NDUFA3

NADH:ubiquinone oxidoreductase subunit A3, the group of NADH:ubiquinone oxidoreductase supernumerary subunits

Basic information

Region (hg38): 19:54102728-54109257

Links

ENSG00000170906 ∙ NCBI:4696 ∙ OMIM:603832 ∙ HGNC:7686 ∙ Uniprot:O95167 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NDUFA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NDUFA3 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						0
missense			3	1		4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	4	1	0

Variants in NDUFA3

This is a list of pathogenic ClinVar variants found in the NDUFA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-54103128-C-A		not specified	Uncertain significance (Jun 16, 2022)
19-54103176-G-A		not specified	Likely benign (Oct 27, 2022)
19-54105937-T-A		not specified	Uncertain significance (Jun 24, 2022)
19-54105958-C-T		not specified	Uncertain significance (Apr 07, 2022)
19-54106819-C-T		not specified	Uncertain significance (Apr 09, 2024)
19-54107096-T-C		not specified	Uncertain significance (Jun 30, 2022)
19-54107144-A-G		not specified	Uncertain significance (May 13, 2024)
19-54108069-C-T		not specified	Uncertain significance (Jan 26, 2023)
19-54108078-C-T		not specified	Uncertain significance (May 30, 2024)
19-54108087-C-T		not specified	Uncertain significance (Jul 25, 2023)
19-54108091-G-A		not specified	Uncertain significance (Dec 26, 2023)
19-54108093-C-A		not specified	Uncertain significance (Mar 19, 2024)
19-54108145-G-A		not specified	Uncertain significance (Sep 06, 2022)
19-54108229-C-T		not specified	Uncertain significance (Mar 15, 2024)
19-54108354-C-T		not specified	Uncertain significance (Dec 18, 2023)
19-54108355-G-A		not specified	Uncertain significance (Mar 23, 2022)
19-54108367-C-T		not specified	Uncertain significance (Nov 17, 2023)
19-54108382-C-G		not specified	Uncertain significance (Jan 26, 2023)
19-54108387-A-G		not specified	Uncertain significance (Dec 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NDUFA3	protein_coding	protein_coding	ENST00000485876	4	6529

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0719	0.755	125732	0	8	125740	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.394	57	49.2	1.16	0.00000275	539
Missense in Polyphen		12	9.9424	1.207		129
Synonymous	0.387	19	21.3	0.893	0.00000127	155
Loss of Function	0.954	2	4.08	0.490	1.72e-7	53

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000217	0.000215
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000550	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000550	0.0000544
South Asian	0.00	0.00
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)

Intolerance Scores

• loftool: 0.394
• rvis_EVS: 0.19
• rvis_percentile_EVS: 66.57

Haploinsufficiency Scores

• pHI: 0.108
• hipred: N
• hipred_score: 0.170
• ghis: 0.485

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.482

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ndufa3

Gene ontology

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