COX11

cytochrome c oxidase copper chaperone COX11, the group of Mitochondrial respiratory chain complex assembly factors

Basic information

Region (hg38): 17:54951902-54968703

Links

ENSG00000166260 ∙ NCBI:1353 ∙ OMIM:603648 ∙ HGNC:2261 ∙ Uniprot:Q9Y6N1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• mitochondrial complex IV deficiency, nuclear type 23 (Limited), mode of inheritance: AR
• mitochondrial complex IV deficiency, nuclear type 23 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Mitochondrial complex IV deficiency, nuclear type 23	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	Audiologic/Otolaryngologic; Biochemical; Musculoskeletal; Neurologic	36030551; 38068960

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COX11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COX11 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						0
missense			8	2		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	9	2	0

Variants in COX11

This is a list of pathogenic ClinVar variants found in the COX11 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-54960583-T-C		not specified	Uncertain significance (Nov 07, 2023)
17-54962752-G-A		not specified	Uncertain significance (Apr 25, 2023)
17-54962778-A-C		Mitochondrial complex IV deficiency, nuclear type 23	Uncertain significance (-)
17-54962797-G-GT		Mitochondrial complex IV deficiency, nuclear type 23	Pathogenic (Mar 11, 2024)
17-54962800-A-G		not specified	Uncertain significance (Feb 28, 2024)
17-54962825-G-T		Mitochondrial complex IV deficiency, nuclear type 23	Pathogenic (Mar 11, 2024)
17-54962834-C-G		Mitochondrial complex IV deficiency, nuclear type 23	Pathogenic (Mar 07, 2023)
17-54962896-T-C		Mitochondrial complex IV deficiency, nuclear type 23	Uncertain significance (-)
17-54964837-C-T		not specified	Uncertain significance (Jun 17, 2024)
17-54968285-C-T		not specified	Uncertain significance (May 15, 2023)
17-54968394-C-T		not specified	Uncertain significance (Sep 16, 2021)
17-54968435-G-A		not specified	Uncertain significance (Aug 10, 2021)
17-54968489-A-G		not specified	Uncertain significance (Dec 17, 2023)
17-54968543-A-C		not specified	Likely benign (Jan 23, 2023)
17-54968546-G-C		not specified	Uncertain significance (Nov 09, 2023)
17-54968559-C-G		not specified	Uncertain significance (Mar 25, 2024)
17-54968576-G-C		not specified	Uncertain significance (Apr 24, 2024)
17-54968611-AA-C		Mitochondrial complex IV deficiency, nuclear type 23	Pathogenic (Mar 11, 2024)
17-54968624-C-G		not specified	Likely benign (Jul 13, 2021)
17-54968634-A-T		not specified	Uncertain significance (Jun 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COX11	protein_coding	protein_coding	ENST00000299335	4	16884

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0161	0.962	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.666	124	147	0.845	0.00000682	1786
Missense in Polyphen		40	54.545	0.73334		675
Synonymous	-0.912	63	54.4	1.16	0.00000259	559
Loss of Function	1.99	5	12.7	0.395	6.13e-7	134

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000184	0.000178
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000893	0.0000879
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Exerts its effect at some terminal stage of cytochrome c oxidase synthesis, probably by being involved in the insertion of the copper B into subunit I. {ECO:0000250}.
• Pathway: Thermogenesis - Homo sapiens (human);Oxidative phosphorylation - Homo sapiens (human);Electron Transport Chain;Copper homeostasis;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)

Recessive Scores

• pRec: 0.170

Intolerance Scores

• loftool: 0.508
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.95

Haploinsufficiency Scores

• pHI: 0.0935
• hipred: Y
• hipred_score: 0.541
• ghis: 0.549

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.922

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cox11

Gene ontology

• Biological process: respiratory gaseous exchange;respiratory chain complex IV assembly;electron transport chain;negative regulation of glucokinase activity;metal ion homeostasis;proton transmembrane transport
• Cellular component: mitochondrion;integral component of mitochondrial inner membrane;protein-containing complex
• Molecular function: cytochrome-c oxidase activity;copper ion binding;protein binding;electron transfer activity