3
Conflicting interpretations of pathogenicity: SIFT, tolerated; Polyphen-2, benign; MutationTaster, disease causing.
Approved on: 2018-08-10
Published on: 2018-12-10
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