4-83264306-G-T
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001358921.2(COQ2):c.1009C>A(p.Arg337=) variant causes a synonymous change. The variant allele was found at a frequency of 0.000000685 in 1,459,948 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
COQ2
NM_001358921.2 synonymous
NM_001358921.2 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.21
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;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| COQ2 | NM_001358921.2 | c.1009C>A | p.Arg337= | synonymous_variant | 7/7 | ENST00000647002.2 | NP_001345850.1 | |
| COQ2 | NM_015697.9 | c.1159C>A | p.Arg387= | synonymous_variant | 7/7 | NP_056512.5 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| COQ2 | ENST00000647002.2 | c.1009C>A | p.Arg337= | synonymous_variant | 7/7 | NM_001358921.2 | ENSP00000495761 | P2 | ||
| COQ2 | ENST00000311469.9 | c.1159C>A | p.Arg387= | synonymous_variant | 7/7 | 1 | ENSP00000310873 | A2 | ||
| COQ2 | ENST00000503915.5 | c.*141C>A | 3_prime_UTR_variant, NMD_transcript_variant | 7/7 | 1 | ENSP00000427146 | ||||
| COQ2 | ENST00000503391.5 | c.*176-1651C>A | intron_variant, NMD_transcript_variant | 2 | ENSP00000426242 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.00000404 AC: 1AN: 247460Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134266
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GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459948Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 726188
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GnomAD4 genome
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at