chr10-124397962-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000274.4(OAT):āc.1300A>Gā(p.Lys434Glu) variant causes a missense change. The variant allele was found at a frequency of 0.0000438 in 1,461,544 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K434T) has been classified as Uncertain significance.
Frequency
Consequence
NM_000274.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OAT | NM_000274.4 | c.1300A>G | p.Lys434Glu | missense_variant | 10/10 | ENST00000368845.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OAT | ENST00000368845.6 | c.1300A>G | p.Lys434Glu | missense_variant | 10/10 | 1 | NM_000274.4 | P1 | |
OAT | ENST00000539214.5 | c.886A>G | p.Lys296Glu | missense_variant | 9/9 | 1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000280 AC: 7AN: 250136Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135456
GnomAD4 exome AF: 0.0000438 AC: 64AN: 1461544Hom.: 0 Cov.: 31 AF XY: 0.0000385 AC XY: 28AN XY: 727072
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Ornithine aminotransferase deficiency Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 13, 2021 | This sequence change replaces lysine with glutamic acid at codon 434 of the OAT protein (p.Lys434Glu). The lysine residue is moderately conserved and there is a small physicochemical difference between lysine and glutamic acid. This variant is present in population databases (rs200785094, ExAC 0.003%). This variant has not been reported in the literature in individuals affected with OAT-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at