NM_005138.3(SCO2):c.227_230del (p.Leu76fs) AND Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Feb 19, 2024
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:: RCV003110139.5

Allele description [Variation Report for NM_005138.3(SCO2):c.227_230del (p.Leu76fs)]

NM_005138.3(SCO2):c.227_230del (p.Leu76fs)

Genes:

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

Variant type:

Microsatellite

Cytogenetic location:

22q13.33

Genomic location:

Preferred name:

NM_005138.3(SCO2):c.227_230del (p.Leu76fs)

HGVS:

NC_000022.11:g.50524183CCAG[1]
NG_011860.1:g.10897TGGC[1]
NG_016235.1:g.7251TGGC[1]
NG_021419.1:g.20968CCAG[1]
NM_001169109.2:c.227_230del
NM_001169110.1:c.227_230del
NM_001169111.2:c.227_230del
NM_001185011.2:c.*808CCAG[1]
NM_005138.3:c.227_230delMANE SELECT
NM_152299.4:c.*808CCAG[1]MANE SELECT
NP_001162580.1:p.Leu76fs
NP_001162581.1:p.Leu76fs
NP_001162582.1:p.Leu76fs
NP_005129.2:p.Leu76fs
LRG_727:g.10897TGGC[1]
NC_000022.10:g.50962611_50962614del
NC_000022.10:g.50962612CCAG[1]
NM_005138.2:c.227_230del

Protein change:

L76fs

Molecular consequence:

NM_001185011.2:c.*808CCAG[1] - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_152299.4:c.*808CCAG[1] - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001169109.2:c.227_230del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001169110.1:c.227_230del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001169111.2:c.227_230del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_005138.3:c.227_230del - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

Condition(s)

Name:: Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1 (MC4DN2)
Synonyms:: CYTOCHROME c OXIDASE DEFICIENCY, FATAL INFANTILE, WITH CARDIOENCEPHALOMYOPATHY; Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency; MITOCHONDRIAL COMPLEX IV DEFICIENCY, NUCLEAR TYPE 2
Identifiers:: MONDO: MONDO:0011451; MedGen: C5399977; Orphanet: 1561; OMIM: 604377

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003762132	Laboratory of Inherited Metabolic Diseases, Research centre for medical genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jan 31, 2023)	maternal	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004202363	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Feb 19, 2024)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003762132

Laboratory of Inherited Metabolic Diseases, Research centre for medical genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jan 31, 2023)

maternal

clinical testing

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

SCV004202363

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Feb 19, 2024)

unknown

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	maternal	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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 Laboratory of Inherited Metabolic Diseases, Research centre for medical genetics, SCV003762132.2

#	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	maternal	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

From Baylor Genetics, SCV004202363.2

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jun 17, 2024

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