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.

not_specified (7 variants)

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. These statistics are base on transcript: NM_000005694.2. 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						0
missense			7 clinvar			7
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	7	0	0

Loading clinvar variants...

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