rs104894507
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_000485.3(APRT):c.294G>A(p.Trp98Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,612,136 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 (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_000485.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APRT | NM_000485.3 | c.294G>A | p.Trp98Ter | stop_gained | 3/5 | ENST00000378364.8 | |
APRT | NM_001030018.2 | c.294G>A | p.Trp98Ter | stop_gained | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APRT | ENST00000378364.8 | c.294G>A | p.Trp98Ter | stop_gained | 3/5 | 1 | NM_000485.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000242 AC: 6AN: 247560Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134848
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1459928Hom.: 0 Cov.: 32 AF XY: 0.00000826 AC XY: 6AN XY: 726260
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74374
ClinVar
Submissions by phenotype
Adenine phosphoribosyltransferase deficiency Pathogenic:4Other:1
Pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jan 06, 2022 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Apr 25, 2022 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 01, 1991 | - - |
Pathogenic, no assertion criteria provided | literature only | APRT Deficiency Research Program of the Rare Kidney Stone Consortium, Landspitali, National University Hospital of Iceland | Sep 01, 2020 | - - |
not provided, no classification provided | literature only | GeneReviews | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at