COX20

cytochrome c oxidase assembly factor COX20, the group of Mitochondrial respiratory chain complex assembly factors

Basic information

Region (hg38): 1:244835616-244845057

Previous symbols: [ "FAM36A" ]

Links

ENSG00000203667NCBI:116228OMIM:614698HGNC:26970Uniprot:Q5RI15AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • 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: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Mitochondrial complex IV deficiency, nuclear type 11ARGeneralGenetic 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; Musculoskeletal; Neurologic23125284; 24202787

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COX20 gene.

  • 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
clinvar
2
clinvar
22
missense
1
clinvar
47
clinvar
1
clinvar
1
clinvar
50
nonsense
1
clinvar
2
clinvar
3
start loss
1
clinvar
1
frameshift
3
clinvar
2
clinvar
5
inframe indel
1
clinvar
3
clinvar
4
splice donor/acceptor (+/-2bp)
3
clinvar
3
splice region
1
3
3
3
10
non coding
1
clinvar
21
clinvar
8
clinvar
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)383480
1-244835677-C-T Likely benign (Jan 15, 2021)389196
1-244835705-A-T not specified Likely benign (Jun 21, 2016)379647
1-244835716-T-C Mitochondrial complex 4 deficiency, nuclear type 11 Uncertain significance (Jul 30, 2024)1320208
1-244835718-G-A Mitochondrial complex 4 deficiency, nuclear type 11 Uncertain significance (Feb 04, 2024)3582898
1-244835720-C-T Likely benign (Jun 11, 2024)1942531
1-244835721-G-A Inborn genetic diseases • Mitochondrial complex 4 deficiency, nuclear type 11 Uncertain significance (Mar 08, 2024)1921674
1-244835721-G-T not specified • Mitochondrial complex 4 deficiency, nuclear type 11 Benign/Likely benign (Jan 27, 2025)214269
1-244835722-C-T Mitochondrial complex 4 deficiency, nuclear type 11 Uncertain significance (Apr 22, 2024)3582912
1-244835723-C-G Likely benign (Jun 07, 2022)1969731
1-244835723-C-T COX20-related disorder Likely benign (Apr 11, 2024)1644151
1-244835724-C-T Mitochondrial complex 4 deficiency, nuclear type 11 Uncertain significance (Apr 01, 2024)3582920
1-244835727-C-T Uncertain significance (May 24, 2024)3608515
1-244835730-G-T Mitochondrial complex 4 deficiency, nuclear type 11 Likely pathogenic (Jan 24, 2024)3582926
1-244835729-G-GGAGCCCGGTGAGCCC Uncertain significance (Apr 04, 2022)591995
1-244835732-G-A Likely benign (Apr 01, 2022)1924682
1-244835733-C-T Mitochondrial complex 4 deficiency, nuclear type 11 Uncertain significance (Jan 28, 2024)3582935
1-244835736-G-A Uncertain significance (Nov 04, 2024)1472963
1-244835738-T-C Mitochondrial complex 4 deficiency, nuclear type 11 Likely benign (Aug 13, 2024)1649891
1-244835739-G-A Uncertain significance (Apr 22, 2022)1916992
1-244835741-G-C Mitochondrial complex 4 deficiency, nuclear type 11 Uncertain significance (Jan 28, 2024)3582940
1-244835744-C-G not specified Likely benign (Mar 31, 2017)509566
1-244835745-G-A Mitochondrial complex 4 deficiency, nuclear type 11 Uncertain significance (Oct 24, 2024)1895670
1-244835747-G-T Mitochondrial complex 4 deficiency, nuclear type 11 Uncertain significance (Mar 07, 2024)3582953
1-244835755-A-G Mitochondrial complex 4 deficiency, nuclear type 11 • COX20-related disorder • Inborn genetic diseases Pathogenic (Oct 09, 2024)383938

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
COX20protein_codingprotein_codingENST00000411948 49736
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.02010.7591256960251257210.0000994
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.2935157.20.8910.00000283749
Missense in Polyphen2023.1480.86401293
Synonymous-1.012519.41.299.24e-7208
Loss of Function0.85235.070.5922.10e-784

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00003340.0000334
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.0001390.000139
European (Non-Finnish)0.00004520.0000440
Middle Eastern0.000.00
South Asian0.0004920.000490
Other0.0001640.000163

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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