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 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.1318G>T

CA16020997

Gene: PAH (HGNC:5053)
Condition: phenylketonuria (MONDO:0009861)
Inheritance Mode: Autosomal recessive inheritance
UUID: 69793eba-f1b8-4e7f-af42-b3a459a72236
Approved on: 2020-05-15
Published on: 2020-05-15

HGVS expressions

NM_001354304.2:c.1318G>T
NM_000277.1:c.1318G>T
NM_000277.2:c.1318G>T
NM_001354304.1:c.1318G>T
NM_000277.3:c.1318G>T
ENST00000307000.7:c.1303G>T
ENST00000551114.2:n.980G>T
ENST00000553106.5:c.1318G>T
ENST00000635477.1:n.422G>T
ENST00000635528.1:n.833G>T
NC_000012.12:g.102839216C>A
CM000674.2:g.102839216C>A
NC_000012.11:g.103232994C>A
CM000674.1:g.103232994C>A
NC_000012.10:g.101757124C>A
NG_008690.1:g.83387G>T
NG_008690.2:g.124195G>T
More

Likely Pathogenic

Met criteria codes 4
PM3_Supporting PP4 PM2 PVS1_Strong

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Phenylketonuria VCEP
The c.1318G>T (p.E440*) is a nonsense variant in exon 13 of 13 of PAH, a gene where loss of function is a known disease mechanism, and is predicted to lead to premature truncation of the protein at amino acid 440/453 (PVS1_Strong). Exon 13 encodes 15 amino acids + stop codon = 3.3% of PAH protein length. Along with Exon 12, Exon 13 forms the oligomerization domain (residues 411–452), which is responsible for the dimerization and tetramerization of the enzyme, important for regulation of PAH activity (e.g., positive cooperativity by the substrate, L-Phe, and decreasing PAH activity at low L-Phe concentration) (see PMID: 23457044; PMID: 22005392). Exon 13 contains the non-truncating Likely Pathogenic p.A447P (Likely Pathogenic by ClinGen PAH VCEP) and Pathogenic p.A447D variants (Likely Pathogenic by ClinGen PAH VCEP; Pathogenic in Clinvar (ID 102595; 4 submitters, 2 stars). Thus PVS1_Strong will be applied for variants resulting in premature truncation of this exon. The variant is absent from ethnically diverse control databases, including gnomAD/ExAC, 1000 Genomes, and ESP (PM2). It has been previously reported in one proband with abnormal blood Phe (BH4 deficiency does not appear to have been formally excluded) (PP4) (PMID: 23842451), in presumed trans with the p.R243* mutation (Pathogenic per PAH VCEP) (0.5 points; PM3_Supporting). Classification: Likely Pathogenic Supporting Criteria: PVS1_Strong; PM2; PM3_Supporting; PP4
Met criteria codes
PM3_Supporting
(PMID: 23842451) in presumed trans with the p.R243* mutation (Pathogenic per PAH VCEP) (0.5 points; PM3_Supporting).
PP4
It has been previously reported in one proband with abnormal blood Phe (BH4 deficiency does not appear to have been formally excluded) (PP4) (PMID: 23842451), in presumed trans with the p.R243* mutation (Pathogenic per PAH VCEP) (0.5 points; PM3_Supporting).
PM2
The variant is absent from ethnically diverse control databases, including gnomAD/ExAC, 1000 Genomes, and ESP (PM2).
PVS1_Strong
The c.1318G>T (p.E440*) is a nonsense variant in exon 13 of 13 of PAH, a gene where loss of function is a known disease mechanism, and is predicted to lead to premature truncation of the protein at amino acid 440/453 (PVS1_Strong). Exon 13 encodes 15 amino acids + stop codon = 3.3% of PAH protein length. Along with Exon 12, Exon 13 forms the oligomerization domain (residues 411–452), which is responsible for the dimerization and tetramerization of the enzyme, important for regulation of PAH activity (e.g., positive cooperativity by the substrate, L-Phe, and decreasing PAH activity at low L-Phe concentration) (see PMID: 23457044; PMID: 22005392). Exon 13 contains the non-truncating Likely Pathogenic p.A447P (Likely Pathogenic by ClinGen PAH VCEP) and Pathogenic p.A447D variants (Likely Pathogenic by ClinGen PAH VCEP; Pathogenic in Clinvar (ID 102595; 4 submitters, 2 stars). Thus PVS1_Strong will be applied for variants resulting in premature truncation of this exon
Curation History
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