NDUFS3
protein-codingNADH:ubiquinone oxidoreductase core subunit S3, the group of NADH:ubiquinone oxidoreductase core subunits
Gene summary
This gene encodes one of the iron-sulfur protein (IP) components of mitochondrial NADH:ubiquinone oxidoreductase (complex I). Mutations in this gene are associated with Leigh syndrome resulting from mitochondrial complex I deficiency.[provided by RefSeq, Apr 2009]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~19.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0032613
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0044970
Submitter: ClinGen
The relationship between *NDUFS3* and *NDUFS3*-related primary mitochondrial disease was evaluated using the ClinGen Clinical Validity Framework as of September 19, 2024. The *NDUFS3* gene encodes a complex I subunit from the iron-sulfur protein fraction of complex I. The *NDUFS3* gene was first reported in relation to autosomal recessive *NDUFS3*-related primary mitochondrial disease in 2004 (PMID: 14729820). *NDUFS3* has been associated with a single disease entity to date; mitochondrial complex I deficiency, nuclear type 8 [OMIM# 618230]. This is one disease entity according to the ClinGen Lumping and Splitting Framework, and has been renamed as *NDUFS3*-related primary mitochondrial disease. Of note, *NDUFS3* was first curated by this Expert Panel for its association with Leigh syndrome spectrum (LSS) on June 10, 2019 (SOP v6), with a final classification of Moderate. This current curation for the association with *NDUFS3*-related primary mitochondrial disease includes cases with LSS. Evidence supporting this gene-disease relationship includes case-level data and experimental data. This curation included five unique variants (four missense, one intronic variant shown to impact splicing) identified in four unrelated cases from four publications (PMIDs: 14729820, 22499348, 30140060, 33097395). Additional cases are reported in the literature, but did not meet criteria to be included in scoring (PMIDs: 36531773, 19167255). Age of onset is childhood. Clinical features in affected individuals include LSS, encephalomyopathy, developmental delay and regression, ataxia, dystonia, optic atrophy, pancreatitis, respiratory insufficiency, and lactic acidosis. Complex I deficiency is seen in muscle biopsy. The mechanism of disease is loss of function. This gene-disease relationship is also supported by a biochemical function shared with other genes associated with primary mitochondrial disease (PMID: 33340416), functional alteration studies in non-patient cells (PMID: 30796225), and a conditional knockout mouse model (PMID: 33148885) with subsequent studies showing rescue of the phenotype with AAV vector-based gene replacement of NDUFS3 (PMID: 39169163). In summary, there is moderate evidence to support the relationship between *NDUFS3* and autosomal recessive *NDUFS3*-related 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 September 19, 2024 (SOP Version 10).
Inheritance Pattern: AR
Disease ID:MONDO:0009723
Submitter: ClinGen
The relationship between NDUFS3 and Leigh syndrome spectrum was evaluated using the ClinGen Clinical Validity Framework as of March 12, 2019. NDUFS3 was first reported in relation to autosomal recessive Leigh syndrome spectrum in 2004 (Benit et al., PMID 14729820). Several variants have been reported in ClinVar, but mostly with limited evidence of pathogenicity. Evidence supporting this gene-disease relationship includes case-level data and experimental data (PMIDs 14729820, 22200994) to reach a case-level evidence score of 3.5 points. This gene-disease association is further supported by the function of the gene product, complex I alterations in cell lines, expression studies, and animal models reaching an experimental score of 5.5 points. The mechanism for disease is complex I deficiency. In summary, NDUFS3 is moderately associated with autosomal recessive Leigh syndrome spectrum. This classification was approved by the NICHD U24 ClinGen Mitochondrial Disease Gene Curation Expert Panel on June 10, 2019 (SOP Version 6).
Inheritance Pattern: AR
Disease ID:MONDO:0032613
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0100133
Submitter: Orphanet
Clinical Genomic Database (CGD)
Manifestation: Biochemical; Cardiovascular; Gastrointestinal; 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
Comments: Medical treatment (eg, riboflavin, ubiquinol) may be beneficial; Individuals may have cardiac involvement
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to NDUFS3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004551.3. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 30 | 31 | |||
| missense | 4 | 78 | 3 | 85 | ||
| nonsense | 1 | 1 | ||||
| start loss | 2 | 2 | ||||
| frameshift | 3 | 3 | 6 | |||
| splice donor/acceptor (+/-2bp) | 1 | 5 | 6 | |||
| Total | 3 | 7 | 88 | 33 | 0 | 131 |
Highest pathogenic variant AF is 0.00002602008
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004542.1 | 7 | MANE Select | |
| Ensembl | ENSP00000263774.4 | 7 | MANE Select | |
| Ensembl | ENSP00000432099.1 | 5 | Standard | |
| Ensembl | ENSP00000432099.1 | 5 | Standard |
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
- substantia nigra development
- negative regulation of cell growth
- mitochondrial respiratory chain complex I assembly
- reactive oxygen species metabolic process
Molecular Function
- NADH dehydrogenase activity
- protein binding
- NADH dehydrogenase (ubiquinone) activity
- electron transfer activity
Cellular Component
- mitochondrion
- mitochondrial respiratory chain complex I
- mitochondrial matrix
- nuclear body
- mitochondrial membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000263774
- Coding exons
- 7
- Length
- 19227
- Individuals with no LoFs
- 125699
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 49
- Defined
- 125748
- p
- 0.000195
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0153 | 150 | 149 | 1.00 | 0.00000958 | 1698 |
| Missense (PolyPhen) | 54 | 59.832 | 0.90253 | 667 | ||
| Synonymous | -0.767 | 68 | 60.4 | 1.13 | 0.00000345 | 542 |
| Loss of Function | 1.50 | 7 | 12.8 | 0.548 | 5.70e-7 | 154 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.00020 | 0.00020 | rare |
| Ashkenazi Jewish | 0.00030 | 0.00030 | rare |
| East Asian | 0.00023 | 0.00022 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00024 | 0.00024 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0.00049 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) that is believed to belong to the minimal assembly required for 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 (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.367
Intolerance Scores
- LoFtool
- 0.405
- RVIS EVS
- -0.16
- RVIS percentile EVS
- 41.64
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- H
- Indispensability pred.
- E
- Indispensability score
- 0.992
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |