rs72556273
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1PM2PM5PP3_Moderate
The NM_000531.6(OTC):c.490T>A(p.Ser164Thr) 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S164P) has been classified as Pathogenic.
Frequency
Consequence
NM_000531.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OTC | NM_000531.6 | c.490T>A | p.Ser164Thr | missense_variant | 5/10 | ENST00000039007.5 | |
OTC | NM_001407092.1 | c.490T>A | p.Ser164Thr | missense_variant | 7/12 | ||
OTC | XM_017029556.2 | c.490T>A | p.Ser164Thr | missense_variant | 5/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTC | ENST00000039007.5 | c.490T>A | p.Ser164Thr | missense_variant | 5/10 | 1 | NM_000531.6 | P1 | |
OTC | ENST00000488812.1 | n.527T>A | non_coding_transcript_exon_variant | 5/6 | 5 | ||||
OTC | ENST00000643344.1 | c.*240T>A | 3_prime_UTR_variant, NMD_transcript_variant | 6/11 |
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD4 exome Cov.: 28
GnomAD4 genome Cov.: 24
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at