COQ4

coenzyme Q4

Basic information

Region (hg38): 9:128322544-128334072

Links

ENSG00000167113 ∙ NCBI:51117 ∙ OMIM:612898 ∙ HGNC:19693 ∙ Uniprot:Q9Y3A0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome (Supportive), mode of inheritance: AR
• neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome (Strong), mode of inheritance: AR
• mitochondrial disease (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Coenzyme Q10 deficiency 7	AR	Biochemical	Treatment with coenzyme Q10 has been described as possibly beneficial	Biochemical; Cardiovascular; Neurologic	22368301; 25658047; 33704555; 33704555; 36047608; 38013626; 38014483

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COQ4 gene.

• Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome (13 variants)
• Spastic ataxia 10, autosomal recessive (2 variants)
• not provided (2 variants)
• Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome;Spastic ataxia 10, autosomal recessive (1 variants)
• Spastic ataxia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COQ4 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			2	72	1	75
missense	4	5	90	3	4	106
nonsense	4	3				7
start loss		1	1			2
frameshift	6	1				7
inframe indel						0
splice donor/acceptor (+/-2bp)		7				7
splice region			6	8		14
non coding				44	9	53
Total	14	17	93	119	14

Highest pathogenic variant AF is 0.0000263

Variants in COQ4

This is a list of pathogenic ClinVar variants found in the COQ4 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-128322588-T-A			Likely benign (Jul 15, 2018)
9-128322834-C-T		not specified	Benign (Jun 30, 2016)
9-128322839-C-G		not specified • Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome	Likely benign (Oct 08, 2021)
9-128322842-C-T		not specified	Likely benign (Jan 25, 2017)
9-128322847-A-G		not specified	Likely benign (May 18, 2017)
9-128322848-C-A		not specified	Likely benign (Jan 25, 2018)
9-128322859-A-G		Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome • Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome;Spastic ataxia 10, autosomal recessive	Conflicting classifications of pathogenicity (Apr 27, 2024)
9-128322860-T-C		Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome	Likely pathogenic (Aug 05, 2019)
9-128322860-T-G		Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome	Uncertain significance (Apr 21, 2022)
9-128322868-C-T		Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome	Likely benign (Nov 13, 2023)
9-128322869-T-A			Uncertain significance (Jul 16, 2024)
9-128322870-G-C		Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome	Likely benign (Oct 19, 2022)
9-128322875-G-A		Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome • Inborn genetic diseases	Uncertain significance (Nov 03, 2023)
9-128322875-GCC-G		Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome	Pathogenic (Nov 18, 2023)
9-128322876-C-T		Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome	Likely benign (Apr 08, 2024)
9-128322877-C-T		Inborn genetic diseases • Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome	Uncertain significance (Dec 03, 2021)
9-128322879-T-C		Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome	Likely benign (Dec 12, 2024)
9-128322879-TGTCCTCCGTCG-T		Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome • Spastic ataxia 10, autosomal recessive;Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome	Pathogenic (Jan 25, 2024)
9-128322881-T-A		Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome	Uncertain significance (Jan 22, 2024)
9-128322882-C-T		Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome	Likely benign (Apr 09, 2023)
9-128322886-C-T		Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome	Uncertain significance (Jun 13, 2022)
9-128322887-G-C		Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome	Uncertain significance (Jun 26, 2022)
9-128322889-C-A		Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome	Likely benign (Jun 15, 2023)
9-128322889-C-T			Uncertain significance (Jun 14, 2023)
9-128322890-G-C		Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome	Uncertain significance (Jan 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COQ4	protein_coding	protein_coding	ENST00000300452	7	11537

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.40e-9	0.0973	125677	0	71	125748	0.000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.364	157	170	0.921	0.0000107	1643
Missense in Polyphen		73	82.796	0.88168		792
Synonymous	-1.24	87	73.5	1.18	0.00000441	589
Loss of Function	-0.0102	13	13.0	1.00	8.22e-7	124

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000365	0.000359
Ashkenazi Jewish	0.00	0.00
East Asian	0.000598	0.000598
Finnish	0.00116	0.00116
European (Non-Finnish)	0.000181	0.000176
Middle Eastern	0.000598	0.000598
South Asian	0.000164	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the coenzyme Q biosynthetic pathway. May play a role in organizing a multi-subunit COQ enzyme complex required for coenzyme Q biosynthesis. Required for steady-state levels of other COQ polypeptides. {ECO:0000255|HAMAP- Rule:MF_03111, ECO:0000269|PubMed:18474229}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.01

Haploinsufficiency Scores

• pHI: 0.136
• hipred: N
• hipred_score: 0.248
• ghis: 0.421

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.666

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Coq4
• Phenotype: 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); homeostasis/metabolism phenotype

Gene ontology

• Biological process: ubiquinone biosynthetic process
• Cellular component: mitochondrion;extrinsic component of mitochondrial inner membrane;protein-containing complex
• Molecular function: protein binding