rs121965047
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PP3_StrongPP5_Moderate
The NM_000274.4(OAT):c.994G>A(p.Val332Met) variant causes a missense change. The variant allele was found at a frequency of 0.000000685 in 1,460,496 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 (★). Synonymous variant affecting the same amino acid position (i.e. V332V) has been classified as Likely benign.
Frequency
Consequence
NM_000274.4 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 |
---|---|---|---|---|---|---|---|
OAT | NM_000274.4 | c.994G>A | p.Val332Met | missense_variant | 8/10 | ENST00000368845.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OAT | ENST00000368845.6 | c.994G>A | p.Val332Met | missense_variant | 8/10 | 1 | NM_000274.4 | P1 | |
OAT | ENST00000539214.5 | c.580G>A | p.Val194Met | missense_variant | 7/9 | 1 | |||
OAT | ENST00000467675.5 | n.795G>A | non_coding_transcript_exon_variant | 7/7 | 5 | ||||
OAT | ENST00000471127.1 | n.504G>A | non_coding_transcript_exon_variant | 2/4 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250456Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135408
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460496Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726604
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Ornithine aminotransferase deficiency Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Jan 31, 2022 | - - |
Likely pathogenic, no assertion criteria provided | literature only | Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) | - | - - |
Gyrate atrophy of choroid and retina with pyridoxine-responsive ornithinemia Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 01, 1993 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at