SELENOO
protein-codingselenoprotein O, the group of Selenoproteins
Gene summary
This gene encodes a selenoprotein that is localized to the mitochondria. It is the largest mammalian selenoprotein, containing the rare amino acid selenocysteine (Sec). Sec is encoded by the UGA codon, which normally signals translation termination. The 3' UTRs of selenoprotein mRNAs contain a conserved stem-loop structure, designated the Sec insertion sequence (SECIS) element, that is necessary for the recognition of UGA as a Sec codon, rather than as a stop signal. The exact function of this selenoprotein is not known, but it is thought to have redox activity. [provided by RefSeq, Dec 2016]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~16.6 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 SELENOO variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_031454.2. 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 | 1 | 5 | ||
| missense | 196 | 9 | 205 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 6 | 6 | ||||
| Total | 0 | 0 | 204 | 11 | 1 | 216 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_113642.1 | 9 | MANE Select | |
| Ensembl | ENSP00000370288.2 | 9 | MANE Select | |
| Ensembl | ENSP00000811180.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Selenium Micronutrient Network
- Selenium Metabolism and Selenoproteins
Cellular Component
- mitochondrion
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000380903
- Coding exons
- 9
- Length
- 16638
- Individuals with no LoFs
- 124438
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 445
- Defined
- 124884
- p
- 0.00179
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.40 | 436 | 361 | 1.21 | 0.0000261 | 4190 |
| Missense (PolyPhen) | 161 | 139.3 | 1.1557 | 1552 | ||
| Synonymous | -3.60 | 228 | 169 | 1.35 | 0.0000138 | 1408 |
| Loss of Function | -0.882 | 24 | 19.8 | 1.21 | 9.13e-7 | 247 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00086 | 0.00083 | rare |
| Latino/Admixed American | 0.0024 | 0.0024 | notable |
| Ashkenazi Jewish | 0.012 | 0.012 | notable |
| East Asian | 0.0019 | 0.0019 | notable |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.0013 | 0.0013 | notable |
| South Asian | 0.0014 | 0.0013 | notable |
| Other | 0.0018 | 0.0018 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May be a redox-active mitochondrial selenoprotein which interacts with a redox target protein. {ECO:0000269|PubMed:24751718}.;
Intolerance Scores
- RVIS EVS
- -0.64
- RVIS percentile EVS
- 16.76
Essentials
- Essential (gene trap)
- N