NM_182476.3(COQ6):c.1078C>T (p.Arg360Trp) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Aug 22, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001877231.12

Allele description [Variation Report for NM_182476.3(COQ6):c.1078C>T (p.Arg360Trp)]

NM_182476.3(COQ6):c.1078C>T (p.Arg360Trp)

Genes:

COQ6:coenzyme Q6, monooxygenase [Gene - OMIM - HGNC]
ENTPD5:ectonucleoside triphosphate diphosphohydrolase 5 (inactive) [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

14q24.3

Genomic location:

Preferred name:

NM_182476.3(COQ6):c.1078C>T (p.Arg360Trp)

HGVS:

NC_000014.9:g.73961359C>T
NG_032805.1:g.16426C>T
NM_001321984.2:c.*174G>A
NM_001330189.2:c.1201-1806G>A
NM_001382258.1:c.1201-5772G>A
NM_001382259.1:c.1201-1806G>A
NM_001382260.1:c.1201-1806G>A
NM_001382262.1:c.1201-5531G>A
NM_001425255.1:c.1078C>T
NM_001425256.1:c.970C>T
NM_001425257.1:c.913C>T
NM_001425258.1:c.895C>T
NM_001425259.1:c.853C>T
NM_001425260.1:c.853C>T
NM_001425261.1:c.853C>T
NM_001425262.1:c.823C>T
NM_001425263.1:c.751C>T
NM_001425264.1:c.538C>T
NM_001425265.1:c.538C>T
NM_182476.3:c.1078C>TMANE SELECT
NM_182480.3:c.1003C>T
NP_001412184.1:p.Arg360Trp
NP_001412185.1:p.Arg324Trp
NP_001412186.1:p.Arg305Trp
NP_001412187.1:p.Arg299Trp
NP_001412188.1:p.Arg285Trp
NP_001412189.1:p.Arg285Trp
NP_001412190.1:p.Arg285Trp
NP_001412191.1:p.Arg275Trp
NP_001412192.1:p.Arg251Trp
NP_001412193.1:p.Arg180Trp
NP_001412194.1:p.Arg180Trp
NP_872282.1:p.Arg360Trp
NP_872286.2:p.Arg335Trp
NC_000014.8:g.74428062C>T

Protein change:

R335W

Links:

dbSNP: rs778856227

NCBI 1000 Genomes Browser:

rs778856227

Molecular consequence:

NM_001321984.2:c.*174G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001330189.2:c.1201-1806G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001382258.1:c.1201-5772G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001382259.1:c.1201-1806G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001382260.1:c.1201-1806G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001382262.1:c.1201-5531G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001425255.1:c.1078C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001425256.1:c.970C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001425257.1:c.913C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001425258.1:c.895C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001425259.1:c.853C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001425260.1:c.853C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001425261.1:c.853C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001425262.1:c.823C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001425263.1:c.751C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001425264.1:c.538C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001425265.1:c.538C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_182476.3:c.1078C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_182480.3:c.1003C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002131553	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Aug 22, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 28173653, 30232548, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002131553

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Aug 22, 2023)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

[Coenzyme Q(10) treatment for one child with COQ6 gene mutation induced nephrotic syndrome and literature review].

Cao Q, Li GM, Xu H, Shen Q, Sun L, Fang XY, Liu HM, Guo W, Zhai YH, Wu BB.

Zhonghua Er Ke Za Zhi. 2017 Feb 2;55(2):135-138. doi: 10.3760/cma.j.issn.0578-1310.2017.02.016. Review. Chinese.

PubMed [citation]

PMID:: 28173653

Stańczyk M, Bałasz-Chmielewska I, Lipska-Ziętkiewicz B, Tkaczyk M.

Pediatr Nephrol. 2018 Dec;33(12):2383-2387. doi: 10.1007/s00467-018-4083-3. Epub 2018 Sep 19.

PubMed [citation]

PMID:: 30232548
PMCID:: PMC6208703

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002131553.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt COQ6 protein function. ClinVar contains an entry for this variant (Variation ID: 1370573). This missense change has been observed in individual(s) with coenzyme Q10 deficiency (PMID: 28173653, 30232548). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is present in population databases (rs778856227, gnomAD 0.003%). This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 360 of the COQ6 protein (p.Arg360Trp).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 24, 2024

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