IDI1

isopentenyl-diphosphate delta isomerase 1

Basic information

Region (hg38): 10:1039152-1049119

Links

ENSG00000067064 ∙ NCBI:3422 ∙ OMIM:604055 ∙ HGNC:5387 ∙ Uniprot:Q13907 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IDI1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IDI1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in IDI1

This is a list of pathogenic ClinVar variants found in the IDI1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-1041317-T-G		not specified	Uncertain significance (Oct 06, 2021)
10-1041342-C-T		not specified	Uncertain significance (Dec 03, 2021)
10-1041386-T-G		not specified	Uncertain significance (Nov 29, 2023)
10-1041473-C-A		not specified	Uncertain significance (Sep 15, 2022)
10-1042635-T-A		not specified	Uncertain significance (Aug 02, 2023)
10-1042698-G-A		not specified	Likely benign (Dec 10, 2024)
10-1042707-C-G		not specified	Uncertain significance (Apr 20, 2023)
10-1042741-C-T		not specified	Uncertain significance (May 05, 2022)
10-1044079-C-A		not specified	Uncertain significance (Dec 20, 2021)
10-1044101-C-G		not specified	Uncertain significance (Dec 09, 2023)
10-1048894-G-A		not specified	Uncertain significance (Jul 06, 2021)
10-1048910-C-G		not specified	Uncertain significance (May 30, 2024)
10-1048945-T-C		not specified	Uncertain significance (Jan 23, 2024)
10-1048970-C-T		not specified	Uncertain significance (Nov 30, 2022)
10-1048978-C-G		not specified	Uncertain significance (Jan 27, 2022)
10-1048981-G-C		not specified	Uncertain significance (May 11, 2022)
10-1048991-G-C		not specified	Uncertain significance (Jul 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IDI1	protein_coding	protein_coding	ENST00000381344	5	9263

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000398	0.849	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.640	130	152	0.854	0.00000762	1861
Missense in Polyphen		36	63.196	0.56966		783
Synonymous	-1.29	70	57.6	1.22	0.00000318	516
Loss of Function	1.35	9	14.6	0.617	8.59e-7	159

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000302	0.000279
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000136	0.000123
Middle Eastern	0.00	0.00
South Asian	0.000197	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• 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:8806705}.
• Pathway: Terpenoid backbone biosynthesis - Homo sapiens (human);Simvastatin Action Pathway;Pravastatin Action Pathway;Atorvastatin Action Pathway;Hyper-IgD syndrome;Cholesteryl ester storage disease;Lysosomal Acid Lipase Deficiency (Wolman Disease);Alendronate Action Pathway;Rosuvastatin Action Pathway;Lovastatin Action Pathway;Mevalonic aciduria;Wolman disease;Risedronate Action Pathway;Cerivastatin Action Pathway;Pamidronate Action Pathway;Fluvastatin Action Pathway;Smith-Lemli-Opitz Syndrome (SLOS);Chondrodysplasia Punctata II, X Linked Dominant (CDPX2);CHILD Syndrome;Desmosterolosis;Hypercholesterolemia;Steroid Biosynthesis;Zoledronate Action Pathway;Ibandronate Action Pathway;Target Of Rapamycin (TOR) Signaling;Cholesterol Biosynthesis;Sterol Regulatory Element-Binding Proteins (SREBP) signalling;Activation of gene expression by SREBF (SREBP);Exercise-induced Circadian Regulation;Metabolism of lipids;Regulation of cholesterol biosynthesis by SREBP (SREBF);<i>trans, trans</i>-farnesyl diphosphate biosynthesis;Squalene and cholesterol biosynthesis;Metabolism;superpathway of cholesterol biosynthesis;Metabolism of steroids;Steroids metabolism;Cholesterol biosynthesis;Activation of gene expression by SREBF (SREBP);mevalonate pathway;superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) (Consensus)

Recessive Scores

• pRec: 0.138

Intolerance Scores

• loftool: 0.447
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.42

Haploinsufficiency Scores

• pHI: 0.436
• hipred: N
• hipred_score: 0.235
• ghis: 0.396

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.986

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Idi1

Gene ontology

• Biological process: cholesterol biosynthetic process;isopentenyl diphosphate biosynthetic process;regulation of cholesterol biosynthetic process;dimethylallyl diphosphate biosynthetic process
• Cellular component: peroxisome;cytosol
• Molecular function: isopentenyl-diphosphate delta-isomerase activity;hydrolase activity;metal ion binding