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]
Link to SEPIO compliant JSON-LD document
  • No ClinVar Id was directly found from the curated document
  • There was no gene found in the curated document received from the VCI/VCEP
  • Gene listed was thus derived from ClinVar and/or CAR
  • See Evidence submitted by expert panel for details.

Variant: NM_001354304.2:c.750_751del

CA16020852

Gene: PAH
Condition: phenylketonuria
Inheritance Mode: Autosomal recessive inheritance
Link to MONDO
UUID: 34f96733-cc4f-4edd-8cf4-908f6379c67f

HGVS expressions

NM_001354304.2:c.750_751del
NC_000012.12:g.102852906_102852907del
CM000674.2:g.102852906_102852907del
NC_000012.11:g.103246684_103246685del
CM000674.1:g.103246684_103246685del
NC_000012.10:g.101770814_101770815del
NG_008690.1:g.69699_69700del
NG_008690.2:g.110507_110508del
ENST00000553106.6:c.753_754del
ENST00000307000.7:c.738_739del
ENST00000549247.6:n.512_513del
ENST00000553106.5:c.753_754del
NM_000277.1:c.753_754del
NM_000277.2:c.753_754del
NM_001354304.1:c.753_754del
NM_000277.3:c.753_754del
NM_001354304.2:c.753_754del

Pathogenic

Met criteria codes 4
PP4 PVS1 PM2 PM3_Supporting

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Phenylketonuria VCEP
The frameshift variant NM_000277.3(PAH):c.750_751del (p.Arg252GlyfsTer30) occurs in exon 7 of 13 and is predicted to result in NMD. The variant is absent from population databases, including gnomAD. One PKU patient has been reported (PMID: 32106880) compound heterozygous for Arg252GlyfsTer30 and Arg158Trp (ClinVar 102693, Pathogenic). In summary, this variant meets criteria to be classified as Pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PVS1, PM2, PM3_supporting, PP4.
Met criteria codes
PP4
PMID: 32106880 Reports an adult PKU patient with Phe level of 142 μmol/L at time of investigation.
PVS1
The frameshift variant Arg252Glyfs occurs in exon 7 of 13 and generates a stop codon at position 281 which is predicted to result in NMD.
PM2
The variant is absent from controls in gnomAD, ExAC, 1000 Genomes, and ESP.
PM3_Supporting
One compound heterozygous patient has been described (PMID: 32106880) with Arg252GlyfsTer30 and Arg158Trp (ClinVar 102693, Pathogenic reviewed by GCEP). Confirmation of trans phase was not reported.
Approved on: 2020-12-08
Published on: 2022-03-11
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