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

    Gene ID: 9997, updated on 2-Nov-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (50523568..50526442, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (51034133..51037007, complement)
    RS_2024_09 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 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. Novel SCO2 mutation (G1521A) presenting as a spinal muscular atrophy type I phenotype. Tarnopolsky MA, et al. Am J Med Genet A, 2004 Mar 15. PMID 14994243
    2. A homozygous mutation in the SCO2 gene causes a spinal muscular atrophy like presentation with stridor and respiratory insufficiency. Pronicki M, et al. Eur J Paediatr Neurol, 2010 May. PMID 19879173
    3. Remodelling of skeletal muscle cells in children with SCO2 gene mutation - ultrastructural study. Matyja E, et al. Folia Neuropathol, 2009. PMID 19353431
    4. Phenotypic consequences of a novel SCO2 gene mutation. Verdijk RM, et al. Am J Med Genet A, 2008 Nov 1. PMID 18924171
    5. Intracellular delivery of full length recombinant human mitochondrial L-Sco2 protein into the mitochondria of permanent cell lines and SCO2 deficient patient's primary cells. Foltopoulou PF, et al. Biochim Biophys Acta, 2010 Jun. PMID 20193760

    See all (116) 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 inner membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in mitochondrion HTP PubMed 
    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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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