COX20
Basic information
Region (hg38): 1:244835616-244845057
Previous symbols: [ "FAM36A" ]
Links
Phenotypes
GenCC
Source:
- cytochrome-c oxidase deficiency disease (Supportive), mode of inheritance: AR
- mitochondrial disease (Definitive), mode of inheritance: AR
- mitochondrial complex 4 deficiency, nuclear type 11 (Strong), mode of inheritance: AR
- mitochondrial complex 4 deficiency, nuclear type 11 (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Mitochondrial complex IV deficiency, nuclear type 11 | 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; Musculoskeletal; Neurologic | 23125284; 24202787 |
ClinVar
This is a list of variants' phenotypes submitted to
- COX20-related disorder (1 variants)
- Mitochondrial complex 4 deficiency, nuclear type 11 (1 variants)
- not provided (1 variants)
- Inborn genetic diseases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the COX20 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 | 20 | 22 | ||||
missense | 47 | 50 | ||||
nonsense | 3 | |||||
start loss | 1 | |||||
frameshift | 5 | |||||
inframe indel | 4 | |||||
splice donor/acceptor (+/-2bp) | 3 | |||||
splice region | 1 | 3 | 3 | 3 | 10 | |
non coding | 21 | 30 | ||||
Total | 1 | 8 | 56 | 42 | 11 |
Highest pathogenic variant AF is 0.0000470
Variants in COX20
This is a list of pathogenic ClinVar variants found in the COX20 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-244835676-C-G | not specified | Likely benign (Mar 02, 2016) | ||
1-244835677-C-T | Likely benign (Jan 15, 2021) | |||
1-244835705-A-T | not specified | Likely benign (Jun 21, 2016) | ||
1-244835716-T-C | Mitochondrial complex 4 deficiency, nuclear type 11 | Uncertain significance (Jul 30, 2024) | ||
1-244835718-G-A | Mitochondrial complex 4 deficiency, nuclear type 11 | Uncertain significance (Feb 04, 2024) | ||
1-244835720-C-T | Likely benign (Jun 11, 2024) | |||
1-244835721-G-A | Inborn genetic diseases • Mitochondrial complex 4 deficiency, nuclear type 11 | Uncertain significance (Mar 08, 2024) | ||
1-244835721-G-T | not specified • Mitochondrial complex 4 deficiency, nuclear type 11 | Benign/Likely benign (Jan 27, 2025) | ||
1-244835722-C-T | Mitochondrial complex 4 deficiency, nuclear type 11 | Uncertain significance (Apr 22, 2024) | ||
1-244835723-C-G | Likely benign (Jun 07, 2022) | |||
1-244835723-C-T | COX20-related disorder | Likely benign (Apr 11, 2024) | ||
1-244835724-C-T | Mitochondrial complex 4 deficiency, nuclear type 11 | Uncertain significance (Apr 01, 2024) | ||
1-244835727-C-T | Uncertain significance (May 24, 2024) | |||
1-244835730-G-T | Mitochondrial complex 4 deficiency, nuclear type 11 | Likely pathogenic (Jan 24, 2024) | ||
1-244835729-G-GGAGCCCGGTGAGCCC | Uncertain significance (Apr 04, 2022) | |||
1-244835732-G-A | Likely benign (Apr 01, 2022) | |||
1-244835733-C-T | Mitochondrial complex 4 deficiency, nuclear type 11 | Uncertain significance (Jan 28, 2024) | ||
1-244835736-G-A | Uncertain significance (Nov 04, 2024) | |||
1-244835738-T-C | Mitochondrial complex 4 deficiency, nuclear type 11 | Likely benign (Aug 13, 2024) | ||
1-244835739-G-A | Uncertain significance (Apr 22, 2022) | |||
1-244835741-G-C | Mitochondrial complex 4 deficiency, nuclear type 11 | Uncertain significance (Jan 28, 2024) | ||
1-244835744-C-G | not specified | Likely benign (Mar 31, 2017) | ||
1-244835745-G-A | Mitochondrial complex 4 deficiency, nuclear type 11 | Uncertain significance (Oct 24, 2024) | ||
1-244835747-G-T | Mitochondrial complex 4 deficiency, nuclear type 11 | Uncertain significance (Mar 07, 2024) | ||
1-244835755-A-G | Mitochondrial complex 4 deficiency, nuclear type 11 • COX20-related disorder • Inborn genetic diseases | Pathogenic (Oct 09, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
COX20 | protein_coding | protein_coding | ENST00000411948 | 4 | 9736 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0201 | 0.759 | 125696 | 0 | 25 | 125721 | 0.0000994 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.293 | 51 | 57.2 | 0.891 | 0.00000283 | 749 |
Missense in Polyphen | 20 | 23.148 | 0.86401 | 293 | ||
Synonymous | -1.01 | 25 | 19.4 | 1.29 | 9.24e-7 | 208 |
Loss of Function | 0.852 | 3 | 5.07 | 0.592 | 2.10e-7 | 84 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000334 | 0.0000334 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.000139 | 0.000139 |
European (Non-Finnish) | 0.0000452 | 0.0000440 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.000492 | 0.000490 |
Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Essential for the assembly of the mitochondrial respiratory chain complex IV (CIV), also known as cytochrome c oxidase (PubMed:23125284). Acts as a chaperone in the early steps of cytochrome c oxidase subunit II (MT-CO2/COX2) maturation, stabilizing the newly synthesized protein and presenting it to metallochaperones SCO1/2 which in turn facilitates the incorporation of the mature MT-CO2/COX2 into the assembling CIV holoenzyme (PubMed:24403053). {ECO:0000269|PubMed:23125284, ECO:0000269|PubMed:24403053}.;
- Disease
- DISEASE: Mitochondrial complex IV deficiency (MT-C4D) [MIM:220110]: A disorder of the mitochondrial respiratory chain with heterogeneous clinical manifestations, ranging from isolated myopathy to severe multisystem disease affecting several tissues and organs. Features include hypertrophic cardiomyopathy, hepatomegaly and liver dysfunction, hypotonia, muscle weakness, exercise intolerance, developmental delay, delayed motor development and mental retardation. Some affected individuals manifest a fatal hypertrophic cardiomyopathy resulting in neonatal death. A subset of patients manifest Leigh syndrome. {ECO:0000269|PubMed:23125284, ECO:0000269|PubMed:24202787, ECO:0000269|PubMed:29154948}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Thermogenesis - Homo sapiens (human);Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Respiratory electron transport;The citric acid (TCA) cycle and respiratory electron transport;Metabolism;TP53 Regulates Metabolic Genes;Transcriptional Regulation by TP53;Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.
(Consensus)
Intolerance Scores
- loftool
- rvis_EVS
- 0.08
- rvis_percentile_EVS
- 59.76
Haploinsufficiency Scores
- pHI
- 0.156
- hipred
- N
- hipred_score
- 0.177
- ghis
- 0.474
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.114
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cox20
- Phenotype
Gene ontology
- Biological process
- aerobic respiration;mitochondrial respiratory chain complex IV assembly
- Cellular component
- mitochondrion;mitochondrial inner membrane;integral component of membrane
- Molecular function
- protein binding