rs757588809
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001292063.2(OTOG):c.3359T>C(p.Leu1120Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000153 in 1,550,434 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L1120R) has been classified as Uncertain significance.
Frequency
Consequence
NM_001292063.2 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OTOG | NM_001292063.2 | c.3359T>C | p.Leu1120Pro | missense_variant | 28/56 | ENST00000399397.6 | |
OTOG | NM_001277269.2 | c.3395T>C | p.Leu1132Pro | missense_variant | 27/55 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTOG | ENST00000399397.6 | c.3359T>C | p.Leu1120Pro | missense_variant | 28/56 | 5 | NM_001292063.2 | P2 | |
OTOG | ENST00000399391.7 | c.3395T>C | p.Leu1132Pro | missense_variant | 27/55 | 5 | A2 | ||
OTOG | ENST00000342528.2 | n.724T>C | non_coding_transcript_exon_variant | 5/22 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000871 AC: 13AN: 149212Hom.: 0 AF XY: 0.0000622 AC XY: 5AN XY: 80376
GnomAD4 exome AF: 0.000157 AC: 219AN: 1398264Hom.: 0 Cov.: 32 AF XY: 0.000151 AC XY: 104AN XY: 689652
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74334
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 30, 2023 | This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 1132 of the OTOG protein (p.Leu1132Pro). This variant is present in population databases (rs757588809, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with OTOG-related conditions. ClinVar contains an entry for this variant (Variation ID: 517377). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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. - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Dec 10, 2020 | In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | May 16, 2017 | The p.Leu1132Pro variant in OTOG has not been previously reported in individuals with hearing loss, but has been identified in 12/67064 European chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs757588809). Although this variant has been seen in the general population, it s frequency is not high enough to rule out a pathogenic role. Computational pred iction tools and conservation analysis suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogeni city. In summary, the clinical significance of the p.Leu1132Pro variant is uncer tain. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at