rs104893866
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PP3_StrongPP5_Moderate
The NM_000320.3(QDPR):āc.449A>Gā(p.Tyr150Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,768 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (ā ). Synonymous variant affecting the same amino acid position (i.e. Y150Y) has been classified as Likely benign.
Frequency
Consequence
NM_000320.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
QDPR | NM_000320.3 | c.449A>G | p.Tyr150Cys | missense_variant | 5/7 | ENST00000281243.10 | |
QDPR | NM_001306140.2 | c.356A>G | p.Tyr119Cys | missense_variant | 4/6 | ||
QDPR | NR_156494.2 | n.473-1583A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
QDPR | ENST00000281243.10 | c.449A>G | p.Tyr150Cys | missense_variant | 5/7 | 1 | NM_000320.3 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461768Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727190
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Dihydropteridine reductase deficiency Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 01, 1998 | - - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Aug 24, 2020 | Not observed in large population cohorts (Lek et al., 2016); Missense variants in this gene are often considered pathogenic (Stenson et al., 2014); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 31589614, 31980526, 11153907, 9744478, 16917893, 22325981, 10896287, 27246466, 21890392) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at