COQ8B

coenzyme Q8B

Basic information

Region (hg38): 19:40691514-40725784

Previous symbols: [ "ADCK4" ]

Links

ENSG00000123815 ∙ NCBI:79934 ∙ OMIM:615567 ∙ HGNC:19041 ∙ Uniprot:Q96D53 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• nephrotic syndrome, type 9 (Strong), mode of inheritance: AR
• familial idiopathic steroid-resistant nephrotic syndrome (Supportive), mode of inheritance: AD
• nephrotic syndrome, type 9 (Definitive), 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
Nephrotic syndrome, type 9	AR	Biochemical; Renal	The condition manifests as steroid-resistant nephrotic syndrome, with focal segmental glomerulosclerosis, and treatment with coenzyme Q10 has been described as beneficial	Renal	24270420

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COQ8B gene.

• Nephrotic syndrome, type 9 (7 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COQ8B 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				49	6	55
missense	1	4	65	8	2	80
nonsense	1	2				3
start loss						0
frameshift	2	2	1			5
inframe indel			1			1
splice donor/acceptor (+/-2bp)	5	1				6
splice region			4	13	2	19
non coding			2	49	14	65
Total	9	9	69	106	22

Highest pathogenic variant AF is 0.0000394

Variants in COQ8B

This is a list of pathogenic ClinVar variants found in the COQ8B region.

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

Position	Type	Phenotype	Significance	ClinVar
19-40691861-G-A			Likely benign (Jul 09, 2018)
19-40691898-C-T			Likely benign (Jul 07, 2018)
19-40692025-A-G		not specified • Nephrotic syndrome, type 9	Benign/Likely benign (Oct 08, 2021)
19-40692038-T-C			Likely benign (Aug 02, 2023)
19-40692087-G-C			Uncertain significance (Mar 22, 2022)
19-40692091-C-T		Inborn genetic diseases	Uncertain significance (Sep 27, 2022)
19-40692092-G-A		not specified • Kidney disorder	Benign (Jan 22, 2024)
19-40692104-A-G			Likely benign (Oct 05, 2023)
19-40692110-C-T		Inborn genetic diseases • Nephrotic syndrome, type 9 • Retinitis pigmentosa	Conflicting classifications of pathogenicity (Jul 12, 2024)
19-40692118-G-A		Nephrotic syndrome, type 9	Uncertain significance (Nov 28, 2023)
19-40692151-C-T			Likely benign (Jul 27, 2023)
19-40692152-G-A			Likely benign (Nov 27, 2023)
19-40692153-A-AT			Uncertain significance (Apr 15, 2022)
19-40692166-G-A			Uncertain significance (Sep 01, 2023)
19-40692182-G-A			Likely benign (Jun 27, 2022)
19-40692202-G-A		Nephrotic syndrome, type 9	Pathogenic (Jan 22, 2024)
19-40692205-G-A		Nephrotic syndrome, type 9	Uncertain significance (Dec 01, 2023)
19-40692211-C-A		Nephrotic syndrome, type 9	Uncertain significance (May 12, 2023)
19-40692222-T-C			Uncertain significance (Nov 16, 2023)
19-40692223-C-A		Nephrotic syndrome, type 9	Pathogenic/Likely pathogenic (Jan 17, 2020)
19-40692223-C-T			Uncertain significance (Dec 11, 2023)
19-40692235-A-G		Inborn genetic diseases	Likely benign (Apr 11, 2024)
19-40692239-C-A			Likely benign (May 27, 2022)
19-40692240-C-T		Nephrotic syndrome, type 9	Pathogenic/Likely pathogenic (Mar 05, 2024)
19-40692246-C-T			Uncertain significance (Apr 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COQ8B	protein_coding	protein_coding	ENST00000324464	14	26679

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.82e-13	0.250	125656	0	92	125748	0.000366

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.890	303	350	0.866	0.0000225	3473
Missense in Polyphen		113	139.3	0.81119		1339
Synonymous	1.68	112	137	0.817	0.00000818	1123
Loss of Function	1.09	23	29.4	0.782	0.00000148	302

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000721	0.000720
Ashkenazi Jewish	0.0000997	0.0000992
East Asian	0.000272	0.000272
Finnish	0.0000976	0.0000924
European (Non-Finnish)	0.000414	0.000404
Middle Eastern	0.000272	0.000272
South Asian	0.000573	0.000555
Other	0.000664	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Atypical kinase involved in the biosynthesis of coenzyme Q, also named ubiquinone, an essential lipid-soluble electron transporter for aerobic cellular respiration (PubMed:24270420). Its substrate specificity is unclear: does not show any protein kinase activity. Probably acts as a small molecule kinase, possibly a lipid kinase that phosphorylates a prenyl lipid in the ubiquinone biosynthesis pathway. Required for podocyte migration (PubMed:24270420). {ECO:0000250|UniProtKB:Q8NI60, ECO:0000269|PubMed:24270420}.
• Disease: DISEASE: Nephrotic syndrome 9 (NPHS9) [MIM:615573]: A form of nephrotic syndrome, a renal disease clinically characterized by progressive renal failure, severe proteinuria, hypoalbuminemia, hyperlipidemia and edema. Kidney biopsies show focal segmental glomerulosclerosis. {ECO:0000269|PubMed:24270420, ECO:0000269|PubMed:25967120}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.0981

Intolerance Scores

• rvis_EVS: 0.03
• rvis_percentile_EVS: 55.79

Haploinsufficiency Scores

• pHI: 0.137
• hipred: N
• hipred_score: 0.196
• ghis: 0.499

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Coq8b

Zebrafish Information Network

• Gene name: coq8b
• Affected structure: podocyte
• Phenotype tag: abnormal
• Phenotype quality: disorganized

Gene ontology

• Biological process: protein phosphorylation;ubiquinone biosynthetic process;cerebellar Purkinje cell layer morphogenesis
• Cellular component: mitochondrion;cytosol;plasma membrane;integral component of membrane;extrinsic component of mitochondrial inner membrane
• Molecular function: protein kinase activity;ATP binding;kinase activity