Variant: NM_000277.3(PAH):c.1066-11G>A

CA251538

607 (ClinVar)

Gene: PAH

Condition: phenylketonuria

Inheritance Mode: Autosomal recessive inheritance

UUID: 2470a255-3083-4956-9ff7-176203d54920

Approved on: 2024-12-30

Published on: 2024-12-31

HGVS expressions

NM_000277.3:c.1066-11G>A
NM_000277.3(PAH):c.1066-11G>A
NC_000012.12:g.102843790C>T
CM000674.2:g.102843790C>T
NC_000012.11:g.103237568C>T
CM000674.1:g.103237568C>T
NC_000012.10:g.101761698C>T
NG_008690.1:g.78813G>A
NG_008690.2:g.119621G>A
ENST00000553106.6:c.1066-11G>A
ENST00000307000.7:c.1051-11G>A
ENST00000549247.6:n.825-11G>A
ENST00000551114.2:n.728-11G>A
ENST00000553106.5:c.1066-11G>A
ENST00000635477.1:c.170-11G>A
ENST00000635528.1:n.581-11G>A
NM_000277.1:c.1066-11G>A
NM_000277.2:c.1066-11G>A
NM_001354304.1:c.1066-11G>A
NM_001354304.2:c.1066-11G>A

Pathogenic

• Met criteria codes: PP4_Moderate PM3_Very Strong PVS1_Strong

• Not Met criteria codes: PP3 PS3 BA1 PM2 BP4 BS1

Expert Panel

Phenylketonuria VCEP

Criteria Specification Information

Criteria Specification: ClinGen Phenylketonuria Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PAH Version 2.0.0

Evidence submitted by expert panel

Phenylketonuria VCEP

The c.1066-11G>A variant in PAH occurs within intron 10. It is predicted to impact splicing of biologically-relevant-exon 11/13. This prediction is confirmed by RT-PCR analysis which showed an in-frame insertion of Gly, Leu, Gln between exon 10 and 11 (PMID: 1769645). Nonsense mediated decay does not occur, but the resulting protein has no enzymatic activity (altered region is critical to protein function, PVS1_strong). At least one patient with this variant displayed blood Phe > 30 mg/dl, which is highly specific for PAH deficiency (PMID: 8990013). BH4 deficiency was ruled out in 1 study (PMID: 23500595). This variant has been detected in at least 23 individuals with PAH deficiency. Of those individuals, 15 were compound heterozygous for the variant and a pathogenic variant [p.R252W, p.R243X, p.R261Q (4 patients), p.R270K, p.I65T (2 patients); 5.5 points] (PMID: 23500595; PMID: 8990013) (PM3_Very strong). The population allele frequency in gnomAD v4 is 0.0003248, which is higher than the PAH VCEP cutoff for PM2 (<0.0002). In summary, this variant meets criteria to be classified as pathogenic for PAH deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen PAH VCEP: PVS1_strong, PP4_Moderate, PM3_very-strong. (VCEP specifications version 2; 12/06/24)

Met criteria codes

• PP4_Moderate: At least one patient with this variant displayed blood Phe > 30 mg/dl, which is highly specific for PAH deficiency (PMID: 8990013). BH4 deficiency ruled out in 1 study with 29 alleles (PMID: 23500595). Upgraded per ClinGen Metabolic workgroup
• PM3_Very Strong: This variant has been detected in at least 23 individuals with PAH deficiency. Of those individuals, 15 were compound heterozygous for the variant and a pathogenic variant [p.R252W, p.R243X, p.R261Q (4 patients), p.R270K, p.I65T (2 patients); 5.5 points] (PMID: 23500595; PMID: 8990013.) (PM3_Very strong)
• PVS1_Strong: mutant cDNA had 9 additional nt. inserted between exon 10 and 11 (In frame insertion of Gly, Leu, Gln), proving creation of a splice acceptor site. Only trace amounts of the normal product could be detected. Presence of the mutant protein in the patient’s liver was shown by Western blot (does not undergo NMD). PAH activity assay showed no conversion of C-14 labeled Phe into Tyr (altered region is critical to protein function). PMID: 1769645

Not Met criteria codes

• PP3: SpliceAI delta scores: Acceptor loss 0.61; Acceptor gain 0.98; Donor gain 0.30
• PS3: Functional studies from patient liver sample support a damaging effect on the gene product (no PAH activity). In vivo sample does not apply.
• BA1: Does not meet PAH EP PM2 cutoff (<0.0002): MAF in 1000G EUR, AF=0.00298 (3/1006); 0.0002424 in gnomAD
• PM2: Does not meet PAH VCEP PM2 cutoff (<0.0002): MAF in 1000G EUR, AF=0.00298 (3/1006); 0.0003248 in gnomAD v4.1.0
• BP4: Predicted in affect splicing in HSF and MaxEnt. Conserved in 25/31 vertebrates.
• BS1: Does not meet PAH EP PM2 cutoff (<0.0002): MAF in 1000G EUR, AF=0.00298 (3/1006); 0.0002424 in gnomAD