SOD3
protein-codingsuperoxide dismutase 3, the group of Superoxide dismutases
Gene summary
This gene encodes a member of the superoxide dismutase (SOD) protein family. SODs are antioxidant enzymes that catalyze the conversion of superoxide radicals into hydrogen peroxide and oxygen, which may protect the brain, lungs, and other tissues from oxidative stress. Proteolytic processing of the encoded protein results in the formation of two distinct homotetramers that differ in their ability to interact with the extracellular matrix (ECM). Homotetramers consisting of the intact protein, or type C subunit, exhibit high affinity for heparin and are anchored to the ECM. Homotetramers consisting of a proteolytically cleaved form of the protein, or type A subunit, exhibit low affinity for heparin and do not interact with the ECM. A mutation in this gene may be associated with increased heart disease risk. [provided by RefSeq, Oct 2015]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~10.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SOD3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003102.4. 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 | 2 | 2 | 4 | |||
| missense | 55 | 3 | 2 | 60 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 56 | 5 | 4 | 65 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003093.2 | 1 | MANE Select | |
| Ensembl | ENSP00000371554.3 | 1 | MANE Select | |
| Ensembl | ENSP00000472134.1 | 1 | Standard | |
| Ensembl | ENSP00000550324.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Degradation of Superoxides
- Selenium Micronutrient Network
- Vitamin B12 Metabolism
- Folate Metabolism
- Nuclear Receptors Meta-Pathway
Biological Process
- response to hypoxia
- removal of superoxide radicals
- cellular response to oxidative stress
- positive regulation of catalytic activity
- response to copper ion
Molecular Function
- superoxide dismutase activity
- copper ion binding
- protein binding
- heparin binding
- zinc ion binding
Cellular Component
- extracellular region
- extracellular space
- nucleus
- cytoplasm
- Golgi lumen
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000382120
- Coding exons
- 1
- Length
- 10931
- Individuals with no LoFs
- 119594
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 62
- Defined
- 119656
- p
- 0.000259
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.11 | 101 | 138 | 0.734 | 0.00000928 | 1467 |
| Missense (PolyPhen) | 29 | 45.346 | 0.63953 | 561 | ||
| Synonymous | 1.24 | 60 | 73.6 | 0.815 | 0.00000560 | 517 |
| Loss of Function | 0.350 | 5 | 5.92 | 0.845 | 3.43e-7 | 46 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.0014 | 0.0013 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00012 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000070 | 0.000065 | rare |
| South Asian | 0.00010 | 0.000099 | rare |
| Other | 0.00089 | 0.00084 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Protect the extracellular space from toxic effect of reactive oxygen intermediates by converting superoxide radicals into hydrogen peroxide and oxygen.;
Recessive Scores
- pRec
- 0.106
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0782
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |