rs180177168
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP3_StrongPP5
The NM_000030.3(AGXT):c.122G>A(p.Gly41Glu) variant causes a missense change. The variant allele was found at a frequency of 0.00000186 in 1,612,874 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 (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G41R) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000030.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGXT | NM_000030.3 | c.122G>A | p.Gly41Glu | missense_variant | 1/11 | ENST00000307503.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGXT | ENST00000307503.4 | c.122G>A | p.Gly41Glu | missense_variant | 1/11 | 1 | NM_000030.3 | P1 | |
AGXT | ENST00000472436.1 | n.142G>A | non_coding_transcript_exon_variant | 1/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000404 AC: 1AN: 247546Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134532
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460674Hom.: 0 Cov.: 34 AF XY: 0.00000138 AC XY: 1AN XY: 726644
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 34 AF XY: 0.0000135 AC XY: 1AN XY: 74346
ClinVar
Submissions by phenotype
Primary hyperoxaluria, type I Pathogenic:1
Pathogenic, no assertion criteria provided | in vitro | Clinical Biochemistry Laboratory, Health Services Laboratory | Nov 27, 2014 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at