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

Gene

• 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

SNPs

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

miRNA

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

Gene ontology (GO)

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

Other IDs

• MIM: 604526
• HGNC: 5385
• e!Ensembl: 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

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Retinitis pigmentosa 46	Likely pathogenic; Pathogenic	rs767275467, rs1600169350	RCV005023103 RCV000005840	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Cervical cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
IDH3B-related disorder	Conflicting classifications of pathogenicity; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Optic atrophy	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Ovarian serous cystadenocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Retinal dystrophy	Uncertain significance; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Retinitis pigmentosa	Conflicting classifications of pathogenicity; Benign; Likely benign; Uncertain significance	ClinVar CTD, Disgenet, GWAS catalog, Orphanet CTD, Disgenet, GWAS catalog, Orphanet CTD, Disgenet, GWAS catalog, Orphanet CTD, Disgenet, GWAS catalog, Orphanet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
RETINITIS PIGMENTOSA 1	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Retinitis Pigmentosa, Recessive	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
STOMACH NEOPLASMS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uveal melanoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Bipolar Disorder	Bipolar Disorder	BEFREE	26782057		★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	HPO_DG			★☆☆☆☆ Found in Text Mining only
Conductive hearing loss	Hearing Loss	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital hypoplasia of penis	Congenital Hypoplasia Of Penis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Disorder of eye	Disorder Of Eye	GENOMICS_ENGLAND_DG			★☆☆☆☆ Found in Text Mining only
Glaucoma	Glaucoma	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hereditary Diffuse Gastric Cancer	Gastric Cancer	CTD_human_DG	21364753		★☆☆☆☆ Found in Text Mining only
Hidradenitis Suppurativa	Hidradenitis suppurativa	BEFREE	30325321		★☆☆☆☆ Found in Text Mining only
Hyperinsulinism	Hyperinsulinism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypogonadism	Hypogonadism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Keratoconus	Keratoconus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	CTD_human_DG	21364753		★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	HPO_DG			★☆☆☆☆ Found in Text Mining only
Optic Atrophy	Optic Atrophy	HPO_DG			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Retinal Dystrophies	Retinal Dystrophy	BEFREE	31736247		★☆☆☆☆ Found in Text Mining only
Retinitis Pigmentosa	Retinitis Pigmentosa	LHGDN	18806796		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Retinitis Pigmentosa	Retinitis Pigmentosa	CTD_human_DG	18806796		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Retinitis Pigmentosa	Retinitis pigmentosa	Pubtator	20011630, 40119724	Associate	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Retinitis pigmentosa	Retinitis Pigmentosa	Orphanet			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Retinitis Pigmentosa	Retinitis Pigmentosa	GENOMICS_ENGLAND_DG			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Retinitis Pigmentosa 46	Retinitis Pigmentosa	UNIPROT_DG	18806796		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis Pigmentosa 46	Retinitis Pigmentosa	GENOMICS_ENGLAND_DG	18806796		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis Pigmentosa 46	Retinitis Pigmentosa	CTD_human_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis Pigmentosa 46	Retinitis Pigmentosa	CLINVAR_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Rod-Cone Dystrophy	Rod-cone dystrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Sensorineural Hearing Loss (disorder)	Hearing Loss	HPO_DG			★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach Neoplasms	CTD_human_DG	21364753		★★☆☆☆ Found in Text Mining + Unknown/Other Associations