COX6B2

cytochrome c oxidase subunit 6B2, the group of Mitochondrial complex IV: cytochrome c oxidase subunits

Basic information

Region (hg38): 19:55349306-55354719

Links

ENSG00000160471 ∙ NCBI:125965 ∙ OMIM:618127 ∙ HGNC:24380 ∙ Uniprot:Q6YFQ2 ∙ 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 COX6B2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COX6B2 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			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	0

Variants in COX6B2

This is a list of pathogenic ClinVar variants found in the COX6B2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-55353732-C-T		not specified	Uncertain significance (Aug 27, 2024)
19-55353765-A-G		not specified	Uncertain significance (Oct 20, 2023)
19-55353961-G-A		not specified	Uncertain significance (Jun 18, 2021)
19-55354434-G-A		not specified	Uncertain significance (Nov 11, 2024)
19-55354440-G-T		not specified	Uncertain significance (Aug 20, 2023)
19-55354441-G-C		not specified	Uncertain significance (Nov 21, 2023)
19-55354497-G-T		not specified	Uncertain significance (Oct 19, 2024)
19-55354500-C-T		not specified	Likely benign (Aug 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COX6B2	protein_coding	protein_coding	ENST00000593184	3	5509

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000642	0.512	124765	0	10	124775	0.0000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.328	58	51.4	1.13	0.00000227	576
Missense in Polyphen		25	22.32	1.1201		248
Synonymous	-0.361	22	19.9	1.10	8.88e-7	140
Loss of Function	0.283	5	5.73	0.872	2.44e-7	61

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000647	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000265
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.000331	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Connects the two COX monomers into the physiological dimeric form. {ECO:0000250}.
• 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) (Consensus)

Intolerance Scores

• loftool: 0.569
• rvis_EVS: 0.39
• rvis_percentile_EVS: 75.87

Haploinsufficiency Scores

• pHI: 0.0755
• hipred: N
• hipred_score: 0.241
• ghis: 0.399

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cox6b2

Gene ontology

• Cellular component: mitochondrion;mitochondrial intermembrane space;mitochondrial crista
• Molecular function: protein binding