NDUFS3

protein-coding

NADH: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

NM_004551.3

Inheritance

AR

ClinVar variants

P:10U:88B:33

Top phenotype

Mitochondrial complex I deficiency, nuclear type 8; Leigh syndrome

gnomAD constraint

pLI —, LoF o/e 0.55

Max pathogenic AF

—

Genomic locus

chr11:47,565,336-47,584,562

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~19.2 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

mitochondrial complex I deficiency, nuclear type 8STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032613

Submitter: PanelApp Australia

mitochondrial diseaseMODERATE

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).

Leigh syndromeMODERATE

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).

mitochondrial complex I deficiency, nuclear type 8STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032613

Submitter: Labcorp Genetics (formerly Invitae)

mitochondrial complex I deficiencySUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0100133

Submitter: Orphanet

Clinical Genomic Database (CGD)

Mitochondrial complex I deficiency, nuclear type 8; Leigh syndromeAR

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

Refs: 11743516; 14729820; 22499348; 33097395Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NDUFS3 variants in ClinVar

9 Conditions Cataloged
not providedTotal: 114
Inborn genetic diseasesTotal: 33
Leigh syndromeTotal: 18
Mitochondrial complex I deficiency, nuclear type 8Total: 17
Mitochondrial complex I deficiency, nuclear type 1Total: 17
not specifiedTotal: 10
NDUFS3-related disorderTotal: 7
Mitochondrial complex I deficiencyTotal: 3

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
30
clinvar
31
missense
4
clinvar
78
clinvar
3
clinvar
85
nonsense
1
clinvar
1
start loss
2
clinvar
2
frameshift
3
clinvar
3
clinvar
6
splice donor/acceptor (+/-2bp)
1
clinvar
5
clinvar
6
Total3788330131

Highest pathogenic variant AF is 0.00002602008

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 40 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_004551.3RefSeqNP_004542.17MANE Select
ENST00000263774.9EnsemblENSP00000263774.47MANE Select
ENST00000528192.5EnsemblENSP00000432099.15Standard
ENST00000528192.6EnsemblENSP00000432099.15Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.01531501491.000.000009581698
Missense (PolyPhen)5459.8320.90253667
Synonymous-0.7676860.41.130.00000345542
Loss of Function1.50712.80.5485.70e-7154

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American0.000200.00020rare
Ashkenazi Jewish0.000300.00030rare
East Asian0.000230.00022rare
Finnish00.0absent
European (Non-Finnish)0.000240.00024rare
South Asian0.000130.00013rare
Other0.000490.00049rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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