4-83264242-GTCT-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP3BS1_Supporting
The NM_001358921.2(COQ2):c.1070_1072delAGA(p.Lys357del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0000107 in 1,593,514 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000097 ( 0 hom. )
Consequence
COQ2
NM_001358921.2 disruptive_inframe_deletion
NM_001358921.2 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.71
Genes affected
COQ2 (HGNC:25223): (coenzyme Q2, polyprenyltransferase) This gene encodes an enzyme that functions in the final steps in the biosynthesis of CoQ (ubiquinone), a redox carrier in the mitochondrial respiratory chain and a lipid-soluble antioxidant. This enzyme, which is part of the coenzyme Q10 pathway, catalyzes the prenylation of parahydroxybenzoate with an all-trans polyprenyl group. Mutations in this gene cause coenzyme Q10 deficiency, a mitochondrial encephalomyopathy, and also COQ2 nephropathy, an inherited form of mitochondriopathy with primary renal involvement. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP3
Nonframeshift variant in repetitive region in NM_001358921.2
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0000198 (3/151632) while in subpopulation EAS AF= 0.00058 (3/5170). AF 95% confidence interval is 0.000157. There are 0 homozygotes in gnomad4. There are 1 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COQ2 | NM_001358921.2 | c.1070_1072delAGA | p.Lys357del | disruptive_inframe_deletion | Exon 7 of 7 | ENST00000647002.2 | NP_001345850.1 | |
COQ2 | NM_015697.9 | c.1220_1222delAGA | p.Lys407del | disruptive_inframe_deletion | Exon 7 of 7 | NP_056512.5 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151514Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000373 AC: 9AN: 241298Hom.: 0 AF XY: 0.0000229 AC XY: 3AN XY: 131102
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GnomAD4 exome AF: 0.00000971 AC: 14AN: 1441882Hom.: 0 AF XY: 0.00000975 AC XY: 7AN XY: 717838
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GnomAD4 genome AF: 0.0000198 AC: 3AN: 151632Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74068
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Coenzyme Q10 deficiency, primary, 1;C3714927:Multiple system atrophy 1, susceptibility to Uncertain:1
Mar 26, 2024
Fulgent Genetics, Fulgent Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Coenzyme Q10 deficiency, primary, 1 Uncertain:1
Jun 07, 2017
SingHealth Duke-NUS Institute of Precision Medicine
Significance: Uncertain significance
Review Status: no assertion criteria provided
Collection Method: curation
- -
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at