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Variant: NM_000277.3(PAH):c.1065+39G>T

CA229317

102503 (ClinVar)

Gene: PAH
Condition: phenylketonuria
Inheritance Mode: Autosomal recessive inheritance
UUID: caf04e58-0600-4563-bab9-149add060c14

HGVS expressions

NM_000277.3:c.1065+39G>T
NM_000277.3(PAH):c.1065+39G>T
NC_000012.12:g.102844297C>A
CM000674.2:g.102844297C>A
NC_000012.11:g.103238075C>A
CM000674.1:g.103238075C>A
NC_000012.10:g.101762205C>A
NG_008690.1:g.78306G>T
NG_008690.2:g.119114G>T
ENST00000553106.6:c.1065+39G>T
ENST00000307000.7:c.1050+39G>T
ENST00000549247.6:n.824+39G>T
ENST00000551114.2:n.727+39G>T
ENST00000553106.5:c.1065+39G>T
ENST00000635477.1:n.169+39G>T
ENST00000635528.1:n.580+39G>T
NM_000277.1:c.1065+39G>T
NM_000277.2:c.1065+39G>T
NM_001354304.1:c.1065+39G>T
NM_001354304.2:c.1065+39G>T

Uncertain Significance

Met criteria codes 3
PP4_Moderate BP4 PM3
Not Met criteria codes 3
BA1 BS1 PM2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Phenylketonuria VCEP
This variant has been detected in one individual with PAH deficiency (PMID: 36104584). This individual was a compound heterozygote for the variant and a pathogenic variant, p.Arg408Gln, in trans (phase confirmed by parental testing) (PMID: 36104584). This individual had plasma phenylalanine >120 μmol/L with the exclusion of a defect of BH4 cofactor metabolism (PP4_Moderate) (PMID: 36104584). The highest population minor allele frequency in gnomAD v2.1.1 is 0.001 (20/19766 alleles) in the East Asian population (none of the population data codes are met). The computational splicing predictor SpliceAI gives a score of 0.05 for donor loss suggesting that the variant has no impact on splicing (BP4). There is a ClinVar entry for this variant (Variation ID: 102503, 1 star review status) with one submitter classifying the variant as a variant of uncertain significance, one submitter classifying the variant as likely benign, and one submitter classifying the variant as benign. Due to conflicting evidence, this variant is classified as a variant of unknown significance for PAH deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen PAH Variant Curation Expert Panel (Specifications Version 2.0): PM3, PP4, BP4.
Met criteria codes
PP4_Moderate
This individual had plasma phenylalanine >120 μmol/L with the exclusion of a defect of BH4 cofactor metabolism (PP4_Moderate) (PMID: 36104584).
BP4
No predicted splice impact by SpliceAI (all scores <0.2)
PM3
This variant has been detected in one individual with PAH deficiency (PMID: 36104584). This individual was a compound heterozygote for the variant and a pathogenic variant, p.Arg408Gln, in trans (phase confirmed by parental testing) (PMID: 36104584).
Not Met criteria codes
BA1
The highest population minor allele frequency in gnomAD v2.1.1 is 0.001 (20/19766 alleles) in the East Asian population (none of the population data codes are met).
BS1
The highest population minor allele frequency in gnomAD v2.1.1 is 0.001 (20/19766 alleles) in the East Asian population (none of the population data codes are met).
PM2
The highest population minor allele frequency in gnomAD v2.1.1 is 0.001 (20/19766 alleles) in the East Asian population (none of the population data codes are met).
Approved on: 2023-07-23
Published on: 2023-07-23
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