COX5B
cytochrome c oxidase subunit 5B, the group of Mitochondrial complex IV: cytochrome c oxidase subunits
Basic information
Region (hg38): 2:97646062-97648383
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the COX5B 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 | 1 | |||||
| missense | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 6 | 2 | 0 |
Variants in COX5B
This is a list of pathogenic ClinVar variants found in the COX5B region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 2-97646098-G-C | not specified | Uncertain significance (Dec 13, 2022) | ||
| 2-97646107-C-T | Likely benign (May 01, 2023) | |||
| 2-97646115-G-A | not specified | Uncertain significance (Feb 13, 2023) | ||
| 2-97646120-C-G | not specified | Uncertain significance (Dec 14, 2022) | ||
| 2-97646179-G-T | not specified | Uncertain significance (Mar 21, 2023) | ||
| 2-97648019-G-A | not specified | Likely benign (May 03, 2023) | ||
| 2-97648043-G-A | not specified | Uncertain significance (Dec 21, 2023) | ||
| 2-97648053-G-A | not specified | Uncertain significance (Jun 05, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| COX5B | protein_coding | protein_coding | ENST00000258424 | 4 | 2344 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.874 | 0.125 | 125733 | 0 | 1 | 125734 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.394 | 62 | 71.4 | 0.869 | 0.00000368 | 803 |
| Missense in Polyphen | 16 | 19.138 | 0.83603 | 260 | ||
| Synonymous | 1.15 | 22 | 30.0 | 0.733 | 0.00000159 | 267 |
| Loss of Function | 2.41 | 0 | 6.76 | 0.00 | 3.67e-7 | 76 |
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) | 0.00000879 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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;AndrogenReceptor;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
- 0.121
Intolerance Scores
- loftool
- rvis_EVS
- 0.24
- rvis_percentile_EVS
- 68.72
Haploinsufficiency Scores
- pHI
- 0.550
- hipred
- Y
- hipred_score
- 0.508
- ghis
- 0.445
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.827
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cox5b
- 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; limbs/digits/tail phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- mitochondrial electron transport, cytochrome c to oxygen;respiratory gaseous exchange;mitochondrial ATP synthesis coupled proton transport
- Cellular component
- mitochondrion;mitochondrial inner membrane
- Molecular function
- cytochrome-c oxidase activity;protein binding;metal ion binding