Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs Other IDs Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	3420
Gene name Gene Name - the full gene name approved by the HGNC.	Isocitrate dehydrogenase (NAD(+)) 3 non-catalytic subunit beta
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	IDH3B
Synonyms (NCBI Gene) Gene synonyms aliases	RP46
Chromosome Chromosome number	20
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	20p13
Summary Summary of gene provided in NCBI Entrez Gene.	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

Show/Hide all(5)

SNP ID	Visualize variation	Clinical significance	Consequence
rs137853020	A>G	Pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs191680997	G>A,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance, benign	Intron variant
rs747812567	G>-	Likely-pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs776399707	C>T	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, coding sequence variant, synonymous variant
rs1600169350	T>-	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant

Show/Hide all(9)

miRTarBase ID	miRNA	Experiments	Reference
MIRT043662	hsa-miR-342-3p	CLASH	23622248
MIRT040424	hsa-miR-615-3p	CLASH	23622248
MIRT035766	hsa-miR-103a-2-5p	CLASH	23622248
MIRT717080	hsa-miR-4709-5p	HITS-CLIP	19536157
MIRT717081	hsa-miR-6884-3p	HITS-CLIP	19536157
MIRT717079	hsa-miR-197-3p	HITS-CLIP	19536157
MIRT717080	hsa-miR-4709-5p	HITS-CLIP	19536157
MIRT717081	hsa-miR-6884-3p	HITS-CLIP	19536157
MIRT717079	hsa-miR-197-3p	HITS-CLIP	19536157

Show/Hide all(21)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000287	Function	Magnesium ion binding	IEA
GO:0004449	Function	Isocitrate dehydrogenase (NAD+) activity	TAS	10601238
GO:0005515	Function	Protein binding	IPI	31515270
GO:0005634	Component	Nucleus	HDA	21630459
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IBA
GO:0005739	Component	Mitochondrion	IDA
GO:0005739	Component	Mitochondrion	IEA
GO:0005739	Component	Mitochondrion	NAS	14555658
GO:0005739	Component	Mitochondrion	TAS	10601238
GO:0005759	Component	Mitochondrial matrix	TAS
GO:0006099	Process	Tricarboxylic acid cycle	IBA
GO:0006099	Process	Tricarboxylic acid cycle	IDA	14555658
GO:0006099	Process	Tricarboxylic acid cycle	IEA
GO:0006102	Process	Isocitrate metabolic process	IBA
GO:0006102	Process	Isocitrate metabolic process	TAS	10601238
GO:0009055	Function	Electron transfer activity	TAS	10601238
GO:0016616	Function	Oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	IEA
GO:0045242	Component	Isocitrate dehydrogenase complex (NAD+)	IDA	14555658
GO:0045242	Component	Isocitrate dehydrogenase complex (NAD+)	IPI	14555658
GO:0051287	Function	NAD binding	IEA

MIM	HGNC	e!Ensembl
604526	5385	ENSG00000101365

Protein

UniProt ID

O43837

Protein name

Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial (Isocitric dehydrogenase subunit beta) (NAD(+)-specific ICDH subunit beta)

Protein function

Plays a structural role to facilitate the assembly and ensure the full activity of the enzyme catalyzing the decarboxylation of isocitrate (ICT) into alpha-ketoglutarate. The heterodimer composed of the alpha (IDH3A) and beta (IDH3B) subunits an

PDB

6KDE , 6KDF , 6KDY , 6KE3 , 7CE3 , 8GRB , 8GRD , 8GRU , 8GS5

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00180	Iso_dh	50 → 376	Isocitrate/isopropylmalate dehydrogenase	Domain

Sequence

MAALSGVRWLTRALVSAGNPGAWRGLSTSAAAHAASRSQAEDVRVEGSFPVTMLPGDGVG
PELMHAVKEVFKAAAVPVEFQEHHLSEVQNMASEEKLEQVLSSMKENKVAIIGKIHTPME
YKGELASYDMRLRRKLDLFANVVHVKSLPGYMTRHNNLDLVIIREQTEGEYSSLEHESAR
GVIECLKIVTRAKSQRIAKFAFDYATKKGRGKVTAVHKANIMKLGDGLFLQCCEEVAELY
PKIKFETMIIDNCCMQLVQNPYQFDVLVMPNLYGNIIDNLAAGLVGGAGVVPGESYSAEY
AVFETGARHPFAQAVGRNIANPTAMLLSASNMLRHLNLEYHSSMIADAVKKVIKVGKVRT
RDMGGYSTTTDFIKSVIGHLQTKGS

Sequence length

385

Interactions

View interactions

Show/Hide Causal Diseases (1)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Retinitis Pigmentosa	retinitis pigmentosa 46	rs1600169350	N/A

Show/Hide Unknown Diseases (3)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Breast Cancer	Postmenopausal breast cancer	N/A	N/A	GWAS
Optic Atrophy	optic atrophy	N/A	N/A	ClinVar
retinal dystrophy	Retinal dystrophy	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (4)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Immunoglobulin G4 Related Disease	Associate	31736247
Neoplasm Metastasis	Associate	23217164
Niemann Pick Disease Type C	Associate	23217164
Retinitis Pigmentosa	Associate	20011630, 40119724

IDH3B (isocitrate dehydrogenase (NAD(+)) 3 non-catalytic subunit beta)