COX6C

cytochrome c oxidase subunit 6C, the group of Mitochondrial complex IV: cytochrome c oxidase subunits

Basic information

Region (hg38): 8:99873199-99893707

Links

ENSG00000164919 ∙ NCBI:1345 ∙ OMIM:124090 ∙ HGNC:2285 ∙ Uniprot:P09669 ∙ 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 COX6C gene.

• Inborn genetic diseases (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COX6C 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			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in COX6C

This is a list of pathogenic ClinVar variants found in the COX6C region.

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

Position	Type	Phenotype	Significance	ClinVar
8-99875122-T-C			Benign (Jul 17, 2018)
8-99875399-T-TATTA		Cohen syndrome	Likely benign (Nov 20, 2023)
8-99875400-A-ATTAT		Cohen syndrome	Likely benign (Dec 19, 2023)
8-99875400-A-ATTATT		Cohen syndrome	Likely benign (Dec 12, 2022)
8-99875403-A-AT		Cohen syndrome	Benign (Oct 25, 2023)
8-99875407-T-C		Cohen syndrome	Likely benign (Oct 13, 2023)
8-99875406-T-TTTGGATCC		Cohen syndrome	Uncertain significance (Jan 10, 2024)
8-99875411-A-C		Cohen syndrome	Likely benign (Aug 09, 2023)
8-99875415-T-C		Cohen syndrome	Uncertain significance (Jun 12, 2022)
8-99875417-G-A		Cohen syndrome	Pathogenic/Likely pathogenic (Aug 30, 2023)
8-99875418-G-GTAGA		Cohen syndrome	Likely pathogenic (May 12, 2017)
8-99875420-A-AGAT		Cohen syndrome • Inborn genetic diseases • VPS13B-related disorder	Conflicting classifications of pathogenicity (Jan 31, 2024)
8-99875422-A-T		Cohen syndrome	Uncertain significance (Sep 27, 2022)
8-99875425-G-A		Cohen syndrome	Uncertain significance (Jul 04, 2021)
8-99875427-G-A		Cohen syndrome	Uncertain significance (Mar 19, 2022)
8-99875429-C-T		Cohen syndrome	Likely benign (Sep 06, 2023)
8-99875430-C-T		Cohen syndrome • Abnormality of the nervous system	Pathogenic/Likely pathogenic (Dec 19, 2023)
8-99875431-G-A		Cohen syndrome • not specified • VPS13B-related disorder	Uncertain significance (Jan 17, 2024)
8-99875431-G-C		Cohen syndrome	Uncertain significance (Jul 24, 2021)
8-99875435-G-A			Likely benign (Feb 01, 2024)
8-99875441-G-A		Cohen syndrome	Likely benign (Aug 30, 2023)
8-99875441-G-C		Cohen syndrome	Likely benign (Feb 14, 2023)
8-99875443-CAG-C		Cohen syndrome	Pathogenic (Sep 14, 2021)
8-99875445-G-C		Inborn genetic diseases	Uncertain significance (Feb 02, 2024)
8-99875447-G-A		Cohen syndrome	Likely benign (Jun 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COX6C	protein_coding	protein_coding	ENST00000520468	2	20863

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0488	0.701	125428	0	3	125431	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0822	45	46.6	0.966	0.00000296	485
Missense in Polyphen		8	9.3148	0.85885		155
Synonymous	1.57	7	14.6	0.478	7.83e-7	146
Loss of Function	0.642	2	3.25	0.616	2.21e-7	36

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000561	0.0000545
Finnish	0.00	0.00
European (Non-Finnish)	0.0000180	0.0000176
Middle Eastern	0.0000561	0.0000545
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport.
• Pathway: Cardiac muscle contraction - Homo sapiens (human);Non-alcoholic fatty liver disease (NAFLD) - Homo sapiens (human);Alzheimer,s disease - Homo sapiens (human);Huntington,s disease - Homo sapiens (human);Thermogenesis - Homo sapiens (human);Oxidative phosphorylation - Homo sapiens (human);Parkinson,s disease - Homo sapiens (human);Electron Transport Chain;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: 0.0800

Intolerance Scores

• loftool: 0.472
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.33

Haploinsufficiency Scores

• pHI: 0.182
• hipred: Y
• hipred_score: 0.585
• ghis: 0.513

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.920

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cox6c

Gene ontology

• Biological process: generation of precursor metabolites and energy;electron transport chain;proton transmembrane transport
• Cellular component: mitochondrion;mitochondrial inner membrane;integral component of membrane
• Molecular function: cytochrome-c oxidase activity