NM_005138.3(SCO2):c.16_17insAGCATGCAGCAGTGACTCA (p.Arg6fs) AND Primary dilated cardiomyopathy

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Dec 3, 2015
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:: RCV000208004.2

Allele description [Variation Report for NM_005138.3(SCO2):c.16_17insAGCATGCAGCAGTGACTCA (p.Arg6fs)]

NM_005138.3(SCO2):c.16_17insAGCATGCAGCAGTGACTCA (p.Arg6fs)

Genes:

NCAPH2:non-SMC condensin II complex subunit H2 [Gene - OMIM - HGNC]
SCO2:synthesis of cytochrome C oxidase 2 [Gene - OMIM - HGNC]

Variant type:

Insertion

Cytogenetic location:

22q13.33

Genomic location:

Preferred name:

NM_005138.3(SCO2):c.16_17insAGCATGCAGCAGTGACTCA (p.Arg6fs)

HGVS:

NC_000022.11:g.50524395_50524396insTGAGTCACTGCTGCATGCT
NG_011860.1:g.10690_10691insAGCATGCAGCAGTGACTCA
NG_016235.1:g.7044_7045insAGCATGCAGCAGTGACTCA
NG_021419.1:g.21180_21181insTGAGTCACTGCTGCATGCT
NM_001169109.2:c.16_17insAGCATGCAGCAGTGACTCA
NM_001169110.1:c.16_17insAGCATGCAGCAGTGACTCA
NM_001169111.2:c.16_17insAGCATGCAGCAGTGACTCA
NM_001185011.2:c.*1020_*1021insTGAGTCACTGCTGCATGCT
NM_005138.3:c.16_17insAGCATGCAGCAGTGACTCAMANE SELECT
NM_152299.4:c.*1020_*1021insTGAGTCACTGCTGCATGCTMANE SELECT
NP_001162580.1:p.Arg6fs
NP_001162580.1:p.Arg6fs
NP_001162581.1:p.Arg6fs
NP_001162582.1:p.Arg6fs
NP_005129.2:p.Arg6fs
NP_005129.2:p.Arg6fs
LRG_727:g.10690_10691insAGCATGCAGCAGTGACTCA
NC_000022.10:g.50962824_50962825insTGAGTCACTGCTGCATGCT
NM_001169109.1:c.16_17insAGCATGCAGCAGTGACTCA
NM_005138.2:c.16_17insAGCATGCAGCAGTGACTCA

Protein change:

R6fs

Links:

dbSNP: rs749838192

NCBI 1000 Genomes Browser:

rs749838192

Molecular consequence:

NM_001185011.2:c.*1020_*1021insTGAGTCACTGCTGCATGCT - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_152299.4:c.*1020_*1021insTGAGTCACTGCTGCATGCT - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001169109.2:c.16_17insAGCATGCAGCAGTGACTCA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001169110.1:c.16_17insAGCATGCAGCAGTGACTCA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001169111.2:c.16_17insAGCATGCAGCAGTGACTCA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_005138.3:c.16_17insAGCATGCAGCAGTGACTCA - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

Condition(s)

Name:: Primary dilated cardiomyopathy (DCM)
Synonyms:: Dilated Cardiomyopathy
Identifiers:: EFO: EFO_0000407; MONDO: MONDO:0005021; MeSH: D002311; MedGen: C0007193; Human Phenotype Ontology: HP:0001644

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000264220	Blueprint Genetics	criteria provided, single submitter (Variant Classification)	Likely pathogenic (Dec 3, 2015)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV001142498	Reproductive Health Research and Development, BGI Genomics	no assertion criteria provided	Likely pathogenic (Jan 6, 2020)	germline	curation

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000264220

Blueprint Genetics

criteria provided, single submitter

(Variant Classification)

Likely pathogenic
(Dec 3, 2015)

germline

clinical testing

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

Citation Link,

SCV001142498

Reproductive Health Research and Development, BGI Genomics

no assertion criteria provided

Likely pathogenic
(Jan 6, 2020)

germline

curation

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	curation
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A novel mutation in the SCO2 gene in a neonate with early-onset cardioencephalomyopathy.

Joost K, Rodenburg R, Piirsoo A, van den Heuvel B, Zordania R, Ounap K.

Pediatr Neurol. 2010 Mar;42(3):227-30. doi: 10.1016/j.pediatrneurol.2009.10.004.

PubMed [citation]

PMID:: 20159436

Details of each submission

From Blueprint Genetics, SCV000264220.2

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

From Reproductive Health Research and Development, BGI Genomics, SCV001142498.1

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

Description

NM_005138.2:c.16_17insAGCATGCAGCAGTGACTCA in the SCO2 gene has an allele frequency of 0.008 in European (Finnish) subpopulation in the gnomAD database. The p.Arg6Glnfs*82 (NM_005138.2:c.16_17insAGCATGCAGCAGTGACTCA) variant has been detected in an patient with Early-Onset Cardioencephalomyopathy, in tans with c.418G>A. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. Taken together, we interprete this variant as Pathogenic/Likely pathogenic. ACMG/AMP Criteria applied: PVS1; PM3.

#	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: Sep 29, 2024

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