The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene label mismatch: PAH vs undefined
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000277.1(PAH):c.1183G>C (p.Ala395Pro)

CA229373

102547 (ClinVar)

Gene: PAH (HGNC:5053)
Condition: phenylketonuria (MONDO:0009861)
Inheritance Mode: Autosomal recessive inheritance
UUID: e90820bd-3677-45f6-9940-20fe8af192fa
Approved on: 2025-08-15
Published on: 2025-08-15

HGVS expressions

NM_000277.1:c.1183G>C
NM_000277.1(PAH):c.1183G>C (p.Ala395Pro)
NC_000012.12:g.102843662C>G
CM000674.2:g.102843662C>G
NC_000012.11:g.103237440C>G
CM000674.1:g.103237440C>G
NC_000012.10:g.101761570C>G
NG_008690.1:g.78941G>C
NG_008690.2:g.119749G>C
ENST00000553106.6:c.1183G>C
ENST00000307000.7:c.1168G>C
ENST00000549247.6:n.942G>C
ENST00000551114.2:n.845G>C
ENST00000553106.5:c.1183G>C
ENST00000635477.1:c.287G>C
ENST00000635528.1:n.698G>C
NM_000277.2:c.1183G>C
NM_001354304.1:c.1183G>C
NM_000277.3:c.1183G>C
NM_001354304.2:c.1183G>C
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Pathogenic

Met criteria codes 5
PM3_Strong PP3_Strong PM2_Supporting PP4_Moderate PS3_Supporting

Evidence Links 2

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Phenylketonuria Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PAH Version 2.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Phenylketonuria VCEP
The NM_000277.3(PAH):c.1183G>C variant is PAH is a missense variant predicted to cause substitution of alanine by proline at amino acid 395 (p.Ala395Pro). At least one patient with this variant displayed plasma phenylalanine concentration persistently above 120umol/L (2mg/dL) AND sequencing of genes in the BH4 cofactor metabolism pathway excluded a defect of BH4 cofactor metabolism, which is highly specific for PAH deficiency (PP4_Moderate, PMIDs: 9634518, 12836060). This variant has been detected in at least 5 individuals with Phenylketonuria. All individuals were compound heterozygous for the variant and distinct pathogenic variants in unknown phase (PM3_strong, PMIDs: 17502162, 12836060, 11999982, 7726156). The highest population minor allele frequency in gnomAD v4.1.0 is 0.00001017 in European (non-Finnish), which is lower than the ClinGen PAH Variant Curation Expert Panel threshold (<0.0002) for PM2_Supporting, meeting this criterion (PM2_Supporting). Mutant PAH enzyme activity showed 14-17% enzyme activity in vitro with < 10 benign/pathogenic variant controls, indicating that this variant impacts protein function (PS3_supporting, PMID: 11161839). The computational predictor REVEL gives a score of 0.988, which meets the threshold of 0.932, evidence that correlates with strong impact to PAH function (PP3_Strong). In summary, this variant meets criteria to be classified as pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PP4_moderate, PM3_strong, PM2_supporting, PS3_supporting, PP3_strong. Version 2.0, 7/16/2024.
Met criteria codes
PM3_Strong
This variant has been detected in at least 5 individuals with Phenylketonuria. All individuals were compound heterozygous for the variant and distinct pathogenic variants in unknown phase (PM3_strong, PMIDs: 17502162, 12836060, 11999982, 7726156).
PP3_Strong
The computational predictor REVEL gives a score of 0.988, which meets the threshold of 0.932, evidence that correlates with strong impact to PAH function (PP3_Strong).
PM2_Supporting
The highest population minor allele frequency in gnomAD v4.1.0 is 0.00001017 in European (non-Finnish), which is lower than the ClinGen PAH Variant Curation Expert Panel threshold (<0.0002) for PM2_Supporting, meeting this criterion (PM2_Supporting).
PP4_Moderate
At least one patient with this variant displayed plasma phenylalanine concentration persistently above 120umol/L (2mg/dL) AND sequencing of genes in the BH4 cofactor metabolism pathway to exclude a defect of BH4 cofactor metabolism, which is highly specific for Phenylketonuria (PP4_Moderate, PMIDs: 9634518, 12836060).

PS3_Supporting
Mutant PAH enzyme activity 17;14 % wt (pcDNA3/IVT) and 15 +/- 7 in E.coli showed <50% enzyme activity in vitro with < 10 benign/pathogenic variant controls indicating that this variant impacts protein function (PS3_supporting, PMID: 11161839).

Curation History
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