NDUFB10

NADH:ubiquinone oxidoreductase subunit B10, the group of NADH:ubiquinone oxidoreductase supernumerary subunits

Basic information

Region (hg38): 16:1959538-1961975

Links

ENSG00000140990 ∙ NCBI:4716 ∙ OMIM:603843 ∙ HGNC:7696 ∙ Uniprot:O96000 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• mitochondrial complex I deficiency (Supportive), mode of inheritance: AR
• mitochondrial complex 1 deficiency, nuclear type 35 (Limited), mode of inheritance: Unknown
• mitochondrial disease (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Mitochondrial complex I deficiency, nuclear type 35	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Biochemical; Cardiovascular	28040730

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NDUFB10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NDUFB10 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				15	3	18
missense			37	6	1	44
nonsense						0
start loss						0
frameshift			3	1		4
inframe indel			2			2
splice donor/acceptor (+/-2bp)						0
splice region			2	2	1	5
non coding		1			1	2
Total	0	1	42	22	5

Variants in NDUFB10

This is a list of pathogenic ClinVar variants found in the NDUFB10 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-1959628-C-T			Uncertain significance (Jan 02, 2024)
16-1959635-G-C		not specified	Uncertain significance (Nov 08, 2022)
16-1959653-A-G		not specified	Uncertain significance (Jul 30, 2024)
16-1959661-C-T		not specified	Uncertain significance (Aug 17, 2022)
16-1959664-C-A			Uncertain significance (Jan 13, 2024)
16-1959666-G-T			Likely benign (Jan 13, 2024)
16-1959681-G-A			Likely benign (Jul 07, 2023)
16-1959689-A-G		not specified	Uncertain significance (May 14, 2024)
16-1959691-C-A		not specified	Uncertain significance (Nov 28, 2023)
16-1959692-C-A		not specified	Uncertain significance (Jun 17, 2024)
16-1959696-C-T			Benign (Jan 29, 2024)
16-1959718-G-T			Uncertain significance (Aug 06, 2023)
16-1959726-C-T			Likely benign (Mar 23, 2022)
16-1959727-G-T		not specified	Uncertain significance (Jun 23, 2022)
16-1959732-C-T			Likely benign (Dec 11, 2023)
16-1959745-C-T			Uncertain significance (Aug 23, 2023)
16-1959754-G-C			Uncertain significance (Jul 28, 2023)
16-1959761-A-G			Benign (Jan 30, 2024)
16-1960711-G-C		Mitochondrial complex I deficiency	Likely pathogenic (Apr 25, 2020)
16-1961143-G-A			Benign (Jan 22, 2024)
16-1961145-C-T			Likely benign (May 12, 2023)
16-1961156-T-C		not specified	Uncertain significance (Apr 09, 2024)
16-1961159-T-C		not specified	Uncertain significance (Sep 11, 2024)
16-1961163-G-C		not specified	Uncertain significance (Oct 25, 2022)
16-1961164-C-T			Uncertain significance (Sep 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NDUFB10	protein_coding	protein_coding	ENST00000268668	4	2468

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00475	0.890	125730	0	15	125745	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.15	139	106	1.31	0.00000581	1133
Missense in Polyphen		54	42.907	1.2585		450
Synonymous	-1.06	48	39.6	1.21	0.00000217	288
Loss of Function	1.38	5	9.61	0.520	4.12e-7	109

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000872	0.0000872
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000716	0.0000703
Middle Eastern	0.000109	0.000109
South Asian	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone. {ECO:0000269|PubMed:27626371}.
• Pathway: Retrograde endocannabinoid signaling - Homo sapiens (human);Non-alcoholic fatty liver disease (NAFLD) - Homo sapiens (human);Alzheimer,s disease - Homo sapiens (human);Huntington,s disease - Homo sapiens (human);Thermogenesis - Homo sapiens (human);Oxidative phosphorylation - Homo sapiens (human);Parkinson,s disease - Homo sapiens (human);Electron Transport Chain;Oxidative phosphorylation;Respiratory electron transport;The citric acid (TCA) cycle and respiratory electron transport;Metabolism;Complex I biogenesis;Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. (Consensus)

Recessive Scores

• pRec: 0.0990

Intolerance Scores

• loftool: 0.369
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.04

Haploinsufficiency Scores

• pHI: 0.0637
• hipred: N
• hipred_score: 0.240
• ghis: 0.585

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.204

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ndufb10

Gene ontology

• Biological process: mitochondrial electron transport, NADH to ubiquinone;mitochondrial respiratory chain complex I assembly
• Cellular component: mitochondrial inner membrane;mitochondrial respiratory chain complex I
• Molecular function: protein binding;NADH dehydrogenase (ubiquinone) activity