COX7A2

cytochrome c oxidase subunit 7A2, the group of Mitochondrial complex IV: cytochrome c oxidase subunits

Basic information

Region (hg38): 6:75237675-75250323

Links

ENSG00000112695 ∙ NCBI:1347 ∙ OMIM:123996 ∙ HGNC:2288 ∙ Uniprot:P14406 ∙ 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 COX7A2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COX7A2 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			9	1		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 COX7A2

This is a list of pathogenic ClinVar variants found in the COX7A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-75237965-G-T		not specified	Uncertain significance (Mar 19, 2024)
6-75240349-C-T		not specified	Likely benign (Dec 02, 2022)
6-75240352-C-G		not specified	Uncertain significance (Nov 07, 2022)
6-75241258-C-T		not specified	Uncertain significance (Jun 19, 2024)
6-75241259-G-A		not specified	Uncertain significance (May 03, 2023)
6-75243727-C-T		not specified	Uncertain significance (Aug 22, 2022)
6-75243748-G-A		not specified	Uncertain significance (Jan 09, 2025)
6-75243760-C-T		not specified	Uncertain significance (Feb 25, 2025)
6-75243768-G-C		not specified	Likely benign (Oct 29, 2024)
6-75243775-A-C		not specified	Uncertain significance (Aug 11, 2024)
6-75243793-G-A		not specified	Likely benign (Mar 07, 2025)
6-75243811-T-C		not specified	Uncertain significance (Jun 29, 2023)
6-75243814-G-A		not specified	Uncertain significance (Nov 10, 2022)
6-75243824-T-A		not specified	Uncertain significance (Dec 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COX7A2	protein_coding	protein_coding	ENST00000370081	4	12649

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00452	0.692	125118	0	3	125121	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.417	75	65.5	1.15	0.00000333	731
Missense in Polyphen		6	12.212	0.49133		163
Synonymous	-1.17	33	25.5	1.30	0.00000121	229
Loss of Function	0.672	4	5.74	0.697	2.43e-7	67

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	0.00	0.00
European (Non-Finnish)	0.00000961	0.00000881
Middle Eastern	0.00	0.00
South Asian	0.0000661	0.0000659
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 (Consensus)

Intolerance Scores

• loftool: 0.520
• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.76

Haploinsufficiency Scores

• pHI: 0.140
• hipred: N
• hipred_score: 0.145
• ghis: 0.528

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.223

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cox7a2

Gene ontology

• Biological process: regulation of oxidative phosphorylation;electron transport chain;mitochondrial respirasome assembly;proton transmembrane transport
• Cellular component: mitochondrial respirasome
• Molecular function: cytochrome-c oxidase activity