chrX-38352699-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PVS1_SupportingPM2PP5_Moderate
The NM_000531.6(OTC):c.3G>A(p.Met1?) variant causes a start lost change. 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 (★).
Frequency
Consequence
NM_000531.6 start_lost
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OTC | NM_000531.6 | c.3G>A | p.Met1? | start_lost | Exon 1 of 10 | ENST00000039007.5 | NP_000522.3 | |
OTC | NM_001407092.1 | c.3G>A | p.Met1? | start_lost | Exon 3 of 12 | NP_001394021.1 | ||
OTC | XM_017029556.2 | c.3G>A | p.Met1? | start_lost | Exon 1 of 9 | XP_016885045.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OTC | ENST00000039007.5 | c.3G>A | p.Met1? | start_lost | Exon 1 of 10 | 1 | NM_000531.6 | ENSP00000039007.4 | ||
ENSG00000250349 | ENST00000465127.1 | c.172-313422G>A | intron_variant | Intron 3 of 8 | 5 | ENSP00000417050.1 | ||||
OTC | ENST00000488812.1 | n.95G>A | non_coding_transcript_exon_variant | Exon 1 of 6 | 5 | |||||
OTC | ENST00000643344.1 | n.3G>A | non_coding_transcript_exon_variant | Exon 1 of 11 | ENSP00000496606.1 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome Cov.: 27
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
Ornithine carbamoyltransferase deficiency Pathogenic:1
For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 97189). Disruption of the initiator codon has been observed in individual(s) with ornithine transcarbamylase deficiency (PMID: 11793483, 16786505, 32272297). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). This sequence change affects the initiator methionine of the OTC mRNA. The next in-frame methionine is located at codon 21. -
not provided Pathogenic:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at