NM_005138.3(SCO2):c.2T>C (p.Met1Thr) AND Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency

Clinical significance:Likely pathogenic

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000985024.2

Allele description [Variation Report for NM_005138.3(SCO2):c.2T>C (p.Met1Thr)]

NM_005138.3(SCO2):c.2T>C (p.Met1Thr)

Genes:
NCAPH2:non-SMC condensin II complex subunit H2 [Gene - OMIM - HGNC]
SCO2:synthesis of cytochrome C oxidase 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
22q13.33
Genomic location:
Preferred name:
NM_005138.3(SCO2):c.2T>C (p.Met1Thr)
HGVS:
  • NC_000022.11:g.50524410A>G
  • NG_011860.1:g.10676T>C
  • NG_016235.1:g.7030T>C
  • NG_021419.1:g.21195A>G
  • NM_001169109.1:c.2T>C
  • NM_001169109.2:c.2T>C
  • NM_001169110.1:c.2T>C
  • NM_001169111.2:c.2T>C
  • NM_001185011.2:c.*1035A>G
  • NM_005138.3:c.2T>CMANE SELECT
  • NM_005138.3:c.2T>CMANE SELECT
  • NM_152299.4:c.*1035A>GMANE SELECT
  • NP_001162580.1:p.Met1Thr
  • NP_001162580.1:p.Met1Thr
  • NP_001162581.1:p.Met1Thr
  • NP_001162582.1:p.Met1Thr
  • NP_005129.2:p.Met1Thr
  • NP_005129.2:p.Met1Thr
  • LRG_727:g.10676T>C
  • NC_000022.10:g.50962839A>G
Protein change:
M1T
Links:
dbSNP: rs1603441682
NCBI 1000 Genomes Browser:
rs1603441682
Molecular consequence:
  • NM_001185011.2:c.*1035A>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_152299.4:c.*1035A>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001169109.1:c.2T>C - initiatior codon variant - [Sequence Ontology: SO:0001582]
  • NM_001169109.2:c.2T>C - initiatior codon variant - [Sequence Ontology: SO:0001582]
  • NM_001169110.1:c.2T>C - initiatior codon variant - [Sequence Ontology: SO:0001582]
  • NM_001169111.2:c.2T>C - initiatior codon variant - [Sequence Ontology: SO:0001582]
  • NM_005138.3:c.2T>C - initiatior codon variant - [Sequence Ontology: SO:0001582]
  • NM_001169109.1:c.2T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001169109.2:c.2T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001169110.1:c.2T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001169111.2:c.2T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_005138.3:c.2T>C - missense variant - [Sequence Ontology: SO:0001583]
Observations:
3

Condition(s)

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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001132957Biochemical Molecular Genetic Laboratory,King Abdulaziz Medical Cityno assertion criteria providedPathogenic
(Aug 25, 2019)
germlineclinical testing

SCV001438821Pathology and Clinical Laboratory Medicine,King Fahad Medical Citycriteria provided, single submitter
Likely pathogenicgermlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
Arabgermlineyes3not providednot providednot providednot providedclinical testing

Details of each submission

From Biochemical Molecular Genetic Laboratory,King Abdulaziz Medical City, SCV001132957.1

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

From Pathology and Clinical Laboratory Medicine,King Fahad Medical City, SCV001438821.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Arab3not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided3not providednot providednot provided

Last Updated: Oct 24, 2021

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