IDH1 isocitrate dehydrogenase (NADP(+)) 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: IDH1provided by HGNC
Official Full Name: isocitrate dehydrogenase (NADP(+)) 1provided by HGNC
Primary source: HGNC:HGNC:5382
See related: Ensembl:ENSG00000138413 MIM:147700; AllianceGenome:HGNC:5382
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: IDH; IDP; IDCD; IDPC; PICD; HEL-216; HEL-S-26
Summary: Isocitrate dehydrogenases catalyze the oxidative decarboxylation of isocitrate to 2-oxoglutarate. These enzymes belong to two distinct subclasses, one of which utilizes NAD(+) as the electron acceptor and the other NADP(+). Five isocitrate dehydrogenases have been reported: three NAD(+)-dependent isocitrate dehydrogenases, which localize to the mitochondrial matrix, and two NADP(+)-dependent isocitrate dehydrogenases, one of which is mitochondrial and the other predominantly cytosolic. Each NADP(+)-dependent isozyme is a homodimer. The protein encoded by this gene is the NADP(+)-dependent isocitrate dehydrogenase found in the cytoplasm and peroxisomes. It contains the PTS-1 peroxisomal targeting signal sequence. The presence of this enzyme in peroxisomes suggests roles in the regeneration of NADPH for intraperoxisomal reductions, such as the conversion of 2, 4-dienoyl-CoAs to 3-enoyl-CoAs, as well as in peroxisomal reactions that consume 2-oxoglutarate, namely the alpha-hydroxylation of phytanic acid. The cytoplasmic enzyme serves a significant role in cytoplasmic NADPH production. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Sep 2013]
Expression: Ubiquitous expression in adrenal (RPKM 116.0), liver (RPKM 110.2) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2q34

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (208236227..208255071, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (208716002..208734866, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (209100951..209119795, complement)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Gaining Insight into the Catalytic Mechanism of the R132H IDH1 Mutant: A Synergistic DFT Cluster and Experimental Investigation.
Title: Gaining Insight into the Catalytic Mechanism of the R132H IDH1 Mutant: A Synergistic DFT Cluster and Experimental Investigation.
Differential isocitrate dehydrogenase 1 and isocitrate dehydrogenase 2 mutation-related landscape in intrahepatic cholangiocarcinoma.
Title: Differential isocitrate dehydrogenase 1 and isocitrate dehydrogenase 2 mutation-related landscape in intrahepatic cholangiocarcinoma.
The interplay mechanism between IDH mutation, MGMT-promoter methylation, and PRMT5 activity in the progression of grade 4 astrocytoma: unraveling the complex triad theory.
Title: The interplay mechanism between IDH mutation, MGMT-promoter methylation, and PRMT5 activity in the progression of grade 4 astrocytoma: unraveling the complex triad theory.
IDH1 mutation produces R-2-hydroxyglutarate (R-2HG) and induces mir-182-5p expression to regulate cell cycle and tumor formation in glioma.
Title: IDH1 mutation produces R-2-hydroxyglutarate (R-2HG) and induces mir-182-5p expression to regulate cell cycle and tumor formation in glioma.
Mutant IDH1 inhibition induces dsDNA sensing to activate tumor immunity.
Title: Mutant IDH1 inhibition induces dsDNA sensing to activate tumor immunity.
Demographic bias in misdiagnosis by computational pathology models.
Title: Demographic bias in misdiagnosis by computational pathology models.
Correlation of IDH1 gene expression error in breast tumor biopsy in patients with invasive ductal carcinoma.
Title: Correlation of IDH1 gene expression error in breast tumor biopsy in patients with invasive ductal carcinoma.
IDH1 p.R132C mutation in prostatic carcinoma with psammomatous calcifications: report of two cases.
Title: IDH1 p.R132C mutation in prostatic carcinoma with psammomatous calcifications: report of two cases.
IDH1[R132H] mutation increases radiotherapy efficacy and a 4-gene radiotherapy-related signature of WHO grade 4 gliomas.
Title: IDH1(R132H) mutation increases radiotherapy efficacy and a 4-gene radiotherapy-related signature of WHO grade 4 gliomas.
The Epigenetic Evolution of Glioma Is Determined by the IDH1 Mutation Status and Treatment Regimen.
Title: The Epigenetic Evolution of Glioma Is Determined by the IDH1 Mutation Status and Treatment Regimen.

Submit: New GeneRIF Correction See all GeneRIFs (892)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Glioma susceptibility 1 MedGen: C2750850 OMIM: 137800 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of isocitrate dehydrogenase 1 (NADP+), soluble (IDH1) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells	PubMed
Knockdown of isocitrate dehydrogenase 1 (NADP+), soluble (IDH1) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH41922 (e-PCR)
- UniSTS:3075

SHGC-2545 (e-PCR)
- UniSTS:89113

SHGC-37075 (e-PCR)
- UniSTS:16702

RH47131 (e-PCR)
- UniSTS:36425

G43665 (e-PCR)
- UniSTS:95076

G30308 (e-PCR)
- UniSTS:76179

RH81021 (e-PCR)
- UniSTS:92129

RH68077 (e-PCR)
- UniSTS:51170

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables NAD binding	IEA Inferred from Electronic Annotation more info
enables NADP binding	IEA Inferred from Electronic Annotation more info
enables cadherin binding	HDA more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables isocitrate dehydrogenase (NADP+) activity	IBA Inferred from Biological aspect of Ancestor more info
enables isocitrate dehydrogenase (NADP+) activity	IDA Inferred from Direct Assay more info	PubMed
enables magnesium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in 2-oxoglutarate metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in NADP metabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in female gonad development	IEA Inferred from Electronic Annotation more info
involved_in glutathione metabolic process	IEA Inferred from Electronic Annotation more info
involved_in glyoxylate cycle	IEA Inferred from Electronic Annotation more info
involved_in isocitrate metabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in isocitrate metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of phospholipid biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in regulation of phospholipid catabolic process	IEA Inferred from Electronic Annotation more info
involved_in response to oxidative stress	IEA Inferred from Electronic Annotation more info
involved_in response to steroid hormone	IEA Inferred from Electronic Annotation more info
involved_in tricarboxylic acid cycle	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular region	TAS Traceable Author Statement more info
located_in ficolin-1-rich granule lumen	TAS Traceable Author Statement more info
is_active_in mitochondrion	IBA Inferred from Biological aspect of Ancestor more info
located_in peroxisomal matrix	TAS Traceable Author Statement more info
is_active_in peroxisome	IBA Inferred from Biological aspect of Ancestor more info
located_in peroxisome	IDA Inferred from Direct Assay more info	PubMed
located_in secretory granule lumen	TAS Traceable Author Statement more info
located_in tertiary granule lumen	TAS Traceable Author Statement more info

General protein information

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Preferred Names: isocitrate dehydrogenase [NADP] cytoplasmic

Names: NADP(+)-specific ICDH; NADP-dependent isocitrate dehydrogenase, cytosolic; NADP-dependent isocitrate dehydrogenase, peroxisomal; epididymis luminal protein 216; epididymis secretory protein Li 26; epididymis secretory sperm binding protein; isocitrate dehydrogenase (NADP(+)) 1, cytosolic; isocitrate dehydrogenase 1 (NADP+), soluble; oxalosuccinate decarboxylase

NP_001269315.1

EC 1.1.1.42

NP_001269316.1

EC 1.1.1.42

NP_005887.2

EC 1.1.1.42

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_023319.2 RefSeqGene

Range

15932..34848

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_610

mRNA and Protein(s)

NM_001282386.1 → NP_001269315.1 isocitrate dehydrogenase [NADP] cytoplasmic

See identical proteins and their annotated locations for NP_001269315.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) has an alternate 5' UTR exon, compared to variant 1. Variants 1, 2 and 3 encode the same protein.

Source sequence(s)

BC021046, DA707595, N21575

Consensus CDS

CCDS2381.1

UniProtKB/Swiss-Prot

O75874, Q567U4, Q6FHQ6, Q7Z3V0, Q93090, Q9NTJ9, Q9UKW8

UniProtKB/TrEMBL

A0A024R3Y6, B2R5M8, Q6FI37, V9HWJ2

Related

ENSP00000410513.1, ENST00000446179.5

Conserved Domains (1) summary

PTZ00435
Location:1 → 411

PTZ00435; isocitrate dehydrogenase; Provisional
NM_001282387.1 → NP_001269316.1 isocitrate dehydrogenase [NADP] cytoplasmic

See identical proteins and their annotated locations for NP_001269316.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) has an alternate 5' UTR exon, compared to variant 1. Variants 1, 2 and 3 encode the same protein.

Source sequence(s)

BC012846, DR158630, N21575

Consensus CDS

CCDS2381.1

UniProtKB/Swiss-Prot

O75874, Q567U4, Q6FHQ6, Q7Z3V0, Q93090, Q9NTJ9, Q9UKW8

UniProtKB/TrEMBL

A0A024R3Y6, B2R5M8, Q6FI37, V9HWJ2

Related

ENSP00000390265.1, ENST00000415913.5

Conserved Domains (1) summary

PTZ00435
Location:1 → 411

PTZ00435; isocitrate dehydrogenase; Provisional
NM_005896.4 → NP_005887.2 isocitrate dehydrogenase [NADP] cytoplasmic

See identical proteins and their annotated locations for NP_005887.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) and variants 2 and 3 encode the same protein.

Source sequence(s)

AC016697, BC021046, DA728868

Consensus CDS

CCDS2381.1

UniProtKB/Swiss-Prot

O75874, Q567U4, Q6FHQ6, Q7Z3V0, Q93090, Q9NTJ9, Q9UKW8

UniProtKB/TrEMBL

A0A024R3Y6, B2R5M8, Q6FI37, V9HWJ2

Related

ENSP00000260985.2, ENST00000345146.7

Conserved Domains (1) summary

PTZ00435
Location:1 → 411

PTZ00435; isocitrate dehydrogenase; Provisional