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:c.1037G>A

CA16020921

458078 (ClinVar)

Gene: PAH (HGNC:5053)
Condition: phenylketonuria (MONDO:0009861)
Inheritance Mode: Autosomal recessive inheritance
UUID: ccb4bee2-16a6-4799-8548-6186508934f3
Approved on: 2026-02-18
Published on: 2026-03-01

HGVS expressions

NM_000277.1:c.1037G>A
NC_000012.12:g.102844364C>T
CM000674.2:g.102844364C>T
NC_000012.11:g.103238142C>T
CM000674.1:g.103238142C>T
NC_000012.10:g.101762272C>T
NG_008690.1:g.78239G>A
NG_008690.2:g.119047G>A
ENST00000553106.6:c.1037G>A
ENST00000307000.7:c.1022G>A
ENST00000549247.6:n.796G>A
ENST00000551114.2:n.699G>A
ENST00000553106.5:c.1037G>A
ENST00000635477.1:c.141G>A
ENST00000635528.1:n.552G>A
NM_000277.2:c.1037G>A
NM_001354304.1:c.1037G>A
NM_000277.3:c.1037G>A
NM_001354304.2:c.1037G>A
More

Likely Pathogenic

Met criteria codes 4
PM2_Supporting PP4_Moderate PP3_Strong PM3
Not Met criteria codes 2
PM1 PM5

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.1037G>A variant in PAH is a missense variant predicted to cause substitution of glycine by glutamic acid at amino acid 346 (p.Gly346Glu). 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 19394257). Of reported individuals, one was compound heterozygous for the variant and a pathogenic variant (unknown phase), and one individual was homozygous for the variant (1 point, PMID: 32668217, PM3). This variant is absent from gnomAD v4.1.0 (PM2_Supporting). The computational predictor REVEL gives a score of 0.979, which meets the threshold of 0.932, evidence that correlates with strong impact to PAH function (PP3_Strong). Two missense variants, c.1036G>A (p.Gly346Arg) and c.1036G>C (p.Gly346Arg) [ClinVar Variation ID 102485, 102486], in the same codon have been classified as Likely pathogenic for PAH deficiency by the ClinGen PAH Variant Curation Expert Panel. However, the PAH VCEP is not applying PM5 as evidence since the p.Gly346Glu variant is also classified as Likely pathogenic. 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 PAH Variant Curation Expert Panel: PP3_strong, PP4_moderate, PM3, PM2_supporting (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).
PP4_Moderate
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 19394257). BH4 deficiency was excluded in all patients by measuring urinary pterins and dried blood dihydropteridine reductase activity.
PP3_Strong
The computational predictor REVEL gives a score of 0.979, which meets the threshold of 0.932, evidence that correlates with strong impact to PAH function (PP3_Strong).
PM3
This variant has been detected in at least two individuals with Phenylketonuria. Of those individuals, one was compound heterozygous for the variant and a pathogenic variant (unknown phase), and one individual was homozygous for the variant (1 point, PMID: 32668217, PM3). genotype not reported in PMID: 19394257.
Not Met criteria codes
PM1
Missense substitution of residues important in the active site architecture and/or substrate and/or cofactor binding of PAH: Gly346. Not applying since PP3 strong applies
PM5
Two missense variants, c.1036G>A (p.Gly346Arg) and c.1036G>C (p.Gly346Arg) [ClinVar Variation ID 102485, 102486], in the same codon have been classified as likely pathogenic for PAH deficiency by the ClinGen PAH Variant Curation Expert Panel [PM5]. Not applying to keep at LP, similar to other missense variants at this aa per PAH VCEP 2/18/26.
Curation History
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