COX17

cytochrome c oxidase copper chaperone COX17, the group of Mitochondrial respiratory chain complex assembly factors

Basic information

Region (hg38): 3:119654513-119677454

Links

ENSG00000138495 ∙ NCBI:10063 ∙ OMIM:604813 ∙ HGNC:2264 ∙ Uniprot:Q14061 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COX17 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COX17 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			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in COX17

This is a list of pathogenic ClinVar variants found in the COX17 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-119654525-A-G		not specified	Uncertain significance (Aug 02, 2023)
3-119654544-C-A		not specified	Uncertain significance (Jun 26, 2024)
3-119654608-C-A		not specified	Uncertain significance (Dec 27, 2023)
3-119654609-G-A		not specified	Uncertain significance (May 10, 2022)
3-119659958-G-A		not specified	Uncertain significance (Feb 12, 2025)
3-119659994-G-T		not specified	Uncertain significance (Apr 20, 2023)
3-119660000-T-C		not specified	Uncertain significance (Apr 22, 2024)
3-119660015-C-T		not specified	Uncertain significance (Jan 03, 2025)
3-119660017-T-C		not specified	Uncertain significance (Feb 09, 2025)
3-119660019-C-A		not specified	Uncertain significance (Dec 06, 2022)
3-119660024-C-T		not specified	Uncertain significance (Aug 26, 2024)
3-119660051-T-A		not specified	Uncertain significance (Jun 29, 2022)
3-119660083-G-A		not specified	Uncertain significance (Dec 16, 2022)
3-119660089-T-C		not specified	Uncertain significance (Jul 12, 2022)
3-119660125-C-T		not specified	Uncertain significance (Jun 04, 2024)
3-119660153-G-C		not specified	Uncertain significance (Jun 10, 2022)
3-119660162-A-G		not specified	Uncertain significance (Sep 20, 2023)
3-119660227-A-G		not specified	Uncertain significance (Aug 12, 2021)
3-119660237-A-G		not specified	Uncertain significance (Feb 08, 2025)
3-119660246-C-G		not specified	Uncertain significance (Jan 17, 2024)
3-119660254-A-G		not specified	Uncertain significance (Aug 07, 2024)
3-119660329-A-G		not specified	Uncertain significance (Dec 01, 2022)
3-119660341-G-T		not specified	Uncertain significance (May 17, 2023)
3-119660342-C-T		not specified	Uncertain significance (Dec 20, 2023)
3-119660354-C-T		not specified	Uncertain significance (Dec 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COX17	protein_coding	protein_coding	ENST00000261070	2	22942

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.199	0.659	124006	0	1	124007	0.00000403

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.229	32	35.9	0.892	0.00000161	401
Missense in Polyphen		13	14.28	0.91036		172
Synonymous	-0.0797	15	14.6	1.03	7.01e-7	117
Loss of Function	0.980	1	2.76	0.363	1.14e-7	41

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000466	0.0000466
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Copper metallochaperone essential for the assembly of the mitochondrial respiratory chain complex IV (CIV), also known as cytochrome c oxidase. Binds two copper ions and delivers them to the metallochaperone SCO1 which transports the copper ions to the Cu(A) site on the cytochrome c oxidase subunit II (MT- CO2/COX2). {ECO:0000269|PubMed:19393246}.
• Pathway: Thermogenesis - Homo sapiens (human);Oxidative phosphorylation - Homo sapiens (human);Electron Transport Chain;Copper homeostasis;Metabolism of proteins;Mitochondrial protein import (Consensus)

Recessive Scores

• pRec: 0.194

Intolerance Scores

• loftool: 0.345
• rvis_EVS: 0.1
• rvis_percentile_EVS: 60.96

Haploinsufficiency Scores

• pHI: 0.285
• hipred: Y
• hipred_score: 0.585
• ghis: 0.593

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.970

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cox17
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; cellular phenotype

Gene ontology

• Biological process: generation of precursor metabolites and energy;copper ion transport;brain development;heart development;positive regulation of cell population proliferation;mitochondrial respiratory chain complex IV assembly;positive regulation of cytochrome-c oxidase activity
• Cellular component: cytoplasm;mitochondrial intermembrane space
• Molecular function: copper ion binding;protein binding;copper chaperone activity;cuprous ion binding