The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • No ClinVar Id was directly found from the curated document
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000277.1:c.878T>C

CA16020884

Gene: PAH (HGNC:5053)
Condition: phenylketonuria (MONDO:0009861)
Inheritance Mode: Autosomal recessive inheritance
UUID: 4f42dda8-77aa-4616-ba24-28556930a2a2
Approved on: 2026-06-17
Published on: 2026-06-17

HGVS expressions

NM_000277.1:c.878T>C
NC_000012.12:g.102851721A>G
CM000674.2:g.102851721A>G
NC_000012.11:g.103245499A>G
CM000674.1:g.103245499A>G
NC_000012.10:g.101769629A>G
NG_008690.1:g.70882T>C
NG_008690.2:g.111690T>C
ENST00000553106.6:c.878T>C
ENST00000307000.7:c.863T>C
ENST00000549247.6:n.637T>C
ENST00000551114.2:n.540T>C
ENST00000553106.5:c.878T>C
ENST00000635477.1:c.39T>C
NM_000277.2:c.878T>C
NM_001354304.1:c.878T>C
NM_000277.3:c.878T>C
NM_001354304.2:c.878T>C
More

Likely Pathogenic

Met criteria codes 4
PP4_Moderate PP3_Strong PM2_Supporting PM5_Supporting
Not Met criteria codes 1
PM3

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.878T>C variant in PAH is a missense variant predicted to cause substitution of leucine by serine at amino acid 293 (p.Leu293Ser). 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: 21147011). This variant is absent from gnomAD v4.1.0 (PM2_Supporting). The computational predictor REVEL gives a score of 0.968, which meets the threshold of 0.932, evidence that correlates with strong impact to PAH function (PP3_Strong). Another missense variant c.877T>A (p.Leu293Met) [CA16020883] 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 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, PM2_supporting, PM5_supporting (PAH VCEP specifications version 2.0.0; approved July 16, 2024).
Met criteria codes
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 PAH deficiency (PP4_Moderate, PMID: 21147011).

PP3_Strong
The computational predictor REVEL gives a score of 0.968, 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).
PM5_Supporting
Another missense variant c.877T>A (p.Leu293Met) [CA16020883] in the same codon has been classified as likely pathogenic for PAH deficiency by the ClinGen PAH Variant Curation Expert Panel (PM5_Supporting).
Not Met criteria codes
PM3
second variant not reported
Curation History
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
ClinGen Terms of Use.
¤ Powered by BCM's Genboree.