IDI2
protein-codingisopentenyl-diphosphate delta isomerase 2
Gene summary
The protein encoded by this gene catalyzes the conversion of isopentenyl diphosphate to dimethylallyl diphosphate, which is a precursor for the synthesis of cholesterol and other isoprenoids. This gene, which is a product of an ancestral gene duplication event, encodes a protein that may be involved in the aggregation of alpha-synuclein in the cerebral cortex of patients with Lewy body disease. In addition, segmental copy number gains in this locus have been associated with sporadic amyotrophic lateral sclerosis. [provided by RefSeq, Jul 2016]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~6.9 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 IDI2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_033261.3. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 39 | 3 | 42 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 40 | 3 | 0 | 43 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_150286.1 | 4 | MANE Select | |
| Ensembl | ENSP00000277517.1 | 4 | MANE Select | |
| Ensembl | ENSP00000625365.1 | 4 | Standard | |
| Ensembl | ENSP00000625365.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Terpenoid backbone biosynthesis - Homo sapiens (human)
- Metabolism of lipids
- <i>trans, trans</i>-farnesyl diphosphate biosynthesis
- Squalene and cholesterol biosynthesis
- Metabolism
Biological Process
- cholesterol biosynthetic process
- isoprenoid biosynthetic process
- isopentenyl diphosphate biosynthetic process
- isopentenyl diphosphate metabolic process
- dimethylallyl diphosphate biosynthetic process
Molecular Function
- isopentenyl-diphosphate delta-isomerase activity
- hydrolase activity
- metal ion binding
Cellular Component
- peroxisome
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000277517
- Coding exons
- 4
- Length
- 6953
- Individuals with no LoFs
- 125421
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 324
- Defined
- 125747
- p
- 0.00130
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.556 | 153 | 135 | 1.13 | 0.00000780 | 1496 |
| Missense (PolyPhen) | 42 | 32.235 | 1.3029 | 424 | ||
| Synonymous | -1.30 | 67 | 54.8 | 1.22 | 0.00000347 | 431 |
| Loss of Function | -1.34 | 11 | 7.14 | 1.54 | 4.55e-7 | 70 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0011 | 0.0010 | notable |
| Latino/Admixed American | 0.0030 | 0.0030 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.00023 | 0.00023 | rare |
| European (Non-Finnish) | 0.0013 | 0.0013 | notable |
| South Asian | 0.0012 | 0.0012 | notable |
| Other | 0.0016 | 0.0016 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP). {ECO:0000269|PubMed:17202134}.;
Intolerance Scores
- LoFtool
- 0.550
- RVIS EVS
- -0.05
- RVIS percentile EVS
- 50.22
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.228
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |