rs66737144
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_000531.6(OTC):c.386+1G>A variant causes a splice donor, intron 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. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Consequence
NM_000531.6 splice_donor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OTC | NM_000531.6 | c.386+1G>A | splice_donor_variant, intron_variant | Intron 4 of 9 | ENST00000039007.5 | NP_000522.3 | ||
OTC | NM_001407092.1 | c.386+1G>A | splice_donor_variant, intron_variant | Intron 6 of 11 | NP_001394021.1 | |||
OTC | XM_017029556.2 | c.386+1G>A | splice_donor_variant, intron_variant | Intron 4 of 8 | XP_016885045.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OTC | ENST00000039007.5 | c.386+1G>A | splice_donor_variant, intron_variant | Intron 4 of 9 | 1 | NM_000531.6 | ENSP00000039007.4 | |||
ENSG00000250349 | ENST00000465127.1 | c.172-284691G>A | intron_variant | Intron 3 of 8 | 5 | ENSP00000417050.1 | ||||
OTC | ENST00000488812.1 | n.423+1G>A | splice_donor_variant, intron_variant | Intron 4 of 5 | 5 | |||||
OTC | ENST00000643344.1 | n.*136+1G>A | splice_donor_variant, intron_variant | Intron 5 of 10 | ENSP00000496606.1 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome Cov.: 23
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
not provided Pathogenic:2
Canonical splice site variant predicted to result in a null allele in a gene for which loss-of-function is a known mechanism of disease; Published functional studies demonstrate skipping of exon 4 in a majority of transcripts (Sacchetto et al., 2021); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25525159, 16786505, 34906067) -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at