rs118203923
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM3PM2PP4_ModeratePP3
This summary comes from the ClinGen Evidence Repository: The c.731C>T (p.Pro244Leu) variant in PAH has been reported in 2 individuals with mild PKU or benign HPA (BH4 deficiency excluded). It was detected in trans with pathogenic variants I65T, PMID:1363838 and p.R261Q )parental analysis not reported PMID:23430859). This variant has extremely low frequency in gnomAD (MAF= 0.00002979) and ExAC (MAF=0.00009). Computational evidence supports a deleterious effect. In summary, this variant meets criteria to be classified as likely pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PP4_Moderate, PM2, PM3, PP3. LINK:https://erepo.genome.network/evrepo/ui/classification/CA229721/MONDO:0009861/006
Frequency
Consequence
ENST00000553106.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PAH | NM_000277.3 | c.731C>T | p.Pro244Leu | missense_variant | 7/13 | ENST00000553106.6 | NP_000268.1 | |
PAH | NM_001354304.2 | c.731C>T | p.Pro244Leu | missense_variant | 8/14 | NP_001341233.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PAH | ENST00000553106.6 | c.731C>T | p.Pro244Leu | missense_variant | 7/13 | 1 | NM_000277.3 | ENSP00000448059 | P1 | |
PAH | ENST00000307000.7 | c.716C>T | p.Pro239Leu | missense_variant | 8/14 | 5 | ENSP00000303500 | |||
PAH | ENST00000549247.6 | n.490C>T | non_coding_transcript_exon_variant | 1/6 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251140Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135718
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461850Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727228
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Phenylketonuria Pathogenic:2
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 01, 1992 | - - |
Likely pathogenic, reviewed by expert panel | curation | ClinGen PAH Variant Curation Expert Panel | May 22, 2020 | The c.731C>T (p.Pro244Leu) variant in PAH has been reported in 2 individuals with mild PKU or benign HPA (BH4 deficiency excluded). It was detected in trans with pathogenic variants I65T, PMID: 1363838 and p.R261Q )parental analysis not reported PMID: 23430859). This variant has extremely low frequency in gnomAD (MAF= 0.00002979) and ExAC (MAF=0.00009). Computational evidence supports a deleterious effect. In summary, this variant meets criteria to be classified as likely pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PP4_Moderate, PM2, PM3, PP3. - |
not provided Other:1
not provided, no classification provided | literature only | DeBelle Laboratory for Biochemical Genetics, MUHC/MCH RESEARCH INSTITUTE | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at