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SCO2 synthesis of cytochrome C oxidase 2 [ Homo sapiens (human) ]

Gene ID: 9997, updated on 7-Apr-2024

Summary

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Official Symbol
SCO2provided by HGNC
Official Full Name
synthesis of cytochrome C oxidase 2provided by HGNC
Primary source
HGNC:HGNC:10604
See related
Ensembl:ENSG00000284194 MIM:604272; AllianceGenome:HGNC:10604
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
TP; MYP6; TYMP; ECGF1; SCO1L; MC4DN2; CEMCOX1; PD-ECGF; TdRPase; Gliostatin
Summary
Cytochrome c oxidase (COX) catalyzes the transfer of electrons from cytochrome c to molecular oxygen, which helps to maintain the proton gradient across the inner mitochondrial membrane that is necessary for aerobic ATP production. Human COX is a multimeric protein complex that requires several assembly factors; this gene encodes one of the COX assembly factors. The encoded protein is a metallochaperone that is involved in the biogenesis of cytochrome c oxidase subunit II. Mutations in this gene are associated with fatal infantile encephalocardiomyopathy and myopia 6. [provided by RefSeq, Oct 2014]
Expression
Ubiquitous expression in spleen (RPKM 14.8), bone marrow (RPKM 14.4) and 25 other tissues See more
Orthologs
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Genomic context

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See SCO2 in Genome Data Viewer
Location:
22q13.33
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (50523568..50526442, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (51034133..51037007, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (50961997..50964871, complement)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene myo-inositol oxygenase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19321 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13983 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13984 Neighboring gene lipase maturation factor 2 Neighboring gene non-SMC condensin II complex subunit H2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50955745-50956678 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13985 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13986 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50965237-50965808 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19324 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19325 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13987 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13988 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13989 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50969361-50969866 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13991 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13992 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13993 Neighboring gene thymidine phosphorylase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13994 Neighboring gene ciliary microtubule associated protein 1B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19326 Neighboring gene ODF3B-KLHDC7B intergenic CAGE-defined mid-level expression enhancer Neighboring gene uncharacterized LOC102724608 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19328 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19329 Neighboring gene Sharpr-MPRA regulatory region 5393 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19330 Neighboring gene KLHDC7B divergent transcript

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Association between SCO2 mutation and extreme myopia in Japanese patients. Wakazono T, et al. Jpn J Ophthalmol, 2016 Jul. PMID 27052445
  2. Leigh disease due to SCO2 mutations revealed at extended autopsy. Szymanska-Debinska T, et al. J Clin Pathol, 2015 May. PMID 25720770
  3. Mutations in SCO2 are associated with autosomal-dominant high-grade myopia. Tran-Viet KN, et al. Am J Hum Genet, 2013 May 2. PMID 23643385, Free PMC Article
  4. Exome sequencing reveals SCO2 mutations in a family presented with fatal infantile hyperthermia. Sambuughin N, et al. J Hum Genet, 2013 Apr. PMID 23364397
  5. Mitochondrial DNA deletions cause the biochemical defect observed in Alzheimer's disease. Krishnan KJ, et al. Neurobiol Aging, 2012 Sep. PMID 21925769

See all (107) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. TCF19 and p53 regulate transcription of TIGAR and SCO2 in HCC for mitochondrial energy metabolism and stress adaptation.
    Title: TCF19 and p53 regulate transcription of TIGAR and SCO2 in HCC for mitochondrial energy metabolism and stress adaptation.
  2. Systemic Mitochondrial Oxidative Phosphorylation Protein Levels Correlate with Neuroimaging Measures in Chronically HIV-Infected Individuals.
    Title: Systemic Mitochondrial Oxidative Phosphorylation Protein Levels Correlate with Neuroimaging Measures in Chronically HIV-Infected Individuals.
  3. High expression of synthesis of cytochrome c oxidase 2 and TP53-induced glycolysis and apoptosis regulator can predict poor prognosis in human lung adenocarcinoma
    Title: High expression of synthesis of cytochrome c oxidase 2 and TP53-induced glycolysis and apoptosis regulator can predict poor prognosis in human lung adenocarcinoma.
  4. We identified one novel possibility of an extreme myopia-causing mutation in SCO2. No other disease-causing mutation was found in 101 extremely myopic Japanese patients, suggesting that SCO2 plays a limited role in Japanese extreme myopia.
    Title: Association between SCO2 mutation and extreme myopia in Japanese patients.
  5. In gastric cancer, the expression of SCO2 and COX were not shown to be associated with the regulatory role of p53, unlike TIGAR expression. Nevertheless, a significantly high recurrence rate was found in a patient group with high COX expression
    Title: Distinctive interrelation of p53 with SCO2, COX, and TIGAR in human gastric cancer.
  6. oxidative stress-induced glycolysis-to-OXPHOS switch is mediated by synthesis of cytochrome c oxidase 2 (SCO2). These findings demonstrate p53-mediated OXPHOS function as a compensatory alteration in Fanconi anemia (FA)hematopoietic stem cells to ensure a functional but mildly impaired energy metabolism and suggest a cautious approach to manipulating p53 signaling in FA.
    Title: SCO2 Mediates Oxidative Stress-Induced Glycolysis to Oxidative Phosphorylation Switch in Hematopoietic Stem Cells.
  7. Geranylgeranoic acid increased the SCO2 gene expression, which might enhance aerobic respiration.
    Title: Upregulation of energy metabolism-related, p53-target TIGAR and SCO2 in HuH-7 cells with p53 mutation by geranylgeranoic acid treatment.
  8. oncoprotein HBXIP enhances glucose metabolism reprogramming through suppressing SCO2 and PDHA1 in breast cancer
    Title: The oncoprotein HBXIP promotes glucose metabolism reprogramming via downregulating SCO2 and PDHA1 in breast cancer.
  9. Cooperation between COA6 and SCO2 in COX2 maturation during cytochrome c oxidase assembly links two mitochondrial cardiomyopathies.
    Title: Cooperation between COA6 and SCO2 in COX2 maturation during cytochrome c oxidase assembly links two mitochondrial cardiomyopathies.
  10. Sco1 is a metallochaperone that selectively transfers Cu(I) ions based on loop recognition, whereas Sco2 is a copper-dependent thiol reductase of the cysteine ligands in the oxidase.
    Title: Loop recognition and copper-mediated disulfide reduction underpin metal site assembly of CuA in human cytochrome oxidase.
Submit: New GeneRIF Correction See all GeneRIFs (41)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1
MedGen: C5399977 OMIM: 604377 GeneReviews: Not available
Compare labs
Myopia 6
MedGen: C1837148 OMIM: 608908 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.
EBI GWAS Catalog
Genome-wide association study of hematological and biochemical traits in a Japanese population.
EBI GWAS Catalog
Seventy-five genetic loci influencing the human red blood cell.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC125823, MGC125825

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables copper chaperone activity IEA
Inferred from Electronic Annotation
more info
  
enables copper ion binding NAS
Non-traceable Author Statement
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-disulfide reductase activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in eye development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in in utero embryonic development IEA
Inferred from Electronic Annotation
more info
  
involved_in intracellular copper ion homeostasis IEA
Inferred from Electronic Annotation
more info
  
involved_in mitochondrial cytochrome c oxidase assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mitochondrial cytochrome c oxidase assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in mitochondrial cytochrome c oxidase assembly TAS
Traceable Author Statement
more info
 PubMed 
involved_in muscle system process IEA
Inferred from Electronic Annotation
more info
  
involved_in respiratory electron transport chain IEA
Inferred from Electronic Annotation
more info
  
involved_in response to activity IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in mitochondrial inner membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondrial matrix TAS
Traceable Author Statement
more info
  
located_in mitochondrion IDA
Inferred from Direct Assay
more info
  
located_in mitochondrion TAS
Traceable Author Statement
more info
 PubMed 
located_in myofibril IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
protein SCO2 homolog, mitochondrial
Names
Platelet-derived endothelial cell growth factor
SCO cytochrome c oxidase assembly protein 2
SCO cytochrome oxidase deficient homolog 2
SCO2, cytochrome c oxidase assembly protein
Thymidine phosphorylase
NP_001162580.1
NP_001162581.1
NP_001162582.1
NP_005129.2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_016235.1 RefSeqGene

    Range
    5842..7872
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001169109.2 → NP_001162580.1  protein SCO2 homolog, mitochondrial precursor

    See identical proteins and their annotated locations for NP_001162580.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein.
    Source sequence(s)
    BM787182, U62317
    Consensus CDS
    CCDS14095.1
    UniProtKB/Swiss-Prot
    O43819, Q3T1B5, Q9UK87
    Related
    ENSP00000444433.1, ENST00000543927.6
    Conserved Domains (1) summary
    cd02968
    Location:101 → 242
    SCO; SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c ...

  2. NM_001169110.1 → NP_001162581.1  protein SCO2 homolog, mitochondrial precursor

    See identical proteins and their annotated locations for NP_001162581.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein.
    Source sequence(s)
    BG392981, U62317
    Consensus CDS
    CCDS14095.1
    UniProtKB/Swiss-Prot
    O43819, Q3T1B5, Q9UK87
    Related
    ENSP00000444242.1, ENST00000535425.5
    Conserved Domains (1) summary
    cd02968
    Location:101 → 242
    SCO; SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c ...

  3. NM_001169111.2 → NP_001162582.1  protein SCO2 homolog, mitochondrial precursor

    See identical proteins and their annotated locations for NP_001162582.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein.
    Source sequence(s)
    U62317
    Consensus CDS
    CCDS14095.1
    UniProtKB/Swiss-Prot
    O43819, Q3T1B5, Q9UK87
    Related
    ENSP00000252785.3, ENST00000252785.3
    Conserved Domains (1) summary
    cd02968
    Location:101 → 242
    SCO; SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c ...

  4. NM_005138.3 → NP_005129.2  protein SCO2 homolog, mitochondrial precursor

    See identical proteins and their annotated locations for NP_005129.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the shortest transcript. Variants 1, 2, 3 and 4 encode the same protein.
    Source sequence(s)
    AL021683, BC102025, BQ878572, CN409692
    Consensus CDS
    CCDS14095.1
    UniProtKB/Swiss-Prot
    O43819, Q3T1B5, Q9UK87
    Related
    ENSP00000379046.4, ENST00000395693.8
    Conserved Domains (1) summary
    cd02968
    Location:101 → 242
    SCO; SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    50523568..50526442 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    51034133..51037007 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O43819.3 GenPept UniProtKB/Swiss-Prot:O43819

Gene LinkOut

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