NDUFS5
NADH:ubiquinone oxidoreductase subunit S5, the group of NADH:ubiquinone oxidoreductase supernumerary subunits
Basic information
Region (hg38): 1:39026318-39034636
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NDUFS5 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 | 1 | |||||
| missense | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 8 | 1 | 2 |
Variants in NDUFS5
This is a list of pathogenic ClinVar variants found in the NDUFS5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-39028754-C-T | Benign (Mar 29, 2018) | |||
| 1-39028763-C-G | not specified | Uncertain significance (Jan 20, 2025) | ||
| 1-39028812-G-A | not specified | Uncertain significance (Apr 22, 2024) | ||
| 1-39028866-G-A | not specified | Uncertain significance (Nov 10, 2022) | ||
| 1-39028911-T-C | not specified | Uncertain significance (Nov 30, 2021) | ||
| 1-39028914-G-A | not specified | Likely benign (Feb 28, 2024) | ||
| 1-39028930-G-A | not specified | Uncertain significance (Jul 06, 2021) | ||
| 1-39034392-A-T | not specified | Uncertain significance (Aug 14, 2023) | ||
| 1-39034396-G-A | not specified | Likely benign (Jan 02, 2025) | ||
| 1-39034405-G-T | not specified | Uncertain significance (Apr 25, 2022) | ||
| 1-39034441-A-G | not specified | Uncertain significance (Dec 12, 2024) | ||
| 1-39034447-A-G | not specified | Uncertain significance (Aug 09, 2021) | ||
| 1-39034468-A-C | not specified | Uncertain significance (Oct 19, 2021) | ||
| 1-39034514-G-A | not specified | Benign (Jun 18, 2015) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NDUFS5 | protein_coding | protein_coding | ENST00000372969 | 2 | 8319 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0264 | 0.803 | 125739 | 0 | 8 | 125747 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.0125 | 69 | 69.3 | 0.996 | 0.00000427 | 697 |
| Missense in Polyphen | 13 | 14.903 | 0.87231 | 210 | ||
| Synonymous | 0.952 | 15 | 20.5 | 0.732 | 0.00000101 | 192 |
| Loss of Function | 1.03 | 3 | 5.65 | 0.531 | 3.72e-7 | 54 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000578 | 0.0000578 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000879 | 0.00000879 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000980 | 0.0000980 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- 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)
Recessive Scores
- pRec
- 0.106
Intolerance Scores
- loftool
- 0.573
- rvis_EVS
- -0.14
- rvis_percentile_EVS
- 42.88
Haploinsufficiency Scores
- pHI
- 0.0971
- hipred
- N
- hipred_score
- 0.171
- ghis
- 0.580
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.231
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ndufs5
- Phenotype
Zebrafish Information Network
- Gene name
- ndufs5
- Affected structure
- liver
- Phenotype tag
- abnormal
- Phenotype quality
- quality
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;mitochondrial intermembrane space
- Molecular function
- NADH dehydrogenase (ubiquinone) activity