IDH3G

isocitrate dehydrogenase (NAD(+)) 3 non-catalytic subunit gamma, the group of Isocitrate dehydrogenases

Basic information

Region (hg38): X:153785766-153794512

Links

ENSG00000067829 ∙ NCBI:3421 ∙ OMIM:300089 ∙ HGNC:5386 ∙ Uniprot:P51553 ∙ 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 IDH3G gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IDH3G 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				2	1	3
Total	0	0	11	2	1

Variants in IDH3G

This is a list of pathogenic ClinVar variants found in the IDH3G region.

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

Position	Type	Phenotype	Significance	ClinVar
X-153785886-C-T		not specified	Uncertain significance (Jul 31, 2024)
X-153785889-G-A		not specified	Uncertain significance (Jul 27, 2024)
X-153785912-C-T		not specified	Uncertain significance (Feb 27, 2023)
X-153785958-T-C		not specified	Uncertain significance (Mar 27, 2023)
X-153786146-GGGCTACAGGA-G			Likely benign (May 01, 2023)
X-153786194-G-A			Likely benign (Oct 01, 2022)
X-153786389-G-C		not specified	Uncertain significance (May 02, 2024)
X-153786820-A-G		not specified	Uncertain significance (May 17, 2023)
X-153786822-A-C		not specified	Uncertain significance (Jul 27, 2022)
X-153787071-C-T		not specified	Uncertain significance (Sep 19, 2022)
X-153787134-A-G		Spastic tetraplegia	Uncertain significance (Jan 01, 2019)
X-153787885-C-A		not specified	Uncertain significance (Aug 05, 2024)
X-153788090-C-T		not specified	Uncertain significance (Apr 19, 2023)
X-153789735-C-T		not specified	Uncertain significance (Jun 28, 2023)
X-153790211-C-G		not specified	Uncertain significance (Jan 23, 2024)
X-153790253-T-C		not specified	Uncertain significance (Nov 24, 2024)
X-153790844-C-T		not specified	Uncertain significance (Feb 06, 2024)
X-153794101-G-A			Benign (Jun 29, 2018)
X-153794266-G-C		not specified	Uncertain significance (Jul 09, 2024)
X-153794290-C-G		not specified	Uncertain significance (Nov 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IDH3G	protein_coding	protein_coding	ENST00000217901	13	8758

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0852	0.906	125736	3	6	125745	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.19	107	193	0.555	0.0000174	2575
Missense in Polyphen		25	73.186	0.3416		1070
Synonymous	-0.197	90	87.7	1.03	0.00000871	790
Loss of Function	2.29	4	12.9	0.311	8.70e-7	229

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000780	0.0000615
Ashkenazi Jewish	0.000150	0.0000992
East Asian	0.0000798	0.0000544
Finnish	0.000126	0.0000924
European (Non-Finnish)	0.0000372	0.0000264
Middle Eastern	0.0000798	0.0000544
South Asian	0.0000524	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulatory subunit which plays a role in the allosteric regulation of the enzyme catalyzing the decarboxylation of isocitrate (ICT) into alpha-ketoglutarate. The heterodimer composed of the alpha (IDH3A) and beta (IDH3B) subunits and the heterodimer composed of the alpha (IDH3A) and gamma (IDH3G) subunits, have considerable basal activity but the full activity of the heterotetramer (containing two subunits of IDH3A, one of IDH3B and one of IDH3G) requires the assembly and cooperative function of both heterodimers. {ECO:0000269|PubMed:28139779}.
• Pathway: Citrate cycle (TCA cycle) - Homo sapiens (human);Warburg Effect;The oncogenic action of Succinate;The oncogenic action of Fumarate;Pyruvate dehydrogenase deficiency (E3);Pyruvate dehydrogenase deficiency (E2);2-ketoglutarate dehydrogenase complex deficiency;Mitochondrial complex II deficiency;Fumarase deficiency;Congenital lactic acidosis;Citric Acid Cycle;Glutaminolysis and Cancer;The oncogenic action of 2-hydroxyglutarate;The oncogenic action of L-2-hydroxyglutarate in Hydroxygluaricaciduria;The oncogenic action of D-2-hydroxyglutarate in Hydroxygluaricaciduria ;TCA Cycle;Citrate cycle;Citric acid cycle (TCA cycle);Pyruvate metabolism and Citric Acid (TCA) cycle;Metabolism of proteins;The citric acid (TCA) cycle and respiratory electron transport;Metabolism;TCA cycle;TCA cycle;superpathway of conversion of glucose to acetyl CoA and entry into the TCA cycle;Mitochondrial protein import (Consensus)

Recessive Scores

• pRec: 0.283

Intolerance Scores

• loftool: 0.509
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.53

Haploinsufficiency Scores

• pHI: 0.0841
• hipred: Y
• hipred_score: 0.685
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.810

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Idh3g

Gene ontology

• Biological process: carbohydrate metabolic process;tricarboxylic acid cycle;isocitrate metabolic process
• Cellular component: nucleoplasm;nucleolus;mitochondrion;mitochondrial matrix
• Molecular function: magnesium ion binding;isocitrate dehydrogenase (NAD+) activity;ATP binding;NAD binding