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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.158G>A (p.Arg53His)

CA229447

102601 (ClinVar)

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

HGVS expressions

NM_000277.2:c.158G>A
NM_000277.1:c.158G>A (p.Arg53His)
XM_011538422.1:c.158G>A (p.Arg53His)
NM_001354304.1:c.158G>A (p.Arg53His)
XM_017019370.2:c.158G>A (p.Arg53His)
ENST00000307000.7:c.143G>A (p.Arg48His)
ENST00000546844.1:c.158G>A (p.Arg53His)
ENST00000548677.2:n.245G>A
ENST00000548928.1:n.80G>A
ENST00000549111.5:n.254G>A
ENST00000550978.6:n.142G>A
ENST00000551337.5:c.158G>A (p.Arg53His)
ENST00000551988.5:n.247G>A
ENST00000553106.5:c.158G>A (p.Arg53His)
ENST00000635500.1:n.126G>A
NC_000012.12:g.102912801C>T
CM000674.2:g.102912801C>T
NC_000012.11:g.103306579C>T
CM000674.1:g.103306579C>T
NC_000012.10:g.101830709C>T
NG_008690.1:g.9802G>A
NG_008690.2:g.50610G>A

Uncertain Significance

Met criteria codes 3
PM3 BS1 PP4
Unmet criteria codes 1
PP3

Expert Panel

Evidence Links 1

Evidence submitted by expert panel
PAH EP
PAH-specific ACMG/AMP criteria applied: BS1: MAF=0.01596 in ExAC (138/8648) and 0.0104 in gnomAD (265/18868 with 3 homozygotes); PP4: Detected in a patient with mild hyperphe (PMID:24401910); PM3: Detected with V388L (LP) (PMID:24401910). In summary this variant meets criteria to be classified as uncertain significance for phenylketonuria in an autosomal recessive manner based on the ACMG/AMP criteria applied as specified by the PAH Expert Panel: (BS1, PP4, PM3).
Met criteria codes
PM3
Detected with V388L (LP)

BS1
MAF=0.01596 in ExAC (138/8648) and 0.0104 in gnomAD (265/18868 with 3 homozygotes)
PP4
Detected in a patient with mild hyperphe

Unmet criteria codes
PP3
Conflicting predictions of pathogenicity: Disease causing in MutationTaster, Benign in Polyphen-2 (HVAR). REVEL=0.789.
Approved on: 2018-08-10
Published on: 2018-10-02
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