The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

  • See Evidence submitted by expert panel for details.

Variant: NM_000277.3(PAH):c.1066-1G>A

CA229322

102509 (ClinVar)

Gene: PAH
Condition: phenylketonuria
Inheritance Mode: Autosomal recessive inheritance
UUID: 0c1a54c0-a213-4fea-a6d1-b8aad5bdfdfa
Approved on: 2020-05-09
Published on: 2020-05-09

HGVS expressions

NM_000277.3:c.1066-1G>A
NM_000277.3(PAH):c.1066-1G>A
NM_000277.1:c.1066-1G>A
NM_000277.2:c.1066-1G>A
NM_001354304.1:c.1066-1G>A
NM_001354304.2:c.1066-1G>A
ENST00000307000.7:c.1051-1G>A
ENST00000549247.6:n.825-1G>A
ENST00000551114.2:n.728-1G>A
ENST00000553106.5:c.1066-1G>A
ENST00000635477.1:n.170-1G>A
ENST00000635528.1:n.581-1G>A
NC_000012.12:g.102843780C>T
CM000674.2:g.102843780C>T
NC_000012.11:g.103237558C>T
CM000674.1:g.103237558C>T
NC_000012.10:g.101761688C>T
NG_008690.1:g.78823G>A
NG_008690.2:g.119631G>A
More

Pathogenic

Met criteria codes 3
PP4_Moderate PVS1 PM2

Evidence Links 2

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Phenylketonuria VCEP
The PAH variant c.1066-1G>A (IVS10-1G>A) is a null variant (acceptor site) located in exon number 11 of the PAH gene. Loss of function in the PAH gene is a known mechanism of disease. Fifteen pathogenic null variants in exon 11 of the PAH gene have been reported. This variant is predicted to disrupt the reading frame by skipping exon 11, altering a region that is critical to protein function (27 pathogenic non-nonsense variants in exon 11 have been reported). The mRNA transcript is predicted to undergo NMD. According to TraP in silico splicing prediction, this alteration is probably damaging (TraP score 0.559). HSF (-35.29 variation) and MaxEnt (-276.58 variation) agree that this alteration of the WT acceptor site most probably affects splicing by breaking the splicing site. The PAH variant c.1066-1G>A (IVS10-1G>A) was found in a Chinese patient with classical PKU (Phe levels >20 mg/dl). BH4 deficiency was excluded by analysis of urinary pterins and dihydropteridine reductase activity in erythrocytes (PMID: 26322415). This variant was also reported in another Chinese patient with undetermined PKU/MHP phenotype (PMID: 26503515). This variant is absent from the gnomAD, ExAC, 1000 Genomes, and ESP population databases. In summary, this variant meets the criteria to be classified as pathogenic. PAH-specific ACMG/AMP criteria applied: PM2, PP4_Moderate, and PVS1.
Met criteria codes
PP4_Moderate
The PAH variant c.1066-1G>A (IVS10-1G>A) was found in a Chinese patient with classical PKU (Phe levels >20 mg/dl). BH4 deficiency was excluded by analysis of urinary pterins and dihydropteridine reductase activity in erythrocytes (PMID: 26322415). This variant was also reported in another Chinese patient with undetermined PKU/MHP phenotype (PMID: 26503515)

PVS1
The PAH variant c.1066-1G>A (IVS10-1G>A) is a null variant (acceptor site) located in exon number 11 of the PAH gene. Loss of function in the PAH gene is a known mechanism of disease. Fifteen pathogenic null variants in exon 11 of the PAH gene have been reported. This variant is predicted to disrupt the reading frame by skipping exon 11, altering a region that is critical to protein function (27 pathogenic non-nonsense variants in exon 11 have been reported). The mRNA transcript is predicted to undergo NMD. According to TraP in silico splicing prediction, this alteration is probably damaging (TraP score 0.559). HSF (-35.29 variation) and MaxEnt (-276.58 variation) agree that this alteration of the WT acceptor site most probably affects splicing by breaking the splicing site.
PM2
The PAH variant c.1066-1G>A (IVS10-1G>A) is absent from the gnomAD, ExAC, 1000 Genomes, and ESP population databases.
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.
¤ Powered by BCM's Genboree.