rs140246430
Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1PM2PM5PP3_ModeratePP5_Very_Strong
The NM_020247.5(COQ8A):c.901C>T(p.Arg301Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000266 in 1,613,556 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R301Q) has been classified as Likely pathogenic.
Frequency
Consequence
NM_020247.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 16 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COQ8A | ENST00000366777.4 | c.901C>T | p.Arg301Trp | missense_variant | Exon 7 of 15 | 1 | NM_020247.5 | ENSP00000355739.3 | ||
ENSG00000288674 | ENST00000366779.6 | n.*5628C>T | non_coding_transcript_exon_variant | Exon 24 of 32 | 2 | ENSP00000355741.2 | ||||
ENSG00000288674 | ENST00000366779.6 | n.*5628C>T | 3_prime_UTR_variant | Exon 24 of 32 | 2 | ENSP00000355741.2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250778Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135786
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461352Hom.: 0 Cov.: 33 AF XY: 0.0000234 AC XY: 17AN XY: 726974
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74362
ClinVar
Submissions by phenotype
Autosomal recessive ataxia due to ubiquinone deficiency Pathogenic:3
Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Feb 15, 2024 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 15, 2016 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jun 29, 2022 | - - |
Inborn genetic diseases Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 17, 2022 | The c.901C>T (p.R301W) alteration is located in exon 7 (coding exon 6) of the COQ8A gene. This alteration results from a C to T substitution at nucleotide position 901, causing the arginine (R) at amino acid position 301 to be replaced by a tryptophan (W). Based on data from gnomAD, the T allele has an overall frequency of <0.01% (10/282150) total alleles studied. The highest observed frequency was 0.01% (8/128598) of European (non-Finnish) alleles. This variant has been detected in conjunction with a COQ8A pathogenic variant in multiple individuals with clinical features of COQ8-related conezyme Q10 deficiency (Galosi, 2019; Schirinzi, 2019). This amino acid position is highly conserved in available vertebrate species. The in silico prediction for this alteration is inconclusive. Based on the available evidence, this alteration is classified as likely pathogenic. - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 22, 2024 | This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 301 of the COQ8A protein (p.Arg301Trp). This variant is present in population databases (rs140246430, gnomAD 0.005%). This missense change has been observed in individual(s) with clinical features of primary coenzyme Q10 deficiency (PMID: 29915382, 30637285, 31890231, 32337771). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 434087). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed for this missense variant. However, the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on COQ8A protein function. Experimental studies have shown that this missense change affects COQ8A function (PMID: 32337771). For these reasons, this variant has been classified as Pathogenic. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at