SCO2

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

Basic information

Region (hg38): 22:50523568-50526461

Previous symbols: [ "MYP6" ]

Links

ENSG00000284194 ∙ NCBI:9997 ∙ OMIM:604272 ∙ HGNC:10604 ∙ Uniprot:O43819 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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
• myopia 6 (Strong), mode of inheritance: AD
• cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1 (Strong), mode of inheritance: AR
• Leigh syndrome (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Myopia 6; Mitochondrial complex IV deficiency, nuclear type 2	AD/AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Biochemical; Cardiovascular; Musculoskeletal; Neurologic; Ophthalmologic	10545952; 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 (21 variants)
• Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1 (5 variants)
• Myopia 6 (2 variants)
• Seizure;Severe global developmental delay (1 variants)
• Tip-toe gait (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	138	2	141
missense	1	1	138	2	2	144
nonsense	9	5				14
start loss		1	2			3
frameshift	12	12	4			28
inframe indel		1	4			5
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3	2	2	7
Total	22	20	152	142	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)
22-50523612-C-T			Likely benign (Jan 23, 2023)
22-50523616-A-G			Uncertain significance (Aug 31, 2022)
22-50523617-C-T			Likely benign (Dec 22, 2023)
22-50523622-C-T			Uncertain significance (Nov 01, 2022)
22-50523623-A-G			Likely benign (May 02, 2023)
22-50523624-C-T			Uncertain significance (Oct 04, 2021)
22-50523625-T-C			Uncertain significance (Jul 06, 2022)
22-50523627-C-T			Uncertain significance (Aug 19, 2022)
22-50523628-G-A		Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1;Myopia 6	Uncertain significance (Sep 20, 2023)
22-50523632-A-G			Likely benign (Aug 18, 2023)
22-50523635-C-G			Likely benign (Nov 17, 2023)
22-50523635-C-T		SCO2-related disorder	Likely benign (Jan 03, 2024)
22-50523636-G-A		Mitochondrial DNA depletion syndrome 1 • Fatal Infantile Cardioencephalomyopathy • Mitochondrial complex IV deficiency, nuclear type 1 • Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1	Benign/Likely benign (Jun 01, 2024)
22-50523637-C-T		Inborn genetic diseases	Uncertain significance (Jun 07, 2024)
22-50523639-A-G		not specified	Uncertain significance (Jun 27, 2023)
22-50523644-C-T			Likely benign (Sep 06, 2021)
22-50523645-C-T		Inborn genetic diseases	Conflicting classifications of pathogenicity (Oct 24, 2022)
22-50523648-C-A			Uncertain significance (Mar 01, 2022)
22-50523648-C-T			Uncertain significance (Sep 13, 2024)
22-50523649-G-A		Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1	Uncertain significance (Jan 31, 2023)
22-50523649-G-T		not specified • Mitochondrial complex IV deficiency, nuclear type 1 • Fatal Infantile Cardioencephalomyopathy • Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1	Conflicting classifications of pathogenicity (Jul 01, 2024)
22-50523650-C-T			Likely benign (Sep 21, 2023)
22-50523653-A-G			Likely benign (Jan 03, 2024)
22-50523653-ACTGT-A			Uncertain significance (Aug 17, 2022)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP