NDUFC2

protein-coding

NADH:ubiquinone oxidoreductase subunit C2, the group of NADH:ubiquinone oxidoreductase supernumerary subunits

Gene summary

Predicted to enable NADH dehydrogenase (ubiquinone) activity. Involved in mitochondrial respiratory chain complex I assembly. Located in mitochondrial inner membrane. Part of respiratory chain complex I. Implicated in nuclear type mitochondrial complex I deficiency and stroke. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_004549.6

Inheritance

AR

ClinVar variants

P:2U:2B:2

Top phenotype

Mitochondrial complex I deficiency, nuclear type 36

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr11:78,068,297-78,079,862

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~11.6 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

mitochondrial diseaseMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0044970

Submitter: ClinGen

The relationship between *NDUFC2* and primary mitochondrial disease was evaluated using the ClinGen Clinical Validity Framework as of December 18, 2023. The *NDUFC2* gene encodes the NADH:ubiquinone oxidoreductase (complex I) subunit C2, which also plays a role in complex I assembly. Defects of this protein lead to complex I deficiency. The first and only report of *NDUFC2* in relation to autosomal recessive primary mitochondrial disease was in 2020 (PMID:32969598) in two unrelated probands with Leigh syndrome spectrum (LSS). While various names could be given to the constellation of features seen in those with *NDUFC2*-related disease, pathogenic variants in this gene cause a primary mitochondrial disease. Therefore, the *NDUFC2* phenotype has been lumped into one disease entity according to the ClinGen Lumping and Splitting Framework. Of note, *NDUFC2* was first curated by this GCEP for its association with LSS on November 23, 2020 (SOP Version 7), with a final classification of Moderate. This current curation for the association with primary mitochondrial disease includes cases with LSS. Evidence supporting this gene-disease relationship includes case-level data and experimental data. This curation included two variants (homozygous missense and homozygous stop-loss) identified in two cases in one publication (PMID: 32969598). This gene-disease association is also supported by functional implication its known biochemical function (PMID: 27509854) and by complexome profiling in patient cells (PMID: 32969598). In summary, there is moderate evidence to support the relationship between *NDUFC2* and primary mitochondrial disease. While more evidence is needed to establish this relationship definitively, no convincing evidence has emerged that contradicts the gene-disease relationship. This classification was approved by the NICHD/NINDS U24 ClinGen Mitochondrial Disease Gene Curation Expert Panel on December 18, 2023 (SOP Version 9).

mitochondrial complex I deficiency, nuclear type 36LIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0030902

Submitter: Labcorp Genetics (formerly Invitae)

mitochondrial complex I deficiency, nuclear type 36MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0030902

Submitter: PanelApp Australia

Leigh syndromeMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0009723

Submitter: ClinGen

The relationship between NDUFC2 and Leigh syndrome spectrum was evaluated using the ClinGen Clinical Validity Framework as of November 23, 2020. The NDUFC2 gene encodes the NADH:ubiquinone oxidoreductase (complex I) subunit C2, which also plays a role in complex I assembly. Defects of this protein lead to complex I deficiency. The NDUFC2 gene was first reported in relation to autosomal recessive Leigh syndrome spectrum in 2020 (PMID: 32969598). Evidence supporting this gene-disease relationship includes case-level data and experimental data. This curation included two variants identified in two cases in one publication (PMID: 32969598). No segregation data were available. Loss of function is implicated as the mechanism of disease. This gene-disease association is also supported by known protein interaction, functional alteration in non-patient cells, and functional alteration in patient cells (PMIDs: 27509854, 27626371, 32969598). In summary, there is moderate evidence to support this gene-disease relationship. While more evidence is needed to establish this relationship definitively, no convincing evidence has emerged that contradicts the gene-disease relationship. This classification was approved by the NICHD U24 ClinGen Mitochondrial Disease Gene Curation Expert Panel on November 23, 2020 (SOP Version 7).

Clinical Genomic Database (CGD)

Mitochondrial complex I deficiency, nuclear type 36AR

Manifestation: Biochemical; Cardiovascular; Neurologic; Ophthalmologic

Intervention: General

Rationale: 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

Refs: 32969598Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NDUFC2 variants in ClinVar

4 Conditions Cataloged
not providedTotal: 4
Mitochondrial complex I deficiency, nuclear type 36Total: 3
not specifiedTotal: 2
Mitochondrial diseaseTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004549.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
2
clinvar
2
missense
1
clinvar
2
clinvar
3
nonsense
0
start loss
0
frameshift
1
clinvar
1
splice donor/acceptor (+/-2bp)
0
Total112206

Highest pathogenic variant AF is 0.000056998473

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_004549.6RefSeqNP_004540.13MANE Select
ENST00000281031.5EnsemblENSP00000281031.43MANE Select
NM_001204054.3RefSeqNP_001190983.13Standard
NM_001204055.2RefSeqNP_001190984.13Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • 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)

Biological Process

  • mitochondrial electron transport, NADH to ubiquinone
  • mitochondrial respiratory chain complex I assembly
  • neutrophil degranulation

Molecular Function

  • NADH dehydrogenase (ubiquinone) activity

Cellular Component

  • cytoplasm
  • mitochondrion
  • mitochondrial inner membrane
  • mitochondrial respiratory chain complex I
  • plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000281031
Coding exons
3
Length
11916
Individuals with no LoFs
117701
Homozygous LoFs
0
Heterozygous LoFs
2
Defined
117703
p
0.00000850
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.2386267.50.9190.00000388748
Missense (PolyPhen)3234.4450.92901340
Synonymous0.06402525.40.9840.00000124232
Loss of Function1.7903.730.001.54e-757

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian0.000110.00011rare
Finnish00.0absent
European (Non-Finnish)00.0absent
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec
0.0703

Intolerance Scores

LoFtool
0.493
RVIS EVS
0.13
RVIS percentile EVS
62.74

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
E
Essential (gene trap)
H
Indispensability pred.
N
Indispensability score
0.0733

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumLowMedium
Primary ImmunodeficiencyMediumLowMedium
CancerMediumMediumMedium
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