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 (346 variants)
Cardioencephalomyopathy,_fatal_infantile,_due_to_cytochrome_c_oxidase_deficiency_1 (78 variants)
Inborn_genetic_diseases (51 variants)
Myopia_6 (27 variants)
Mitochondrial_complex_IV_deficiency,_nuclear_type_1 (19 variants)
not_specified (18 variants)
SCO2-related_disorder (9 variants)
Fatal_Infantile_Cardioencephalomyopathy (4 variants)
Mitochondrial_DNA_depletion_syndrome_1 (3 variants)
Alagille_syndrome_due_to_a_JAG1_point_mutation (1 variants)
Tip-toe_gait (1 variants)
Severe_global_developmental_delay (1 variants)
Primary_dilated_cardiomyopathy (1 variants)
Seizure (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. These statistics are base on transcript: NM_000005138.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	156 clinvar	1 clinvar	159
missense	3 clinvar	7 clinvar	161 clinvar	11 clinvar	1 clinvar	183
nonsense	10 clinvar	7 clinvar				17
start loss		2	1			3
frameshift	14 clinvar	16 clinvar	4 clinvar			34
splice donor/acceptor (+/-2bp)						0
Total	27	32	168	167	2

Highest pathogenic variant AF is 0.00038998353

Loading clinvar variants...

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP