NM_001358921.2(COQ2):c.138dup (p.Ala47fs) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Mar 20, 2024
Review status:: criteria provided, conflicting classifications

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:: RCV000930683.10

Allele description [Variation Report for NM_001358921.2(COQ2):c.138dup (p.Ala47fs)]

NM_001358921.2(COQ2):c.138dup (p.Ala47fs)

Genes:

LOC112997540:Sharpr-MPRA regulatory region 13773 [Gene]
COQ2:coenzyme Q2, polyprenyltransferase [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

4q21.23

Genomic location:

Preferred name:

NM_001358921.2(COQ2):c.138dup (p.Ala47fs)

Other names:

p.Ala97Argfs*56

HGVS:

NC_000004.12:g.83284632dup
NG_015825.1:g.5288dup
NG_061533.1:g.97dup
NM_001358921.2:c.138dupMANE SELECT
NM_015697.8:c.288dup
NM_015697.9:c.288dup
NP_001345850.1:p.Ala47fs
NP_056512.5:p.Ala97fs
NC_000004.11:g.84205779_84205780insG
NC_000004.11:g.84205785dup
NM_015697.7:c.288dup
NM_015697.7:c.288dupC

Protein change:

A47fs

Links:

dbSNP: rs759310292

NCBI 1000 Genomes Browser:

rs759310292

Molecular consequence:

NM_001358921.2:c.138dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_015697.9:c.288dup - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

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
SCV001076338	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Oct 22, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004014609	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Jul 17, 2023)	germline	clinical testing	Citation Link,
SCV005413644	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Mar 20, 2024)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 33187544, 35483523, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001076338

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Oct 22, 2023)

germline

clinical testing

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

SCV004014609

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Jul 17, 2023)

germline

clinical testing

Citation Link,

SCV005413644

Mayo Clinic Laboratories, Mayo Clinic

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Mar 20, 2024)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	2	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Compound heterozygous inheritance of two novel COQ2 variants results in familial coenzyme Q deficiency.

Abdelhakim AH, Dharmadhikari AV, Ragi SD, de Carvalho JRL Jr, Xu CL, Thomas AL, Buchovecky CM, Mansukhani MM, Naini AB, Liao J, Jobanputra V, Maumenee IH, Tsang SH.

Orphanet J Rare Dis. 2020 Nov 13;15(1):320. doi: 10.1186/s13023-020-01600-8.

PubMed [citation]

PMID:: 33187544
PMCID:: PMC7662744

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001076338.4

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

#	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

From GeneDx, SCV004014609.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 30487145, 35483523, 33187544)

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

From Mayo Clinic Laboratories, Mayo Clinic, SCV005413644.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	not provided	not provided	clinical testing	PubMed (3)

Description

PM2, PVS1

#	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		2	not provided	not provided	not provided

Last Updated: Nov 24, 2024

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