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:c.512G>A

CA16020809

Gene: PAH (HGNC:5053)
Condition: phenylketonuria (MONDO:0009861)
Inheritance Mode: Autosomal recessive inheritance
UUID: 9ded6bce-1853-4671-8b51-6b4f3600c485
Approved on: 2025-11-29
Published on: 2025-11-29

HGVS expressions

NM_000277.1:c.512G>A
NC_000012.12:g.102855330C>T
CM000674.2:g.102855330C>T
NC_000012.11:g.103249108C>T
CM000674.1:g.103249108C>T
NC_000012.10:g.101773238C>T
NG_008690.1:g.67273G>A
NG_008690.2:g.108081G>A
ENST00000553106.6:c.512G>A
ENST00000307000.7:c.497G>A
ENST00000549111.5:n.608G>A
ENST00000551988.5:n.533G>A
ENST00000553106.5:c.512G>A
NM_000277.2:c.512G>A
NM_001354304.1:c.512G>A
NM_000277.3:c.512G>A
NM_001354304.2:c.512G>A
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Likely Pathogenic

Met criteria codes 4
PM5_Supporting PP4_Moderate PP3_Moderate PM2_Supporting

Evidence Links 0

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.512G>A variant in PAH is a missense variant predicted to cause substitution of glycine by glutamic acid at amino acid 171 (p.Gly171Glu). 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, PMID: 26575882, 31332730). This variant is absent from gnomAD v4.1.0 (PM2_Supporting). The computational predictor REVEL gives a score of 0.926, which is above the threshold of 0.773 but below 0.932, evidence that correlates with moderate impact to PAH function (PP3_Moderate). Another missense variant c.512G>C (p.Gly171Ala) [ClinVar Variation ID: 102717] in the same codon has been classified as likely pathogenic for PAH deficiency by the ClinGen PAH Variant Curation Expert Panel (PM5_Supporting). In summary, this variant meets criteria to be classified as likely 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, PP3_moderate, PM5_supporting (PAH VCEP specifications version 2.0.0; approved July 16, 2024).
Met criteria codes
PM5_Supporting
Another missense variant c.512G>C (p.Gly171Ala) [ClinVar Variation ID: 102717] in the same codon has been classified as likely pathogenic for PAH deficiency by the ClinGen PAH Variant Curation Expert Panel (PM5_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 excluded a defect of BH4 cofactor metabolism, which is highly specific for PAH deficiency (PP4_Moderate, PMID: 26575882, 31332730).
PP3_Moderate
The computational predictor REVEL gives a score of 0.926, which is above the threshold of 0.773 but below 0.932, evidence that correlates with moderate impact to PAH function (PP3_Moderate).
PM2_Supporting
This variant is absent from gnomAD v4.1.0 (PM2_Supporting).
Curation History
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