COQ3

coenzyme Q3, methyltransferase, the group of 7BS small molecule methyltransferases

Basic information

Region (hg38): 6:99369401-99394195

Links

ENSG00000132423 ∙ NCBI:51805 ∙ OMIM:605196 ∙ HGNC:18175 ∙ Uniprot:Q9NZJ6 ∙ 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 COQ3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COQ3 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		1
missense			19	2		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	3	0

Variants in COQ3

This is a list of pathogenic ClinVar variants found in the COQ3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-99369637-C-T		not specified	Uncertain significance (Aug 09, 2021)
6-99369650-G-T		not specified	Uncertain significance (Jul 14, 2024)
6-99369710-T-C		not specified	Likely benign (Aug 12, 2024)
6-99369758-A-T		not specified	Uncertain significance (Oct 14, 2023)
6-99369759-A-T		not specified	Uncertain significance (Oct 14, 2023)
6-99369799-A-G		not specified	Uncertain significance (Sep 20, 2023)
6-99369802-G-A		not specified	Uncertain significance (Nov 07, 2022)
6-99371430-G-A		not specified	Uncertain significance (Aug 10, 2021)
6-99371517-G-A		not specified	Uncertain significance (Nov 29, 2023)
6-99371560-T-C		not specified	Uncertain significance (Oct 10, 2023)
6-99371584-C-G		not specified	Uncertain significance (Oct 20, 2024)
6-99375947-A-G		not specified	Uncertain significance (Dec 15, 2021)
6-99375962-T-C		not specified	Uncertain significance (Jul 26, 2022)
6-99375978-G-T		not specified	Uncertain significance (Dec 10, 2024)
6-99376004-G-A		not specified	Uncertain significance (Jan 10, 2023)
6-99376035-T-C		not specified	Uncertain significance (Apr 05, 2023)
6-99376065-C-T			Likely benign (Dec 31, 2019)
6-99376067-C-T		not specified	Uncertain significance (May 26, 2022)
6-99376129-G-A			Likely benign (Mar 01, 2022)
6-99376146-C-G		not specified	Uncertain significance (Nov 17, 2023)
6-99376164-C-G		not specified	Uncertain significance (Sep 01, 2021)
6-99377471-T-G		not specified	Uncertain significance (Jan 24, 2024)
6-99383770-T-C		not specified	Likely benign (Dec 28, 2022)
6-99383773-A-G		not specified	Uncertain significance (Oct 28, 2024)
6-99383808-C-A		not specified	Uncertain significance (Nov 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COQ3	protein_coding	protein_coding	ENST00000254759	7	24805

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.43e-8	0.283	125724	0	23	125747	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0749	192	189	1.02	0.00000876	2373
Missense in Polyphen		49	44.046	1.1125		545
Synonymous	-1.01	83	72.1	1.15	0.00000356	725
Loss of Function	0.561	13	15.4	0.846	6.48e-7	201

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000148	0.000148
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.0000544	0.0000544
South Asian	0.000105	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: O-methyltransferase that catalyzes the 2 O-methylation steps in the ubiquinone biosynthetic pathway. {ECO:0000255|HAMAP- Rule:MF_03190}.
• 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: 0.108

Intolerance Scores

• loftool: 0.864
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.25

Haploinsufficiency Scores

• pHI: 0.345
• hipred: N
• hipred_score: 0.144
• ghis: 0.441

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.735

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Coq3

Gene ontology

• Biological process: glycerol metabolic process;ubiquinone biosynthetic process;regulation of ubiquinone biosynthetic process;methylation
• Cellular component: mitochondrion;mitochondrial matrix;extrinsic component of mitochondrial inner membrane
• Molecular function: hexaprenyldihydroxybenzoate methyltransferase activity;protein binding;O-methyltransferase activity;2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity;3-demethylubiquinone-9 3-O-methyltransferase activity;decaprenyldihydroxybenzoate methyltransferase activity;3-demethylubiquinone-10 3-O-methyltransferase activity