X-38352581-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001407092.1(OTC):c.-79-37C>T variant causes a intron change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001407092.1 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OTC | NM_001407092.1 | c.-79-37C>T | intron_variant | Intron 2 of 11 | NP_001394021.1 | |||
OTC | NM_000531.6 | c.-116C>T | upstream_gene_variant | ENST00000039007.5 | NP_000522.3 | |||
OTC | XM_017029556.2 | c.-116C>T | upstream_gene_variant | XP_016885045.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENSG00000250349 | ENST00000465127.1 | c.172-313540C>T | intron_variant | Intron 3 of 8 | 5 | ENSP00000417050.1 | ||||
OTC | ENST00000039007.5 | c.-116C>T | upstream_gene_variant | 1 | NM_000531.6 | ENSP00000039007.4 | ||||
OTC | ENST00000488812.1 | n.-24C>T | upstream_gene_variant | 5 | ||||||
OTC | ENST00000643344.1 | n.-116C>T | upstream_gene_variant | ENSP00000496606.1 |
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD4 exome Cov.: 6
GnomAD4 genome Cov.: 22
ClinVar
Submissions by phenotype
Ornithine carbamoyltransferase deficiency Pathogenic:1Uncertain:1
The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the gnomAD database. This variant occurs in a non-coding region of the OTC gene. It does not change the encoded amino acid sequence of the OTC protein. This variant has been observed in individual(s) with clinical features of OTC deficiency (PMID: 29282796; Invitae). 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. Studies have shown that this variant alters OTC gene expression (PMID: 29282796). ClinVar contains an entry for this variant (Variation ID: 487343). -
The patient had clinical and biochemical symptoms of OTC deficiency, and no disease causing sequence variants in the OTC coding sequence and canonical splice sites. Functional testing in cultured cells indicates reduced expression of reporter gene. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at