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 obtained from curated document aligns with the Allele Registry but not with ClinVar data
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Variant: NM_000277.1(PAH):c.716G>C (p.Gly239Ala)

CA229709

102799 (ClinVar)

Gene: PAH (HGNC:5053)
Condition: phenylketonuria (MONDO:0009861)
Inheritance Mode: Autosomal recessive inheritance
UUID: 7c030087-a253-4d91-bd92-6b2be0405a35
Approved on: 2025-11-29
Published on: 2025-11-29

HGVS expressions

NM_000277.1(PAH):c.716G>C (p.Gly239Ala)
NM_000277.1:c.716G>C
NC_000012.12:g.102852941C>G
CM000674.2:g.102852941C>G
NC_000012.11:g.103246719C>G
CM000674.1:g.103246719C>G
NC_000012.10:g.101770849C>G
NG_008690.1:g.69662G>C
NG_008690.2:g.110470G>C
ENST00000553106.6:c.716G>C
ENST00000307000.7:c.701G>C
ENST00000549247.6:n.475G>C
ENST00000553106.5:c.716G>C
NM_000277.2:c.716G>C
NM_001354304.1:c.716G>C
NM_000277.3:c.716G>C
NM_001354304.2:c.716G>C
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Pathogenic

Met criteria codes 5
PM2_Supporting PP3_Strong PP4_Moderate PM3 PM5

Evidence Links 1

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 c.716G>C variant in PAH is a missense variant predicted to cause substitution of glycine by alanine at amino acid 239 (p.Gly239Ala). At least one patient with this variant displayed plasma phenylalanine concentration persistently above 120umol/L (2mg/dL) AND normal urine pterins and normal DHPR activity excluded a defect of BH4 cofactor metabolism, which is highly specific for PAH deficiency (PP4_Moderate, PMID: 9391881, 23357515, 26503515). Of those individuals, one was compound heterozygous for the variant and a pathogenic variant confirmed in trans by parental testing (PMID: 30050108). This variant is absent from gnomAD v4.1.0 (PM2_Supporting). The computational predictor REVEL gives a score of 0.983, which meets the threshold of 0.932, evidence that correlates with strong impact to PAH function (PP3_Strong). Another missense variant c.716G>A (p.Gly239Asp) [ClinVar Variation ID: 102798] in the same codon has been classified as pathogenic for PAH deficiency by the ClinGen PAH Variant Curation Expert Panel (PM5). In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive PAH deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen PAH Variant Curation Expert Panel: PP4_Moderate, PM2_supporting, PM3, PM5, PP3_strong. (PAH VCEP specifications version 2.0.0; approved July 16, 2024).
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v4.1.0 (PM2_Supporting).
PP3_Strong
The computational predictor REVEL gives a score of 0.983, which meets the threshold of 0.932, evidence that correlates with strong impact to PAH function (PP3_Strong).
PP4_Moderate
PMID 9391881, PMID: 23357515: listed in one allele in a Czech patient with classic PKU. PMID: 26503515 reported in a Chines PKU patient. dihydropteridine reductase activity, urinary biopterin and neopterin ratio, and tetrahydrobiopterin loading, were collected.

PM3
detected in trans with p.R243Q (P 10 submitters) PMID: 30050108 validation tests on parents were performed using Sanger sequencing.
PM5
p.Gly239Asp is Pathogenic by PAH VCEP, p.Gly239Val uncertain significance
Curation History
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