IDI1

gene
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Summary

IDI1 (isopentenyl-diphosphate delta isomerase 1, HGNC:5387) is a protein-coding gene on chromosome 10p15.3, encoding Isopentenyl-diphosphate Delta-isomerase 1 (Q13907). Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP).

IDI1 encodes a peroxisomally-localized enzyme that catalyzes the interconversion of isopentenyl diphosphate (IPP) to its highly electrophilic isomer, dimethylallyl diphosphate (DMAPP), which are the substrates for the successive reaction that results in the synthesis of farnesyl diphosphate and, ultimately, cholesterol. It has been shown in peroxisomal deficiency diseases such as Zellweger syndrome and neonatal adrenoleukodystrophy that there is reduction in IPP isomerase activity.

Source: NCBI Gene 3422 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 48 total
  • MANE Select transcript: NM_004508

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:5387
Approved symbolIDI1
Nameisopentenyl-diphosphate delta isomerase 1
Location10p15.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000067064
Ensembl biotypeprotein_coding
OMIM604055
Entrez3422

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000381344, ENST00000427898, ENST00000429642, ENST00000482091, ENST00000491735, ENST00000695775

RefSeq mRNA: 4 — MANE Select: NM_004508 NM_001317955, NM_001317956, NM_001317957, NM_004508

CCDS: CCDS7056, CCDS91201

Canonical transcript exons

ENST00000381344 — 5 exons

ExonStartEnd
ENSE0000148834610394191041504
ENSE0000350007110433011043393
ENSE0000363818210439991044171
ENSE0000378587610426321042762
ENSE0000396499610488641049119

Expression profiles

Bgee: expression breadth ubiquitous, 295 present calls, max score 99.62.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 43.5164 / max 816.2354, expressed in 1812 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
10787736.39541807
1078784.21631234
1078792.61051369
1078760.170456
1078750.123947

Top tissues by expression

295 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
adrenal tissueUBERON:001830399.62gold quality
amniotic fluidUBERON:000017399.21gold quality
ponsUBERON:000098898.46gold quality
ventricular zoneUBERON:000305398.46gold quality
superior vestibular nucleusUBERON:000722798.34gold quality
ganglionic eminenceUBERON:000402398.30gold quality
endometrium epitheliumUBERON:000481198.30gold quality
embryoUBERON:000092297.97gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451197.88gold quality
pigmented layer of retinaUBERON:000178297.72gold quality
frontal poleUBERON:000279597.71gold quality
medulla oblongataUBERON:000189697.52gold quality
C1 segment of cervical spinal cordUBERON:000646997.50gold quality
spinal cordUBERON:000224097.48gold quality
biceps brachiiUBERON:000150797.45gold quality
lateral nuclear group of thalamusUBERON:000273697.41gold quality
cortical plateUBERON:000534397.36gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450297.26gold quality
inferior vagus X ganglionUBERON:000536397.26gold quality
substantia nigra pars compactaUBERON:000196597.23gold quality
dorsal root ganglionUBERON:000004497.22gold quality
medial globus pallidusUBERON:000247797.16gold quality
cranial nerve IIUBERON:000094197.12gold quality
deltoidUBERON:000147697.12gold quality
hindlimb stylopod muscleUBERON:000425297.09gold quality
olfactory segment of nasal mucosaUBERON:000538697.09gold quality
ventral tegmental areaUBERON:000269197.03gold quality
dorsal plus ventral thalamusUBERON:000189797.00gold quality
gastrocnemiusUBERON:000138896.98gold quality
Brodmann (1909) area 10UBERON:001354196.96gold quality

Single-cell (SCXA)

Detected in 8 experiment(s), a significant marker in 5.

ExperimentMarker?Max mean expression
E-HCAD-25yes3955.17
E-MTAB-10485yes1292.07
E-GEOD-84465yes22.75
E-GEOD-135922yes13.48
E-MTAB-6819no1066.19
E-MTAB-7606no546.71
E-MTAB-3929no409.65
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

76 targeting IDI1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-340-5P100.0072.504437
HSA-MIR-4455100.0065.481587
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-428299.9975.366408
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-1213699.9872.815713
HSA-MIR-499A-5P99.9870.791323
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-806899.9873.852376
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-60799.9773.625593
HSA-MIR-6888-3P99.9765.951170
HSA-MIR-365899.9673.874379
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-314399.9371.963104
HSA-MIR-6835-3P99.9370.492904
HSA-MIR-338-5P99.9272.342951
HSA-MIR-95-5P99.8972.173973
HSA-MIR-221-5P99.8665.451052
HSA-MIR-807399.8665.211118
HSA-MIR-5582-3P99.8672.484221
HSA-MIR-369-3P99.8570.522264
HSA-MIR-5003-3P99.8569.292517
HSA-MIR-3180-5P99.8269.122422
HSA-MIR-4639-5P99.8167.371028
HSA-MIR-451799.7669.191867
HSA-MIR-64699.6867.841645
HSA-MIR-46699.6770.852863
HSA-MIR-7157-5P99.6669.331829

Literature-anchored findings (GeneRIF, showing 4)

  • only one of the two isoforms (IDI1) is highly conserved, ubiquitously expressed and most likely responsible for housekeeping isomerase activity (PMID:14629038)
  • Within the 40-kb region on 10p15.3 subtelomere, which harbours two genes encoding isopentenyl diphosphate isomerase 1 (IDI1) and IDI2, there was found a segmental copy-number gain in a large proportion of sporadic amyotrophic lateral sclerosis patients. (PMID:20955688)
  • The present findings suggest that IDI1 and IDI2 may be associated with the production of cholesterol metabolites in neurons, leading to alpha-synuclein aggregation during the process of Lewy body formation. (PMID:25950736)
  • Canonical pathway analysis, using Ingenuity Pathway Analysis software, revealed that the only genes in the “superpathway of cholesterol biosynthesis” were Idi1 (upregulated) and Hmgcs2 (downregulated). The Idi1 and Hmgcs2 genes have regulatory roles in atrial lipotoxic myopathy associated with atrial enlargement (PMID:30567295)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioidi1ENSDARG00000019976
mus_musculusIdi1ENSMUSG00000058258
rattus_norvegicusIdi1ENSRNOG00000016690
drosophila_melanogasterIdiFBGN0038876
caenorhabditis_elegansWBGENE00019460

Paralogs (1): IDI2 (ENSG00000148377)

Protein

Protein identifiers

Isopentenyl-diphosphate Delta-isomerase 1Q13907 (reviewed: Q13907)

Alternative names: Isopentenyl pyrophosphate isomerase 1

All UniProt accessions (3): Q13907, A0A8Q3WKR8, C9JD53

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP).

Subunit / interactions. Monomer.

Subcellular location. Peroxisome.

Cofactor. Binds 1 Mg(2+) ion per subunit.

Pathway. Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from isopentenyl diphosphate: step 1/1.

Similarity. Belongs to the IPP isomerase type 1 family.

Isoforms (2)

UniProt IDNamesCanonical?
Q13907-11yes
Q13907-22

RefSeq proteins (4): NP_001304884, NP_001304885, NP_001304886, NP_004499* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000086NUDIX_hydrolase_domDomain
IPR011876IsopentenylPP_isomerase_typ1Family
IPR015797NUDIX_hydrolase-like_dom_sfHomologous_superfamily

Pfam: PF00293

Enzyme classification (BRENDA):

  • EC 5.3.3.2 — isopentenyl-diphosphate DELTA-isomerase (BRENDA: 50 organisms, 36 substrates, 92 inhibitors, 76 Km, 23 kcat entries)

Substrate kinetics (BRENDA)

3 substrates with measured Km, best-characterized 3. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
ISOPENTENYL DIPHOSPHATE0.0008–15.372
NADH0.0874–0.09042
DIMETHYLALLYL DIPHOSPHATE0.0171

Catalyzed reactions (Rhea), 1 shown:

  • isopentenyl diphosphate = dimethylallyl diphosphate (RHEA:23284)

UniProt features (47 total): helix 13, strand 11, binding site 8, sequence conflict 5, turn 3, active site 2, chain 1, domain 1, modified residue 1, splice variant 1, short sequence motif 1

Structure

Experimental structures (PDB)

4 structures.

PDBMethodResolution (Å)
2DHOX-RAY DIFFRACTION1.6
2ICJX-RAY DIFFRACTION1.7
2ICKX-RAY DIFFRACTION1.93
2I6KX-RAY DIFFRACTION2

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q13907-F197.140.96

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (2): 86; 148

Ligand- & substrate-binding residues (8): 87; 146; 148; 36; 40; 51; 70; 74

Post-translational modifications (1): 176

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-2426168Activation of gene expression by SREBF (SREBP)
R-HSA-9969896Lanosterol biosynthesis
R-HSA-191273Cholesterol biosynthesis

MSigDB gene sets: 303 (showing top): GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, JI_RESPONSE_TO_FSH_UP, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, PATIL_LIVER_CANCER, PUJANA_CHEK2_PCC_NETWORK, GOBP_PHOSPHOLIPID_BIOSYNTHETIC_PROCESS, SENESE_HDAC1_AND_HDAC2_TARGETS_DN, WEI_MYCN_TARGETS_WITH_E_BOX, SMITH_TERT_TARGETS_DN, GOBP_SMALL_MOLECULE_BIOSYNTHETIC_PROCESS, KOKKINAKIS_METHIONINE_DEPRIVATION_96HR_UP, YU_MYC_TARGETS_UP, UEDA_PERIFERAL_CLOCK, DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_DN

GO Biological Process (10): cholesterol biosynthetic process (GO:0006695), isoprenoid biosynthetic process (GO:0008299), isopentenyl diphosphate biosynthetic process (GO:0009240), response to stilbenoid (GO:0035634), dimethylallyl diphosphate biosynthetic process (GO:0050992), lipid metabolic process (GO:0006629), steroid biosynthetic process (GO:0006694), steroid metabolic process (GO:0008202), cholesterol metabolic process (GO:0008203), sterol biosynthetic process (GO:0016126)

GO Molecular Function (7): magnesium ion binding (GO:0000287), isopentenyl-diphosphate delta-isomerase activity (GO:0004452), manganese ion binding (GO:0030145), metal ion binding (GO:0046872), protein binding (GO:0005515), isomerase activity (GO:0016853), intramolecular oxidoreductase activity (GO:0016860)

GO Cellular Component (3): cytoplasm (GO:0005737), peroxisome (GO:0005777), cytosol (GO:0005829)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Regulation of cholesterol biosynthesis by SREBP (SREBF)1
Cholesterol biosynthesis1
Metabolism of steroids1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
lipid biosynthetic process2
phospholipid biosynthetic process2
sterol metabolic process2
cellular anatomical structure2
cholesterol metabolic process1
sterol biosynthetic process1
secondary alcohol biosynthetic process1
isoprenoid metabolic process1
isoprenoid biosynthetic process1
isopentenyl diphosphate metabolic process1
response to chemical1
dimethylallyl diphosphate metabolic process1
primary metabolic process1
steroid metabolic process1
lipid metabolic process1
secondary alcohol metabolic process1
steroid biosynthetic process1
metal ion binding1
intramolecular oxidoreductase activity, transposing C=C bonds1
transition metal ion binding1
cation binding1
binding1
catalytic activity1
isomerase activity1
intracellular anatomical structure1
microbody1
cytoplasm1

Protein interactions and networks

STRING

1204 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
IDI1MVDP53602843
IDI1SQLEQ14534842
IDI1FDFT1P37268842
IDI1HMGCS1Q01581828
IDI1FDPSP14324825
IDI1MVKQ03426810
IDI1HMGCRP04035809
IDI1GGPS1O95749805
IDI1PMVKQ15126799
IDI1DHCR7Q9UBM7769
IDI1MSMO1Q15800767
IDI1CYP51A1Q16850764
IDI1INSIG1O15503739
IDI1HSD17B7P56937731
IDI1DHCR24Q15392717

IntAct

13 interactions, top by confidence:

ABTypeScore
IDI1VWA8psi-mi:“MI:0915”(physical association)0.400
IDI1psi-mi:“MI:0915”(physical association)0.370
IDI1WT1psi-mi:“MI:0915”(physical association)0.370
HSCBRBP5psi-mi:“MI:0914”(association)0.350
KSR1FBLL1psi-mi:“MI:0914”(association)0.350
LRRK2psi-mi:“MI:0914”(association)0.350
repMYCBP2psi-mi:“MI:0914”(association)0.350
IDI1BLMHpsi-mi:“MI:0914”(association)0.350
FECHPOTEFpsi-mi:“MI:0914”(association)0.350
FN1ESYT2psi-mi:“MI:0914”(association)0.350
IMMP1LNUDT19psi-mi:“MI:2364”(proximity)0.270

BioGRID (46): VWA8 (Affinity Capture-MS), VWA8 (Affinity Capture-MS), IDI1 (Two-hybrid), IDI1 (Proximity Label-MS), IDI1 (Affinity Capture-MS), IDI1 (Affinity Capture-MS), IDI1 (Affinity Capture-MS), IDI1 (Affinity Capture-MS), ZNF655 (Two-hybrid), IDI1 (Affinity Capture-MS), IDI1 (Proximity Label-MS), IDI1 (Affinity Capture-MS), IDI1 (Proximity Label-MS), IDI1 (Proximity Label-MS), IDI1 (Proximity Label-MS)

ESM2 similar proteins: A0A7C9FSB8, A2TLM1, A6H7H7, B8BKI7, B9N1F9, B9SQI7, D2XV59, E0CSI1, F1N9S8, O00178, O08582, O35586, O35760, O48964, O48965, O76031, O81770, P11029, P11497, P58044, P69341, Q0J035, Q13085, Q13907, Q14165, Q1LZ95, Q1LZ96, Q28559, Q2R483, Q38929, Q39471, Q39472, Q39664, Q3UMR5, Q42553, Q4R4W5, Q5NVE1, Q5R8R6, Q5SWU9, Q5U2U0

Diamond homologs: A0A1D8PLI2, A0A7C9FSB8, A1T5G2, A4FK76, A8GDW2, A9AST0, A9MRI5, B1VTW2, B5F9P6, I1RZ92, O35586, O35760, O42641, O48964, O48965, P15496, P58044, Q0RBQ7, Q10132, Q13907, Q1LZ95, Q38929, Q39471, Q39472, Q39664, Q42553, Q4R4W5, Q4WM52, Q5E7U8, Q5NWG5, Q5R8R6, Q5YYB6, Q6A5Z1, Q6D3F5, Q7N0A6, Q82MJ7, Q8BFZ6, Q9BXS1, Q9NH02, Q9X7Q6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

48 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance37
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

719 predictions. Top by Δscore:

VariantEffectΔscore
10:1041504:CCTAA:Cacceptor_loss1.0000
10:1041505:C:CAacceptor_loss1.0000
10:1041505:C:CCacceptor_gain1.0000
10:1041506:T:Gacceptor_loss1.0000
10:1042627:GTTAC:Gdonor_loss1.0000
10:1042628:TTAC:Tdonor_loss1.0000
10:1042629:TA:Tdonor_loss1.0000
10:1042631:C:CAdonor_loss1.0000
10:1042631:CCT:Cdonor_gain1.0000
10:1042759:CAAC:Cacceptor_gain1.0000
10:1042764:T:Gacceptor_loss1.0000
10:1043298:AAC:Adonor_loss1.0000
10:1043299:A:ACdonor_gain1.0000
10:1043299:A:ATdonor_loss1.0000
10:1043300:C:CCdonor_gain1.0000
10:1043300:C:CGdonor_loss1.0000
10:1043389:TAATC:Tacceptor_gain1.0000
10:1043390:AATC:Aacceptor_gain1.0000
10:1043391:ATC:Aacceptor_gain1.0000
10:1043391:ATCC:Aacceptor_loss1.0000
10:1043392:TC:Tacceptor_gain1.0000
10:1043393:CC:Cacceptor_gain1.0000
10:1043393:CCT:Cacceptor_loss1.0000
10:1043394:C:CCacceptor_gain1.0000
10:1043394:CTG:Cacceptor_loss1.0000
10:1043395:T:Cacceptor_loss1.0000
10:1043401:C:CTacceptor_gain1.0000
10:1043402:A:Tacceptor_gain1.0000
10:1042647:T:TAdonor_gain0.9900
10:1042652:G:Cdonor_gain0.9900

AlphaMissense

1878 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
10:1042734:A:CH88Q0.996
10:1042734:A:TH88Q0.996
10:1042736:G:CH88D0.996
10:1043371:A:CS55R0.996
10:1043371:A:TS55R0.996
10:1043373:T:GS55R0.996
10:1043305:A:CF77L0.995
10:1043305:A:TF77L0.995
10:1043307:A:GF77L0.995
10:1043327:C:GR70T0.995
10:1043374:A:CF54L0.995
10:1043374:A:TF54L0.995
10:1043376:A:GF54L0.995
10:1044033:C:AK36N0.995
10:1044033:C:GK36N0.995
10:1042749:A:CN83K0.994
10:1042749:A:TN83K0.994
10:1043314:C:AK74N0.994
10:1043314:C:GK74N0.994
10:1043326:T:AR70S0.994
10:1043326:T:GR70S0.994
10:1043385:G:CH51D0.993
10:1044023:G:CH40D0.993
10:1044024:A:CC39W0.993
10:1042663:A:GL112P0.992
10:1041285:A:GW196R0.991
10:1041285:A:TW196R0.991
10:1041427:T:AE148D0.991
10:1041427:T:GE148D0.991
10:1042737:A:CS87R0.991

dbSNP variants (sampled 300 via entrez): RS1000115722 (10:1049307 C>A,T), RS1000127747 (10:1046000 A>C), RS1000216791 (10:1039848 G>A), RS1000336083 (10:1048078 G>A), RS1000340233 (10:1051424 G>A), RS1000783377 (10:1039409 T>C,G), RS1001465854 (10:1040150 G>A), RS1001552146 (10:1047931 C>T), RS1001669736 (10:1052479 A>G), RS1001673336 (10:1047601 T>C), RS1001743449 (10:1052748 G>A,C), RS1001810412 (10:1052353 T>C), RS1001919698 (10:1047721 G>C), RS1002168730 (10:1050785 A>G), RS1002507679 (10:1056184 A>C)

Disease associations

OMIM: gene MIM:604055 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: enzyme — Lanosterol biosynthesis pathway

Most potent curated ligand interactions (1 total), top 1:

LigandActionAffinityParameter
NE21650Inhibition4.2pIC50

CTD chemical–gene interactions

124 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
perfluorooctane sulfonic aciddecreases expression5
Valproic Acidaffects expression, decreases expression4
Cyclosporineaffects cotreatment, affects expression, decreases expression4
bisphenol Adecreases methylation, increases expression, affects expression, affects methylation, affects cotreatment3
sodium arseniteaffects cotreatment, increases abundance, increases expression, decreases expression3
Cisplatinaffects cotreatment, increases expression, affects expression3
Acetaminophendecreases expression, increases expression2
Benzo(a)pyrenedecreases expression2
Quercetindecreases expression2
Tunicamycindecreases expression2
Aflatoxin B1affects expression, decreases expression, decreases methylation2
beta-Naphthoflavonedecreases expression2
aristolochic acid Idecreases expression, increases expression1
afuresertibincreases expression1
6,7-dimethoxy-2-(pyrrolidin-1-yl)-N-(5-(pyrrolidin-1-yl)pentyl)quinazolin-4-amineincreases expression1
bisphenol Fincreases expression1
TAK-243increases sumoylation1
dicrotophosdecreases expression1
22-hydroxycholesteroldecreases expression1
methyleugenoldecreases expression1
alpha phellandrenedecreases expression1
triphenyl phosphateaffects expression1
2-methyl-4-isothiazolin-3-oneincreases expression1
trichostatin Aaffects expression1
dodecyldimethylamine oxideincreases expression1
o,p’-DDTdecreases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
cobaltous chlorideincreases expression1
perfluorooctanoic acidincreases expression1
manganese chlorideaffects cotreatment, decreases expression, increases abundance1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.