COQ9

coenzyme Q9

Basic information

Region (hg38): 16:57447424-57461270

Previous symbols: [ "C16orf49" ]

Links

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

Phenotypes

GenCC

Source: genCC

• coenzyme Q10 deficiency, primary, 1 (Definitive), mode of inheritance: AR
• encephalopathy-hypertrophic cardiomyopathy-renal tubular disease syndrome (Strong), mode of inheritance: AR
• mitochondrial disease (Definitive), mode of inheritance: AR
• Leigh syndrome (Limited), 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 (206 variants)
• Encephalopathy-hypertrophic cardiomyopathy-renal tubular disease syndrome (48 variants)
• not specified (19 variants)
• Inborn genetic diseases (17 variants)
• Coenzyme Q10 deficiency (2 variants)
• COQ9-related condition (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.

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	38	1	40
missense			99	8	1	108
nonsense	5					5
start loss						0
frameshift	4					4
inframe indel			1			1
splice donor/acceptor (+/-2bp)	2	2				4
splice region			2	9		11
non coding			15	37	14	66
Total	11	2	116	83	16

Highest pathogenic variant AF is 0.0000329

Variants in COQ9

This is a list of pathogenic ClinVar variants found in the COQ9 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-57447469-C-G		Coenzyme Q10 deficiency	Uncertain significance (Jun 14, 2016)
16-57447479-G-C		Encephalopathy-hypertrophic cardiomyopathy-renal tubular disease syndrome	Uncertain significance (Apr 27, 2017)
16-57447481-C-G		Encephalopathy-hypertrophic cardiomyopathy-renal tubular disease syndrome	Uncertain significance (Jan 12, 2018)
16-57447481-C-T		Coenzyme Q10 deficiency	Uncertain significance (Jun 14, 2016)
16-57447488-G-A		not specified	Likely benign (Feb 02, 2016)
16-57447488-G-C		not specified	Likely benign (Feb 05, 2018)
16-57447507-T-TGGC			Uncertain significance (Sep 07, 2022)
16-57447510-C-T			Uncertain significance (Sep 20, 2021)
16-57447510-CGG-TGA			Uncertain significance (Sep 16, 2018)
16-57447514-G-A			Likely benign (Dec 17, 2023)
16-57447516-C-T			Uncertain significance (Feb 10, 2022)
16-57447517-G-T			Likely benign (Jun 01, 2023)
16-57447519-C-A			Uncertain significance (Aug 22, 2022)
16-57447519-C-G		Inborn genetic diseases	Uncertain significance (Jun 26, 2023)
16-57447519-C-T		Inborn genetic diseases	Uncertain significance (Feb 05, 2024)
16-57447522-T-C			Uncertain significance (Dec 08, 2021)
16-57447523-A-G		not specified	Likely benign (Dec 04, 2023)
16-57447525-C-T		Encephalopathy-hypertrophic cardiomyopathy-renal tubular disease syndrome • Inborn genetic diseases	Uncertain significance (Oct 10, 2023)
16-57447530-G-C			Uncertain significance (Jan 17, 2020)
16-57447531-C-T			Conflicting classifications of pathogenicity (Jan 29, 2024)
16-57447532-G-A			Uncertain significance (Aug 17, 2023)
16-57447533-C-T		Inborn genetic diseases	Uncertain significance (Dec 29, 2023)
16-57447538-C-T			Likely benign (Jan 22, 2024)
16-57447539-C-G		not specified	Likely benign (Mar 25, 2014)
16-57447542-G-A			Uncertain significance (Mar 11, 2022)

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
0.00000553	0.884	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

Haploinsufficiency Scores

• pHI: 0.128
• hipred: N
• hipred_score: 0.204
• ghis: 0.413

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

Mouse Genome Informatics

• Gene name: Coq9
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); growth/size/body region phenotype; muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype

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