SELENOI
protein-codingselenoprotein I, the group of Selenoproteins
Gene summary
The multi-pass transmembrane protein encoded by this gene belongs to the CDP-alcohol phosphatidyltransferase class-I family. It catalyzes the transfer of phosphoethanolamine from CDP-ethanolamine to diacylglycerol to produce phosphatidylethanolamine, which is involved in the formation and maintenance of vesicular membranes, regulation of lipid metabolism, and protein folding. This protein is a selenoprotein, containing the rare selenocysteine (Sec) amino acid at its active site. 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. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2016]
- EPT1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~87.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0032905
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0700092
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Craniofacial; 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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SELENOI variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_033505.4. 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 | 1 | 7 | 1 | 9 | ||
| missense | 2 | 41 | 3 | 46 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 4 | 0 | 42 | 10 | 1 | 57 |
Highest pathogenic variant AF is 0.0000050425374
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_277040.1 | 10 | MANE Select | |
| Ensembl | ENSP00000260585.7 | 10 | MANE Select | |
| Ensembl | ENSP00000415280.1 | 4 | Standard | |
| Ensembl | ENSP00000391804.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Ether lipid metabolism - Homo sapiens (human)
- Glycerophospholipid metabolism - Homo sapiens (human)
- Phosphonate and phosphinate metabolism - Homo sapiens (human)
- Selenium Micronutrient Network
- Selenium Metabolism and Selenoproteins
Biological Process
- phosphatidylethanolamine biosynthetic process
Molecular Function
- ethanolaminephosphotransferase activity
- phosphotransferase activity, for other substituted phosphate groups
- metal ion binding
Cellular Component
- endoplasmic reticulum membrane
- Golgi apparatus
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000260585
- Coding exons
- 10
- Length
- 87345
- Individuals with no LoFs
- 124629
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 8
- Defined
- 124637
- p
- 0.0000321
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.67 | 131 | 197 | 0.665 | 0.00000938 | 2556 |
| Missense (PolyPhen) | 36 | 79.3 | 0.45397 | 1079 | ||
| Synonymous | -0.0981 | 77 | 75.9 | 1.01 | 0.00000389 | 768 |
| Loss of Function | 3.41 | 4 | 20.8 | 0.193 | 9.68e-7 | 259 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000065 | 0.000065 | rare |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000047 | 0.000046 | rare |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes phosphatidylethanolamine biosynthesis from CDP-ethanolamine. It thereby plays a central role in the formation and maintenance of vesicular membranes. Involved in the formation of phosphatidylethanolamine via 'Kennedy' pathway.;
Intolerance Scores
- RVIS EVS
- -0.21
- RVIS percentile EVS
- 38.58
Essentials
- Essential (gene trap)
- K