chr4-83264242-GTCT-G
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP3
The NM_001358921.2(COQ2):βc.1070_1072delβ(p.Lys357del) variant causes a 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 (β ).
Frequency
Genomes: π 0.000020 ( 0 hom., cov: 32)
Exomes π: 0.0000097 ( 0 hom. )
Consequence
COQ2
NM_001358921.2 inframe_deletion
NM_001358921.2 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 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP3
Nonframeshift variant in repetitive region in NM_001358921.2
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COQ2 | NM_001358921.2 | c.1070_1072del | p.Lys357del | inframe_deletion | 7/7 | ENST00000647002.2 | NP_001345850.1 | |
COQ2 | NM_015697.9 | c.1220_1222del | p.Lys407del | inframe_deletion | 7/7 | NP_056512.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COQ2 | ENST00000647002.2 | c.1070_1072del | p.Lys357del | inframe_deletion | 7/7 | NM_001358921.2 | ENSP00000495761 | P2 | ||
COQ2 | ENST00000311469.9 | c.1220_1222del | p.Lys407del | inframe_deletion | 7/7 | 1 | ENSP00000310873 | A2 | ||
COQ2 | ENST00000503915.5 | c.*202_*204del | 3_prime_UTR_variant, NMD_transcript_variant | 7/7 | 1 | ENSP00000427146 | ||||
COQ2 | ENST00000503391.5 | c.*176-1590_*176-1588del | intron_variant, NMD_transcript_variant | 2 | ENSP00000426242 |
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
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jul 21, 2021 | - - |
Coenzyme Q10 deficiency, primary, 1 Uncertain:1
Uncertain significance, no assertion criteria provided | curation | SingHealth Duke-NUS Institute of Precision Medicine | Jun 07, 2017 | - - |
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