COX7A2L

cytochrome c oxidase subunit 7A2 like, the group of Mitochondrial respiratory chain complex assembly factors

Basic information

Region (hg38): 2:42333546-42425088

Links

ENSG00000115944 ∙ NCBI:9167 ∙ OMIM:605771 ∙ HGNC:2289 ∙ Uniprot:O14548 ∙ 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 COX7A2L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COX7A2L 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in COX7A2L

This is a list of pathogenic ClinVar variants found in the COX7A2L region.

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

Position	Type	Phenotype	Significance	ClinVar
2-42351235-T-C		not specified	Uncertain significance (Jan 16, 2024)
2-42351347-C-T		not specified	Uncertain significance (Jan 02, 2024)
2-42353288-G-C		not specified	Uncertain significance (Apr 09, 2024)
2-42353315-G-A		not specified	Uncertain significance (Dec 21, 2023)
2-42361096-G-T		not specified	Uncertain significance (Apr 06, 2024)
2-42361124-G-A		not specified	Uncertain significance (Dec 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COX7A2L	protein_coding	protein_coding	ENST00000378669	3	91543

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000115	0.113	125701	0	46	125747	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.808	82	63.8	1.28	0.00000337	721
Missense in Polyphen		17	16.144	1.053		192
Synonymous	0.172	26	27.1	0.958	0.00000149	235
Loss of Function	-0.714	8	6.10	1.31	3.57e-7	65

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000206	0.000206
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000107	0.000105
Middle Eastern	0.0000545	0.0000544
South Asian	0.000832	0.000817
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the regulation of oxidative phosphorylation and energy metabolism (By similarity). Necessary for the assembly of mitochondrial respiratory supercomplex (By similarity). {ECO:0000250|UniProtKB:Q61387}.
• 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: 0.108

Intolerance Scores

• loftool: 0.637
• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.156
• hipred: N
• hipred_score: 0.190
• ghis: 0.626

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.241

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cox7a2l

Gene ontology

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