rs886037736
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_032620.4(GTPBP3):c.32_33delinsGTG(p.Gln11ArgfsTer98) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Consequence
GTPBP3
NM_032620.4 frameshift
NM_032620.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.788
Genes affected
GTPBP3 (HGNC:14880): (GTP binding protein 3, mitochondrial) This locus encodes a GTP-binding protein. The encoded protein is localized to the mitochondria and may play a role in mitochondrial tRNA modification. Polymorphisms at this locus may be associated with severity of aminoglycoside-induced deafness, a disease associated with a mutation in the 12S rRNA. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Sep 2010]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 11 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 40 pathogenic variants in the truncated region.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 19-17337643-AA-GTG is Pathogenic according to our data. Variant chr19-17337643-AA-GTG is described in ClinVar as [Pathogenic]. Clinvar id is 180619.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GTPBP3 | NM_032620.4 | c.32_33delinsGTG | p.Gln11ArgfsTer98 | frameshift_variant | 1/9 | ENST00000324894.13 | |
GTPBP3 | NM_001128855.3 | c.32_33delinsGTG | p.Gln11ArgfsTer98 | frameshift_variant | 1/9 | ||
GTPBP3 | NM_133644.4 | c.32_33delinsGTG | p.Gln11ArgfsTer98 | frameshift_variant | 1/8 | ||
GTPBP3 | NM_001195422.1 | c.120-365_120-364delinsGTG | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GTPBP3 | ENST00000324894.13 | c.32_33delinsGTG | p.Gln11ArgfsTer98 | frameshift_variant | 1/9 | 1 | NM_032620.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Combined oxidative phosphorylation defect type 23 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 04, 2014 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at