rs72556281
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 8P and 4B. PM1PM5PP3_StrongBS2
The NM_000531.6(OTC):c.520G>A(p.Ala174Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000664 in 1,205,605 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A174P) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000531.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OTC | NM_000531.6 | c.520G>A | p.Ala174Thr | missense_variant | Exon 5 of 10 | ENST00000039007.5 | NP_000522.3 | |
OTC | NM_001407092.1 | c.520G>A | p.Ala174Thr | missense_variant | Exon 7 of 12 | NP_001394021.1 | ||
OTC | XM_017029556.2 | c.520G>A | p.Ala174Thr | missense_variant | Exon 5 of 9 | XP_016885045.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000895 AC: 1AN: 111772Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33972
GnomAD4 exome AF: 0.00000640 AC: 7AN: 1093833Hom.: 0 Cov.: 28 AF XY: 0.00000835 AC XY: 3AN XY: 359303
GnomAD4 genome AF: 0.00000895 AC: 1AN: 111772Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33972
ClinVar
Submissions by phenotype
Ornithine carbamoyltransferase deficiency Uncertain:3
Uncertain significance, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 07, 2021 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | May 17, 2022 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | All of Us Research Program, National Institutes of Health | Jul 29, 2024 | This missense variant replaces alanine with threonine at codon 174 of the OTC protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function. To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with OTC-related disorders in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. - |
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Dec 14, 2017 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Apr 14, 2017 | The A174T variant in the OTC gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. A missense variant at the same codon (A174P) has been reported previously, using alternate nomenclature, as de novo in a female who presented with Reye like" illness with hyperammonemia and orotic aciduria. However, no enzymatic studies were performed to confirm a diagnosis of OTC deficiency (Tsai et al., 1993). The A174T variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The A174T variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret A174T as a variant of uncertain significance." - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at