COQ5

coenzyme Q5, methyltransferase, the group of 7BS small molecule methyltransferases

Basic information

Region (hg38): 12:120503279-120534434

Links

ENSG00000110871 ∙ NCBI:84274 ∙ OMIM:616359 ∙ HGNC:28722 ∙ Uniprot:Q5HYK3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• coenzyme q10 deficiency, primary, 9 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Coenzyme Q10 deficiency, primary, 1	AR	Biochemical	Treatment with coenzyme Q10 has been described as beneficial	Biochemical; Neurologic	29044765

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COQ5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COQ5 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				3	2	5
missense			17	6		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding						0
Total	0	0	17	9	2

Variants in COQ5

This is a list of pathogenic ClinVar variants found in the COQ5 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-120503834-C-T		not specified	Uncertain significance (Aug 14, 2023)
12-120503982-C-T			Benign (Jul 04, 2018)
12-120504010-T-A		not specified	Uncertain significance (Sep 07, 2022)
12-120504026-C-T		not specified	Uncertain significance (Apr 29, 2024)
12-120504087-C-T		COQ5-related disorder	Likely benign (May 02, 2018)
12-120504909-A-T		not specified	Uncertain significance (Apr 04, 2023)
12-120504943-C-T		not specified	Uncertain significance (Jul 05, 2023)
12-120510020-A-C		not specified	Uncertain significance (Jun 10, 2024)
12-120510087-G-T			Uncertain significance (Oct 01, 2019)
12-120510102-T-A		not specified	Uncertain significance (Aug 16, 2022)
12-120510130-G-C		COQ5-related disorder	Benign (Dec 31, 2019)
12-120516621-T-G		not specified	Uncertain significance (May 05, 2023)
12-120516644-C-T		not specified	Likely benign (Apr 27, 2023)
12-120516645-G-A		not specified	Uncertain significance (Aug 08, 2023)
12-120516650-C-T		not specified	Uncertain significance (Feb 14, 2024)
12-120516660-A-G		not specified	Likely benign (Feb 12, 2024)
12-120516680-T-G		not specified	Uncertain significance (Dec 07, 2021)
12-120516746-T-C			Likely benign (May 12, 2018)
12-120516788-C-T		Coenzyme q10 deficiency, primary, 9	Conflicting classifications of pathogenicity (Aug 25, 2023)
12-120522206-G-A		COQ5-related disorder	Likely benign (Jan 14, 2020)
12-120522233-A-C		COQ5-related disorder	Likely benign (Aug 20, 2019)
12-120522252-A-G			Likely benign (Dec 01, 2023)
12-120522254-C-T		COQ5-related disorder	Benign (Jul 23, 2019)
12-120522259-G-C		not specified	Uncertain significance (Apr 19, 2024)
12-120522299-A-G			Likely benign (Jul 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COQ5	protein_coding	protein_coding	ENST00000288532	7	31161

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000284	0.937	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.363	191	177	1.08	0.00000965	2147
Missense in Polyphen		73	79.324	0.92028		956
Synonymous	0.726	60	67.6	0.888	0.00000351	618
Loss of Function	1.72	10	17.8	0.561	8.68e-7	203

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.000489	0.000489
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000149	0.000149
Middle Eastern	0.000489	0.000489
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Methyltransferase required for the conversion of 2- polyprenyl-6-methoxy-1,4-benzoquinol (DDMQH2) to 2-polyprenyl-3- methyl-6-methoxy-1,4-benzoquinol (DMQH2). {ECO:0000255|HAMAP- Rule:MF_03191}.
• Pathway: Ubiquinone and other terpenoid-quinone biosynthesis - Homo sapiens (human);Ubiquinone Biosynthesis;Metabolism;Ubiquinol biosynthesis;Metabolism of cofactors;Metabolism of vitamins and cofactors;ubiquinol-10 biosynthesis (Consensus)

Recessive Scores

• pRec: 0.173

Intolerance Scores

• loftool: 0.867
• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.74

Haploinsufficiency Scores

• pHI: 0.0733
• hipred: N
• hipred_score: 0.177
• ghis: 0.543

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.179

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Coq5

Gene ontology

• Biological process: ubiquinone biosynthetic process;methylation
• Cellular component: mitochondrion;mitochondrial inner membrane;mitochondrial matrix;extrinsic component of mitochondrial inner membrane;protein-containing complex
• Molecular function: protein binding;2-octaprenyl-6-methoxy-1,4-benzoquinone methylase activity;2-decaprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity