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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	3420
Gene name	Isocitrate dehydrogenase (NAD(+)) 3 non-catalytic subunit beta
Gene symbol	IDH3B
Synonyms (NCBI Gene)	RP46
Chromosome	20
Chromosome location	20p13
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

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

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

	KEGG		Reactome
	Citrate cycle (TCA cycle) Metabolic pathways Carbon metabolism 2-Oxocarboxylic acid metabolism Biosynthesis of amino acids		Citric acid cycle (TCA cycle)

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Retinitis pigmentosa 46	Likely pathogenic; Pathogenic	rs767275467, rs1600169350	RCV005023103 RCV000005840

Show/Hide Unknown Diseases (15)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Cervical cancer	Benign	rs57362041	RCV005923220
Cholangiocarcinoma	Benign	rs6107100	RCV005920105
Colon adenocarcinoma	Likely benign	rs748350969	RCV005928321
Gastric cancer	Benign; Likely benign	rs75395630, rs375766433	RCV005924670 RCV005933279
IDH3B-related disorder	Conflicting classifications of pathogenicity; Likely benign	rs191680997, rs556473702, rs375766433, rs202127751, rs113021673	RCV003935056 RCV003927594 RCV003937257 RCV003932348 RCV003908065
Lung cancer	Benign	rs75395630	RCV005924672
Malignant lymphoma, large B-cell, diffuse	Benign	rs75395630, rs6107100	RCV005924669 RCV005920103
Optic atrophy	Uncertain significance	rs761437016	RCV004816587
Ovarian serous cystadenocarcinoma	Benign	rs57362041	RCV005923221
Retinal dystrophy	Uncertain significance; Conflicting classifications of pathogenicity	rs370105557, rs757627319, rs374613588, rs761550849, rs2514750893, rs762623115, rs2514750966, rs377682152, rs2514758137, rs2514758349, rs781157150, rs202127751, rs761437016, rs532273295	RCV004815387 RCV004815394 RCV003888924 RCV003888898 RCV003890394 RCV003890395 RCV003890396 RCV003890397 RCV003890398 RCV003890400 RCV004816584 RCV004816585 RCV004816586 RCV004813790
Retinitis pigmentosa	Conflicting classifications of pathogenicity; Benign; Likely benign; Uncertain significance	rs191680997, rs8296, rs376112899, rs886056568, rs886056570, rs143110856, rs139159095, rs886056572, rs886056573, rs140155681, rs75848934, rs886056571, rs202127751, rs778097475, rs760619105 View all (22 more)	RCV000395761 RCV000350400 RCV000347016 RCV000362059 RCV000358185 RCV000260091 RCV000383200 RCV000288605 RCV000304066 RCV000295524 RCV000266890 RCV000263764 RCV000318929 RCV000386679 RCV000292272 RCV000343632 RCV000307368 RCV000303339 RCV000373525 RCV000334005 RCV000397694 RCV000310665 RCV000347329 RCV001137365 RCV001138024 RCV001138025 RCV001138026 RCV001141015 RCV001141016 RCV001142861 RCV001138118 RCV001138119 RCV001138441 RCV001141014 RCV001142859 RCV001142860 RCV001138117
Retinitis Pigmentosa, Recessive	Uncertain significance	rs781157150	RCV000401029
Uterine carcinosarcoma	Benign	rs75395630, rs6107100	RCV005924671 RCV005920104
Uterine corpus endometrial carcinoma	Benign	rs57362041, rs75395630	RCV005923222 RCV005924673
Uveal melanoma	Benign	rs6107100	RCV005920102

Show/Hide Text Mining Associations (4)

Disease Name	Relationship Type	References
Associations from Text MiningDisease 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)