Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • No ClinVar Id was directly found from the curated document
  • No CSPEC related information was provided by the message!
  • No Criteria Specification was provided in the publication event for the variant classifaction.
  • The Criteria Specification shown below is a best-estimate based on the VCEP, gene, disease, and publication date.

Variant: NM_001354304.2:c.1016C>T

CA386493446

Gene: PAH (HGNC:5053)
Condition: phenylketonuria (MONDO:0009861)
Inheritance Mode: Autosomal recessive inheritance
UUID: 51ea6579-cf3b-43d0-89ad-226c776fe307
Approved on: 2022-07-30
Published on: 2022-07-30

HGVS expressions

NM_001354304.2:c.1016C>T
NC_000012.12:g.102844385G>A
CM000674.2:g.102844385G>A
NC_000012.11:g.103238163G>A
CM000674.1:g.103238163G>A
NC_000012.10:g.101762293G>A
NG_008690.1:g.78218C>T
NG_008690.2:g.119026C>T
ENST00000553106.6:c.1016C>T
ENST00000307000.7:c.1001C>T
ENST00000549247.6:n.775C>T
ENST00000551114.2:n.678C>T
ENST00000553106.5:c.1016C>T
ENST00000635477.1:n.120C>T
ENST00000635528.1:n.531C>T
NM_000277.1:c.1016C>T
NM_000277.2:c.1016C>T
NM_001354304.1:c.1016C>T
NM_000277.3:c.1016C>T
More

Likely Pathogenic

Met criteria codes 4
PP4 PP3 PM2 PM3
Not Met criteria codes 1
PM5

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Phenylketonuria VCEP
This c.1016 C>T (p.Ser339Phe) variant was detected in a patient with mPKU in trans with the pathogenic variant p. Ex6-96A>G (PMID: 28982351). This variant was absent in population databases. Multiple lines of computational evidence support a deleterious effect. In summary, this variant meets criteria to be classified as likely pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PM3, PM2, PP3, PP4.
Met criteria codes
PP4
Variant was detected in a patient affected with mPKU. Variable sites in patient genes were aligned with the corresponding sites from the respective parents. This was seen in trans with a pathogenic variant listed in ClinVar. Those with BH4 cofactor deficiency were excluded PMID: 28982351
PP3
Predicted to be damaging (SIFT), possibly damaging (PolyPhen2), Disease causing (MutationTaster). REVEL=0.716
PM2
This variant is absent from population databases gnomAD and ExAC
PM3
This variant was detected in trans with the pathogenic variant p. Ex6-96A>G (evaluated by an expert panel and seen in multiple entries in ClinVar) in a patient with mPKU (PMID: 28982351). points=1.
Not Met criteria codes
PM5
No other variants at this amino acid site were documented in ClinVar.
Curation History
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