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GeneBe

SCO2

synthesis of cytochrome C oxidase 2, the group of Mitochondrial respiratory chain complex assembly factors

Basic information

Region (hg38): 22:50523567-50526461

Previous symbols: [ "MYP6" ]

Links

ENSG00000284194NCBI:9997OMIM:604272HGNC:10604Uniprot:O43819AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1 (Definitive), mode of inheritance: AR
  • autosomal recessive axonal charcot-marie-tooth disease due to copper metabolism defect (Supportive), mode of inheritance: AR
  • Leigh syndrome (Definitive), mode of inheritance: AR
  • myopia 6 (Strong), mode of inheritance: AD
  • cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Myopia 6; Mitochondrial complex IV deficiency, nuclear type 2AD/ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingBiochemical; Cardiovascular; Musculoskeletal; Neurologic; Ophthalmologic10545952; 10749987; 12538779; 15210538; 18924171; 22231385; 23364397; 23643385

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCO2 gene.

  • not provided (251 variants)
  • Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1 (53 variants)
  • Cytochrome-c oxidase deficiency disease (27 variants)
  • not specified (15 variants)
  • Inborn genetic diseases (15 variants)
  • Fatal Infantile Cardioencephalomyopathy (10 variants)
  • Mitochondrial DNA depletion syndrome 1 (9 variants)
  • Myopia 6 (7 variants)
  • Myopia 6;Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1 (5 variants)
  • Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1;Myopia 6 (3 variants)
  • SCO2-related condition (2 variants)
  • Seizure;Severe global developmental delay (1 variants)
  • Tip-toe gait (1 variants)
  • Primary dilated cardiomyopathy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCO2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
1
clinvar
79
clinvar
2
clinvar
82
missense
1
clinvar
1
clinvar
132
clinvar
1
clinvar
2
clinvar
137
nonsense
6
clinvar
4
clinvar
10
start loss
1
clinvar
2
clinvar
3
frameshift
6
clinvar
9
clinvar
4
clinvar
19
inframe indel
1
clinvar
4
clinvar
5
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
3
clinvar
2
clinvar
2
clinvar
7
Total 13 16 146 82 6

Highest pathogenic variant AF is 0.000105

Variants in SCO2

This is a list of pathogenic ClinVar variants found in the SCO2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
22-50523612-C-G Uncertain significance (Jun 24, 2022)1806547
22-50523612-C-T Likely benign (Jan 23, 2023)2897829
22-50523616-A-G Uncertain significance (Aug 31, 2022)1495670
22-50523617-C-T Likely benign (Dec 22, 2023)1642324
22-50523622-C-T Uncertain significance (Nov 01, 2022)2653399
22-50523623-A-G Likely benign (May 02, 2023)1597355
22-50523624-C-T Uncertain significance (Oct 04, 2021)1384089
22-50523625-T-C Uncertain significance (Jul 06, 2022)1518963
22-50523627-C-T Uncertain significance (Aug 19, 2022)1300717
22-50523628-G-A Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1;Myopia 6 Uncertain significance (Sep 20, 2023)1523095
22-50523632-A-G Likely benign (Aug 18, 2023)3020754
22-50523635-C-G Likely benign (Nov 17, 2023)2900593
22-50523635-C-T SCO2-related condition Likely benign (Jan 03, 2024)2046423
22-50523636-G-A Cytochrome-c oxidase deficiency disease • Mitochondrial DNA depletion syndrome 1 • Fatal Infantile Cardioencephalomyopathy • Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1 Benign/Likely benign (Jan 31, 2024)139088
22-50523637-C-T Uncertain significance (Aug 23, 2021)1398857
22-50523639-A-G not specified Uncertain significance (Jun 27, 2023)2573539
22-50523644-C-T Likely benign (Sep 06, 2021)1624793
22-50523645-C-T Inborn genetic diseases Conflicting classifications of pathogenicity (Oct 24, 2022)2041236
22-50523648-C-A Uncertain significance (Mar 01, 2022)1163688
22-50523648-C-T Uncertain significance (Jan 04, 2023)215129
22-50523649-G-A Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1 Uncertain significance (Jan 31, 2023)2413131
22-50523649-G-T not specified • Cytochrome-c oxidase deficiency disease • Fatal Infantile Cardioencephalomyopathy • Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1 Conflicting classifications of pathogenicity (Jan 31, 2024)139087
22-50523650-C-T Likely benign (Sep 21, 2023)764239
22-50523653-A-G Likely benign (Jan 03, 2024)2043278
22-50523653-ACTGT-A Uncertain significance (Aug 17, 2022)1424997

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP