COQ9

coenzyme Q9

Basic information

Region (hg38): 16:57447425-57461270

Previous symbols: [ "C16orf49" ]

Links

ENSG00000088682 ∙ NCBI:57017 ∙ OMIM:612837 ∙ HGNC:25302 ∙ Uniprot:O75208 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Leigh syndrome (Limited), mode of inheritance: AR
• mitochondrial disease (Definitive), mode of inheritance: AR
• encephalopathy-hypertrophic cardiomyopathy-renal tubular disease syndrome (Strong), mode of inheritance: AR
• encephalopathy-hypertrophic cardiomyopathy-renal tubular disease syndrome (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Coenzyme Q10 deficiency 5	AR	Biochemical	Treatment with coenzyme Q10 can be beneficial	Biochemical; Musculoskeletal; Neurologic; Renal	11562630; 19375058

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COQ9 gene.

• not_provided (271 variants)
• Inborn_genetic_diseases (58 variants)
• Encephalopathy-hypertrophic_cardiomyopathy-renal_tubular_disease_syndrome (42 variants)
• not_specified (17 variants)
• COQ9-related_disorder (15 variants)
• Coenzyme_Q10_deficiency (2 variants)
• Leigh_syndrome (2 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COQ9 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020312.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				78		78
missense	1		137	16	1	155
nonsense	9					9
start loss						0
frameshift	6		1			7
splice donor/acceptor (+/-2bp)	3	5	1			9
Total	19	5	139	94	1

Highest pathogenic variant AF is 0.000047087222

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COQ9	protein_coding	protein_coding	ENST00000262507	9	13851

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125711	0	37	125748	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.216	183	175	1.05	0.0000111	2044
Missense in Polyphen		50	49.349	1.0132		575
Synonymous	0.183	63	64.9	0.971	0.00000377	624
Loss of Function	1.53	11	18.0	0.611	9.78e-7	194

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000387	0.000387
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.000109	0.000109
South Asian	0.000197	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Lipid-binding protein involved in the biosynthesis of coenzyme Q, also named ubiquinone, an essential lipid-soluble electron transporter for aerobic cellular respiration. Binds a phospholipid of at least 10 carbons in each acyl group. May be required to present its bound-lipid to COQ7. {ECO:0000269|PubMed:25339443}.
• Disease: DISEASE: Coenzyme Q10 deficiency, primary, 5 (COQ10D5) [MIM:614654]: A form of coenzyme Q10 deficiency, an autosomal recessive disorder with variable manifestations consistent with 5 major phenotypes. The phenotypes include an encephalomyopathic form with seizures and ataxia; a multisystem infantile form with encephalopathy, cardiomyopathy and renal failure; a predominantly cerebellar form with ataxia and cerebellar atrophy; Leigh syndrome with growth retardation; and an isolated myopathic form. {ECO:0000269|PubMed:19375058}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Metabolism;Ubiquinol biosynthesis;Metabolism of cofactors;Metabolism of vitamins and cofactors (Consensus)

Recessive Scores

• pRec: 0.0865

Intolerance Scores

• loftool: 0.313
• rvis_EVS: 0.68
• rvis_percentile_EVS: 85.04

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.812

Gene Damage Prediction

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

Gene ontology

• Biological process: mitochondrial electron transport, NADH to ubiquinone;ubiquinone biosynthetic process
• Cellular component: mitochondrion;mitochondrial inner membrane
• Molecular function: protein binding;lipid binding;protein homodimerization activity