NDUFB9

NADH:ubiquinone oxidoreductase subunit B9, the group of NADH:ubiquinone oxidoreductase supernumerary subunits|LYR motif containing

Basic information

Region (hg38): 8:124539101-124580648

Links

ENSG00000147684 ∙ NCBI:4715 ∙ OMIM:601445 ∙ HGNC:7704 ∙ Uniprot:Q9Y6M9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• mitochondrial complex 1 deficiency, nuclear type 24 (Limited), mode of inheritance: AR
• mitochondrial complex I deficiency (Supportive), mode of inheritance: AR
• mitochondrial complex 1 deficiency, nuclear type 24 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Mitochondrial complex I deficiency, nuclear type 24	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; Neurologic	22200994

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NDUFB9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NDUFB9 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				17	1	18
missense			33	2	1	36
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region			3	2		5
non coding				18	12	30
Total	0	0	36	37	14

Variants in NDUFB9

This is a list of pathogenic ClinVar variants found in the NDUFB9 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-124539123-A-G			Benign (Jun 14, 2018)
8-124539136-A-G		Mitochondrial complex 1 deficiency, nuclear type 24	Likely benign (Oct 08, 2021)
8-124539140-G-T		not specified	Likely benign (Mar 10, 2016)
8-124539144-A-G		not specified	Benign (Dec 02, 2013)
8-124539151-C-G		not specified	Benign (Feb 21, 2014)
8-124539156-C-T		not specified	Likely benign (Jul 20, 2017)
8-124539161-C-T		not specified	Likely benign (Mar 31, 2017)
8-124539169-G-T		not specified	Likely benign (Jan 30, 2018)
8-124539187-A-G		not specified	Conflicting classifications of pathogenicity (Feb 09, 2024)
8-124539195-C-T			Likely benign (Dec 13, 2017)
8-124539197-T-G		not specified	Uncertain significance (Jan 07, 2022)
8-124539209-C-T		not specified	Likely benign (Jan 17, 2023)
8-124539210-C-T		not specified • Mitochondrial complex 1 deficiency, nuclear type 24	Benign/Likely benign (Apr 01, 2024)
8-124539212-A-G			Uncertain significance (Mar 03, 2023)
8-124539215-T-G			Uncertain significance (Jan 25, 2024)
8-124539251-G-A		not specified	Uncertain significance (Aug 11, 2022)
8-124539265-C-G		not specified	Uncertain significance (May 26, 2023)
8-124539267-C-G			Likely benign (Apr 12, 2022)
8-124539268-G-C			Uncertain significance (Jan 08, 2024)
8-124539270-G-A			Likely benign (Aug 18, 2017)
8-124539294-G-A			Likely benign (Jun 23, 2018)
8-124539326-C-T			Benign (Jun 23, 2018)
8-124539527-G-C			Likely benign (Jul 07, 2018)
8-124542802-CTTTTCTTT-C			Likely benign (Sep 20, 2019)
8-124542846-A-C			Benign (Jun 26, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NDUFB9	protein_coding	protein_coding	ENST00000276689	4	29408

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000163	0.889	125724	0	24	125748	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.000386	104	104	1.00	0.00000600	1154
Missense in Polyphen		25	23.11	1.0818		270
Synonymous	0.0967	38	38.8	0.980	0.00000201	325
Loss of Function	1.45	8	13.8	0.579	8.63e-7	133

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000160	0.000158
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed to be not 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: 0.147

Intolerance Scores

• loftool: 0.577
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.06

Haploinsufficiency Scores

• pHI: 0.0920
• hipred: N
• hipred_score: 0.267
• ghis: 0.476

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ndufb9

Gene ontology

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