NDUFA12

NADH:ubiquinone oxidoreductase subunit A12, the group of NADH:ubiquinone oxidoreductase supernumerary subunits

Basic information

Region (hg38): 12:94895296-95003748

Links

ENSG00000184752 ∙ NCBI:55967 ∙ OMIM:614530 ∙ HGNC:23987 ∙ Uniprot:Q9UI09 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• mitochondrial complex 1 deficiency, nuclear type 23 (Moderate), mode of inheritance: AR
• Leigh syndrome with leukodystrophy (Supportive), mode of inheritance: AR
• mitochondrial complex 1 deficiency, nuclear type 23 (Strong), mode of inheritance: AR
• mitochondrial complex 1 deficiency, nuclear type 23 (Definitive), mode of inheritance: AR
• Leigh syndrome (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Mitochondrial complex I deficiency, nuclear type 23; Leigh syndrome	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; Gastrointestinal; Neurologic; Ophthalmologic	21617257; 33715266; 35141356
Medical treatment (eg, riboflavin, ubiquinol) may be beneficial; Individuals may have cardiac involvement

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NDUFA12 gene.

• not provided (56 variants)
• not specified (10 variants)
• Inborn genetic diseases (7 variants)
• Mitochondrial complex 1 deficiency, nuclear type 23 (6 variants)
• Leigh syndrome (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NDUFA12 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	10	1	13
missense			23	1		24
nonsense	3	1				4
start loss		1				1
frameshift	1		3			4
inframe indel			2			2
splice donor/acceptor (+/-2bp)		1				1
splice region			1	1		2
non coding				8	8	16
Total	4	3	30	19	9

Highest pathogenic variant AF is 0.000112

Variants in NDUFA12

This is a list of pathogenic ClinVar variants found in the NDUFA12 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-94971378-G-A			Likely benign (Nov 29, 2019)
12-94971441-T-C			Uncertain significance (Jun 30, 2022)
12-94971475-G-C		Inborn genetic diseases	Uncertain significance (Nov 04, 2022)
12-94971477-ATCT-A		Inborn genetic diseases	Conflicting classifications of pathogenicity (Nov 01, 2022)
12-94971482-CT-C		Mitochondrial complex 1 deficiency, nuclear type 23	Pathogenic (Sep 01, 2021)
12-94971496-A-C		Inborn genetic diseases	Uncertain significance (Apr 11, 2023)
12-94971499-A-G			Uncertain significance (Mar 13, 2022)
12-94971529-C-T		Inborn genetic diseases	Uncertain significance (Aug 04, 2023)
12-94971540-T-C			Uncertain significance (-)
12-94971545-C-T		not specified	Likely benign (Jan 22, 2024)
12-94971551-A-G			Likely benign (May 27, 2022)
12-94971553-T-A		Inborn genetic diseases	Uncertain significance (Jan 08, 2024)
12-94971561-C-A			Uncertain significance (Jul 23, 2022)
12-94971561-C-T			Uncertain significance (Aug 26, 2021)
12-94971572-TG-T		not specified	Uncertain significance (Nov 15, 2022)
12-94971587-A-G			Likely benign (Apr 14, 2023)
12-94971597-G-T			Uncertain significance (Dec 11, 2023)
12-94971600-A-G		Leigh syndrome	Uncertain significance (Jul 04, 2022)
12-94971604-T-A		Inborn genetic diseases	Likely benign (Dec 28, 2023)
12-94971615-C-T		Inborn genetic diseases	Uncertain significance (Oct 13, 2023)
12-94971616-G-A			Uncertain significance (Mar 15, 2022)
12-94971618-T-C		not specified	Uncertain significance (Oct 24, 2022)
12-94971904-A-AT			Benign (Aug 13, 2019)
12-94993980-C-T			Benign (Jun 14, 2018)
12-94994008-C-T			Benign (Jun 28, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NDUFA12	protein_coding	protein_coding	ENST00000327772	4	106716

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000743	0.527	125721	0	26	125747	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00353	83	83.1	0.999	0.00000456	947
Missense in Polyphen		22	27.002	0.81475		363
Synonymous	-0.921	36	29.6	1.22	0.00000155	273
Loss of Function	0.536	7	8.71	0.804	4.62e-7	88

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000358	0.000358
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000323	0.000323
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
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}.
• Disease: DISEASE: Leigh syndrome (LS) [MIM:256000]: An early-onset progressive neurodegenerative disorder characterized by the presence of focal, bilateral lesions in one or more areas of the central nervous system including the brainstem, thalamus, basal ganglia, cerebellum and spinal cord. Clinical features depend on which areas of the central nervous system are involved and include subacute onset of psychomotor retardation, hypotonia, ataxia, weakness, vision loss, eye movement abnormalities, seizures, and dysphagia. {ECO:0000269|PubMed:21617257}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• 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;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: 0.112

Intolerance Scores

• loftool: 0.759
• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.2

Haploinsufficiency Scores

• pHI: 0.0939
• hipred: N
• hipred_score: 0.218
• ghis: 0.612

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.845

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ndufa12

Gene ontology

• Biological process: response to oxidative stress;respiratory gaseous exchange;mitochondrial respiratory chain complex I assembly;mitochondrial ATP synthesis coupled electron transport
• Cellular component: mitochondrion;mitochondrial inner membrane;mitochondrial respiratory chain complex I;cytosol
• Molecular function: NADH dehydrogenase (ubiquinone) activity;electron transfer activity