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_000277.2(PAH):c.181A>G (p.Asn61Asp)

CA229470

102617 (ClinVar)

Gene: PAH (HGNC:5053)
Condition: phenylketonuria (MONDO:0009861)
Inheritance Mode: Autosomal recessive inheritance
UUID: 7dd2b63c-450a-4270-bf25-412535e6065c
Approved on: 2025-07-18
Published on: 2025-07-18

HGVS expressions

NM_000277.2(PAH):c.181A>G (p.Asn61Asp)
NM_000277.2:c.181A>G
NC_000012.12:g.102894906T>C
CM000674.2:g.102894906T>C
NC_000012.11:g.103288684T>C
CM000674.1:g.103288684T>C
NC_000012.10:g.101812814T>C
NG_008690.1:g.27697A>G
NG_008690.2:g.68505A>G
ENST00000553106.6:c.181A>G
ENST00000307000.7:c.166A>G
ENST00000546844.1:c.181A>G
ENST00000548677.2:n.268A>G
ENST00000548928.1:n.103A>G
ENST00000549111.5:n.277A>G
ENST00000550978.6:c.165A>G
ENST00000551337.5:c.181A>G
ENST00000551988.5:n.270A>G
ENST00000553106.5:c.181A>G
ENST00000635500.1:n.149A>G
NM_000277.1:c.181A>G
NM_001354304.1:c.181A>G
NM_000277.3:c.181A>G
NM_001354304.2:c.181A>G
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Likely Pathogenic

Met criteria codes 5
PM2_Supporting PP3 PM5 PP4_Moderate PM3_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 NM_000277.3(PAH):c.181A>G variant in PAH is a missense variant predicted to cause substitution of asparagine to aspartic acid at amino acid 61 (p.Asn61Asp). 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 (PMID:12501224) (PP4_Moderate). This individual was compound heterozygous for the variant and a pathogenic variant p.R261Q in unknown phase (PMID: 12501224, PM3_Supporting). This variant is absent from gnomAD v4.1.0 (PM2_Supporting). The computational predictor REVEL gives a score of 0.703, which is above the threshold of 0.644 but below 0.773, evidence that correlates with supporting impact to PAH function (PP3). 2 different missense variants c.182A>G (p.Asn61Ser) and c.183C>A (p.Asn61Lys) in the same codon have been classified as pathogenic/likely pathogenic for PAH deficiency by the ClinGen PAH Variant Curation Expert Panel (PM5). In summary, this variant meets the criteria to be classified as likely pathogenic for autosomal recessive PAH deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen Phenylketonuria VCEP: PP4_moderate, PP3, PM2_supporting, PM3_supporting, PM5 (Version 2.0, 7/16/2024).
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v4.1.0 (PM2_Supporting)
PP3
The computational predictor REVEL gives a score of 0.703, which is above the threshold of 0.644 but below 0.773, evidence that correlates with supporting impact to PAH function (PP3).
PM5
2 difference missense variant c.182A>G (p.Asn61Ser) & c.183C>A (p.Asn61Lys) in the same codon has been classified as pathogenic/likely pathogenic for PAH deficiency by the ClinGen PAH Variant Curation Expert Panel (PM5).
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 (PMID:12501224) (PP4_Moderate).
PM3_Supporting
This variant has been detected in at least 1 individual with Phenylketonuria. Of those individuals, 1 was compound heterozygous for the variant and a pathogenic variant p.R261Q (PMID: 12501224, PM3_Supporting).
Curation History
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