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Variant: NM_000277.2(PAH):c.307G>T (p.Gly103Cys)

CA6748984

553638 (ClinVar)

Gene: PAH
Condition: phenylketonuria
Inheritance Mode: Autosomal recessive inheritance
UUID: 508f9867-dc09-41bb-897d-7936dd45c772

HGVS expressions

NM_000277.2:c.307G>T
NM_000277.2(PAH):c.307G>T (p.Gly103Cys)
NC_000012.12:g.102894780C>A
CM000674.2:g.102894780C>A
NC_000012.11:g.103288558C>A
CM000674.1:g.103288558C>A
NC_000012.10:g.101812688C>A
NG_008690.1:g.27823G>T
NG_008690.2:g.68631G>T
ENST00000553106.6:c.307G>T
ENST00000307000.7:c.292G>T
ENST00000546844.1:c.307G>T
ENST00000548928.1:n.229G>T
ENST00000549111.5:n.403G>T
ENST00000550978.6:n.291G>T
ENST00000551337.5:c.307G>T
ENST00000551988.5:n.396G>T
ENST00000553106.5:c.307G>T
NM_000277.1:c.307G>T
NM_001354304.1:c.307G>T
NM_000277.3:c.307G>T
NM_001354304.2:c.307G>T
NM_000277.3(PAH):c.307G>T (p.Gly103Cys)

Uncertain Significance

Met criteria codes 4
PP4 PM2_Supporting PP3_Moderate PM3_Supporting
Not Met criteria codes 1
PM5

Evidence Links 2

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Phenylketonuria VCEP
The c.307G>T (p.Gly103Cys) variant in PAH has been reported in 2 patients with PKU (BH4 deficiency not assessed/reported) (PP4; PMID: 17502162, 24368688). It was detected in unknown phase with a pathogenic variant c.1066-11G>A (PMID: 17502162) and a likely pathogenic variant p.Y154F (PMID: 24368688). This variant has extremely low frequency in ExAC (MAF=0.00001). Computational evidence supports a deleterious effect (REVEL=0.819). In summary, this variant meets criteria to be classified as uncertain significance for PAH. PAH-specific ACMG/AMP criteria applied: PP4, PM2_supporting, PM3_supporting, PP3_moderate.
Met criteria codes
PP4
c.307G>T was identified in 1 patient with PKU. Bh4 deficiency not assessed/reported. PMID: 17502162

PM2_Supporting
Extremely low frequency in gnomAD (MAF=0.000008793). Filtered variant: failed RF filter.
PP3_Moderate
SIFT (T), PolyPhen-2 (D,P), MutationTaster (D), REVEL=0.819.
PM3_Supporting
Detected with c.1066-11G>A (known pathogenic variant) PMID: 17502162; and p.Y154F (LP) PMID: 24368688. phase unknown. 0.75 points

Not Met criteria codes
PM5
G103D (VUS by PAH VCEP), G103S (LP by PAH VCEP)
Approved on: 2023-07-23
Published on: 2023-07-23
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