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

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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

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

Pathogenic

Met criteria codes 3
PVS1 PM2 PP4_Moderate

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
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.
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)

Approved on: 2020-05-09
Published on: 2020-05-09
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