IDI2

isopentenyl-diphosphate delta isomerase 2

Basic information

Region (hg38): 10:1018910-1025859

Links

ENSG00000148377 ∙ NCBI:91734 ∙ OMIM:615389 ∙ HGNC:23487 ∙ Uniprot:Q9BXS1 ∙ 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 IDI2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IDI2 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			19	3		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	3	0

Variants in IDI2

This is a list of pathogenic ClinVar variants found in the IDI2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-1019551-G-A		not specified	Uncertain significance (Mar 19, 2024)
10-1019574-C-A		not specified	Uncertain significance (Oct 26, 2021)
10-1019581-C-T		not specified	Uncertain significance (Oct 13, 2023)
10-1019592-C-A		not specified	Uncertain significance (Apr 12, 2022)
10-1019602-A-G		not specified	Uncertain significance (Dec 14, 2021)
10-1019646-C-G		not specified	Uncertain significance (Nov 01, 2022)
10-1019722-G-A		not specified	Uncertain significance (Jan 23, 2023)
10-1019791-T-A		not specified	Uncertain significance (Oct 20, 2023)
10-1020774-C-G		not specified	Uncertain significance (Oct 25, 2023)
10-1020801-C-T		not specified	Likely benign (Dec 07, 2023)
10-1020823-C-A		not specified	Uncertain significance (Jun 30, 2023)
10-1020828-A-G		not specified	Uncertain significance (Jun 21, 2023)
10-1020835-C-G		not specified	Uncertain significance (Dec 12, 2023)
10-1022695-C-T		not specified	Likely benign (Oct 04, 2022)
10-1022698-T-C		not specified	Uncertain significance (Dec 09, 2023)
10-1022727-C-T		not specified	Uncertain significance (Dec 15, 2023)
10-1022754-C-T		not specified	Uncertain significance (Oct 26, 2022)
10-1022763-C-T		not specified	Uncertain significance (Jul 28, 2021)
10-1022767-G-A		not specified	Uncertain significance (May 04, 2023)
10-1024614-C-T		not specified	Likely benign (Jun 16, 2023)
10-1024630-C-G		not specified	Uncertain significance (Mar 08, 2024)
10-1024632-A-G		not specified	Uncertain significance (Jul 12, 2023)
10-1024694-G-C		not specified	Uncertain significance (Jun 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IDI2	protein_coding	protein_coding	ENST00000277517	4	6953

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.31e-9	0.0216	125421	2	324	125747	0.00130

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.556	153	135	1.13	0.00000780	1496
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00414	0.00408
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000231	0.000231
European (Non-Finnish)	0.00134	0.00134
Middle Eastern	0.000109	0.000109
South Asian	0.00121	0.00118
Other	0.00164	0.00163

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:17202134}.
• Pathway: Terpenoid backbone biosynthesis - Homo sapiens (human);Metabolism of lipids;<i>trans, trans</i>-farnesyl diphosphate biosynthesis;Squalene and cholesterol biosynthesis;Metabolism;superpathway of cholesterol biosynthesis;Metabolism of steroids;Steroids metabolism;Cholesterol biosynthesis;mevalonate pathway;superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) (Consensus)

Intolerance Scores

• loftool: 0.550
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.22

Haploinsufficiency Scores

• pHI: 0.150
• hipred: N
• hipred_score: 0.123
• ghis: 0.501

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.228

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Idi2

Gene ontology

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