Evidence Repository
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_001354304.2:c.442-4403_509+883del

CA916084429

Gene: PAH
Condition: phenylketonuria
Inheritance Mode: Autosomal recessive inheritance
Link to MONDO
UUID: fe18266f-4396-4995-aee4-caccb06c4bae

HGVS expressions

NM_001354304.2:c.442-4403_509+883del
NC_000012.12:g.102865713_102871066del
CM000674.2:g.102865713_102871066del
NC_000012.11:g.103259491_103264844del
CM000674.1:g.103259491_103264844del
NC_000012.10:g.101783621_101788974del
NG_008690.1:g.51537_56890del
NG_008690.2:g.92345_97698del
ENST00000553106.6:c.442-4403_509+883del
ENST00000307000.7:c.427-4403_494+883del
ENST00000549111.5:n.538-4403_605+883del
ENST00000551988.5:n.530+6396_531-10381del
ENST00000553106.5:c.442-4403_509+883del
NM_000277.1:c.442-4403_509+883del
NM_000277.2:c.442-4403_509+883del
NM_001354304.1:c.442-4403_509+883del
NM_000277.3:c.442-4403_509+883del

Pathogenic

Met criteria codes 3
PP4_Moderate PM2 PVS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Phenylketonuria VCEP
The p.Ex5del5321 variant is a 5321bp deletion in Exon 5 of PAH, a gene where loss of function is a known disease mechanism, and is predicted to lead to a frameshift at His170, premature protein truncation, and NMD (PVS1). One heterozygote for the deletion is present in gnomAD, corresponding to an allele frequency of 0.000046 (structural variant version, gnomAD SVs v2.1), less than the 0.0002 cutoff for use of PM2 (PM2). It has been previously reported in one patient with PKU (BH4 deficiency excluded by sequencing of the genes in the BH4 cofactor metabolism pathway) (PP4_Moderate) (PMID: 23942198) in presumed trans with the p.G332R variant (unclassified/VUS). Classification: Pathogenic Supporting Criteria: PVS1; PM2; PP4_Moderate
Met criteria codes
PP4_Moderate
It has been previously reported in one patient with PKU (BH4 deficiency excluded by sequencing of the genes in the BH4 cofactor metabolism pathway) (PP4_Moderate) (PMID: 23942198) in presumed trans with the p.G332R variant (unclassified/VUS).
PM2
One heterozygote for the deletion is present in gnomAD, corresponding to an allele frequency of 0.000046 (structural variant version, gnomAD SVs v2.1), less than the 0.0002 cutoff for use of PM2 (PM2).
PVS1
The p.Ex5del5321 variant is a 5321bp deletion in Exon 5 of PAH, a gene where loss of function is a known disease mechanism, and is predicted to lead to a frameshift at His170, premature protein truncation, and NMD (PVS1).
Approved on: 2020-06-05
Published on: 2021-03-21
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