rs72554332
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1PM2PM5PP3_StrongPP5_Very_Strong
The NM_000531.6(OTC):c.238A>G(p.Lys80Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K80N) has been classified as Pathogenic.
Frequency
Consequence
NM_000531.6 missense
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 |
---|---|---|---|---|---|---|---|
OTC | NM_000531.6 | c.238A>G | p.Lys80Glu | missense_variant | 3/10 | ENST00000039007.5 | |
OTC | NM_001407092.1 | c.238A>G | p.Lys80Glu | missense_variant | 5/12 | ||
OTC | XM_017029556.2 | c.238A>G | p.Lys80Glu | missense_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTC | ENST00000039007.5 | c.238A>G | p.Lys80Glu | missense_variant | 3/10 | 1 | NM_000531.6 | P1 | |
OTC | ENST00000488812.1 | n.330A>G | non_coding_transcript_exon_variant | 3/6 | 5 | ||||
OTC | ENST00000643344.1 | c.238A>G | p.Lys80Glu | missense_variant, NMD_transcript_variant | 3/11 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome Cov.: 25
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
not provided Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 05, 2012 | - - |
Pathogenic, no assertion criteria provided | literature only | GenMed Metabolism Lab | - | - - |
Ornithine carbamoyltransferase deficiency Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Jul 19, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at