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NM_020247.5(COQ8A):c.993C>T (p.Phe331=) AND Autosomal recessive ataxia due to ubiquinone deficiency

Germline classification:
Benign (5 submissions)
Last evaluated:
Jun 28, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000003830.23

Allele description [Variation Report for NM_020247.5(COQ8A):c.993C>T (p.Phe331=)]

NM_020247.5(COQ8A):c.993C>T (p.Phe331=)

Gene:
COQ8A:coenzyme Q8A [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q42.13
Genomic location:
Preferred name:
NM_020247.5(COQ8A):c.993C>T (p.Phe331=)
Other names:
p.F331F:TTC>TTT
HGVS:
  • NC_000001.11:g.226982947C>T
  • NG_012825.2:g.90412C>T
  • NM_020247.5:c.993C>TMANE SELECT
  • NP_064632.2:p.Phe331=
  • LRG_1092t1:c.993C>T
  • LRG_1092:g.90412C>T
  • LRG_1092p1:p.Phe331=
  • NC_000001.10:g.227170648C>T
  • NG_012825.1:g.47711C>T
  • NM_020247.4:c.993C>T
  • NP_064632.2:p.Leu314_Gln360del
  • p.Phe331Phe
Links:
OMIM: 606980.0010; dbSNP: rs41303129
NCBI 1000 Genomes Browser:
rs41303129
Molecular consequence:
  • NM_020247.5:c.993C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Autosomal recessive ataxia due to ubiquinone deficiency
Synonyms:
Spinocerebellar ataxia, autosomal recessive 9; Coenzyme Q10 deficiency, primary, 4
Identifiers:
MONDO: MONDO:0012784; MedGen: C2677589; Orphanet: 139485; OMIM: 612016

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000023995OMIM
no assertion criteria provided
Pathogenic
(Mar 1, 2008)
germlineliterature only

PubMed (1)
[See all records that cite this PMID]

SCV000355249Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)
Benign
(Mar 6, 2018)
germlineclinical testing

Citation Link,

SCV000494096GeneReviews
no classification provided
not providedgermlineliterature only

PubMed (1)
[See all records that cite this PMID]

SCV000884981ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2024)
Benign
(Jun 28, 2023)
germlineclinical testing

Citation Link,

SCV002803569Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Benign
(Jul 20, 2021)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, literature only

Citations

PubMed

ADCK3, an ancestral kinase, is mutated in a form of recessive ataxia associated with coenzyme Q10 deficiency.

Lagier-Tourenne C, Tazir M, López LC, Quinzii CM, Assoum M, Drouot N, Busso C, Makri S, Ali-Pacha L, Benhassine T, Anheim M, Lynch DR, Thibault C, Plewniak F, Bianchetti L, Tranchant C, Poch O, DiMauro S, Mandel JL, Barros MH, Hirano M, Koenig M.

Am J Hum Genet. 2008 Mar;82(3):661-72. doi: 10.1016/j.ajhg.2007.12.024.

PubMed [citation]
PMID:
18319074
PMCID:
PMC2427193

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From OMIM, SCV000023995.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In a patient of French and Algerian ancestry with CoQ10 deficiency-4 manifest as cerebellar ataxia (COQ10D4; 612016), Lagier-Tourenne et al. (2008) found compound heterozygosity for 2 mutations in the ADCK3 gene: a mutation in a predicted exonic splice enhancer in exon 8 (993C-T), and a 1645G-A transition in exon 14, resulting in a gly549-to-ser substitution (G549S; 606980.0011). The exon 8 mutation resulted in skipping of exon 8 leading to an in-frame deletion of 47 amino acids (Lys314_Gln360del).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Illumina Laboratory Services, Illumina, SCV000355249.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From GeneReviews, SCV000494096.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000884981.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Fulgent Genetics, Fulgent Genetics, SCV002803569.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 20, 2024