The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_000277.1(PAH):c.715G>A (p.Gly239Ser)

CA229706

102797 (ClinVar)

Gene: PAH (HGNC:5053)
Condition: phenylketonuria (MONDO:0009861)
Inheritance Mode: Autosomal recessive inheritance
UUID: e84bc878-ccba-4772-8c4c-81be78117db9
Approved on: 2025-11-29
Published on: 2025-11-29

HGVS expressions

NM_000277.1(PAH):c.715G>A (p.Gly239Ser)
NM_000277.1:c.715G>A
NC_000012.12:g.102852942C>T
CM000674.2:g.102852942C>T
NC_000012.11:g.103246720C>T
CM000674.1:g.103246720C>T
NC_000012.10:g.101770850C>T
NG_008690.1:g.69661G>A
NG_008690.2:g.110469G>A
ENST00000553106.6:c.715G>A
ENST00000307000.7:c.700G>A
ENST00000549247.6:n.474G>A
ENST00000553106.5:c.715G>A
NM_000277.2:c.715G>A
NM_001354304.1:c.715G>A
NM_000277.3:c.715G>A
NM_001354304.2:c.715G>A
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Pathogenic

Met criteria codes 5
PP4_Moderate PM3 PM5 PP3_Strong PM2_Supporting

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.715G>A variant in PAH is a missense variant predicted to cause substitution of glycine by serine at amino acid 239 (p.Gly239Ser). 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: 7833954, 9634518, 15503242, 26210745). Of those individuals, four were compound heterozygous for the variant and distinct pathogenic or likely pathogenic variants [unknown phase] (1.75 PM3 points). This variant is absent from gnomAD v4.1.0 (PM2_Supporting). The computational predictor REVEL gives a score of 0.959, 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
PP4_Moderate
PMID 7833954 G239S/IVS12nt1 in a French patient with typical PKU. PMID: 9634518 exclusion of a defect in tetrahydrobiopterin metabolism PMID: 15503242 reported in a Korean patient with classical PKU. Urinary pterin analysis and dihydropteridine reductase (DHPR) assay were performed to exclude 6-pyruvoyltetrahydropterin synthase (PTPS) deficiencies.

PM3
1.75 points: PMID 7833954 G239S/IVS12nt1 in a patient with typical PKU DNA from parents was not available. detected with P281L (LP PAH VCEP), phasing not confirmed. PMID: 15503242 p.I65V c.193A>G (P PAH VCEP), p.R176Q c.527G>A (P PAH VCEP) parental analysis not reported PMID: 26210745

PM5
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).
PP3_Strong
The computational predictor REVEL gives a score of 0.959, which meets the threshold of 0.932, evidence that correlates with strong impact to PAH function (PP3_Strong).
PM2_Supporting
This variant is absent from gnomAD v4.1.0 (PM2_Supporting).
Curation History
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