GDI2

GDP dissociation inhibitor 2

Basic information

Region (hg38): 10:5765222-5842132

Links

ENSG00000057608 ∙ NCBI:2665 ∙ OMIM:600767 ∙ HGNC:4227 ∙ Uniprot:P50395 ∙ 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 GDI2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GDI2 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			15	1	1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	15	1	1

Variants in GDI2

This is a list of pathogenic ClinVar variants found in the GDI2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-5766051-A-C		not specified	Uncertain significance (Jun 16, 2023)
10-5766082-T-A		not specified	Uncertain significance (Feb 17, 2022)
10-5766139-C-T		not specified	Uncertain significance (Mar 31, 2023)
10-5766140-G-A		not specified	Uncertain significance (Apr 26, 2023)
10-5766530-C-G		not specified	Uncertain significance (Jun 16, 2023)
10-5766630-C-T		not specified	Uncertain significance (Aug 08, 2022)
10-5768224-T-C		not specified	Uncertain significance (May 22, 2023)
10-5768297-T-C			Benign (Aug 15, 2018)
10-5768316-C-G		not specified	Uncertain significance (Sep 30, 2024)
10-5773898-T-C		not specified	Uncertain significance (Mar 31, 2023)
10-5785253-T-C		not specified	Likely benign (Feb 28, 2023)
10-5785868-G-C		not specified	Uncertain significance (Oct 06, 2024)
10-5785942-G-T		not specified	Uncertain significance (Jan 30, 2024)
10-5785966-A-G		not specified	Uncertain significance (Jun 10, 2024)
10-5785976-G-C		not specified	Uncertain significance (Sep 17, 2021)
10-5785996-G-A		not specified	Uncertain significance (Jan 08, 2024)
10-5794941-T-C		not specified	Uncertain significance (Jun 30, 2022)
10-5795001-A-T		not specified	Uncertain significance (Nov 17, 2021)
10-5796803-G-T		not specified	Uncertain significance (Mar 07, 2023)
10-5800591-C-T			Benign (Aug 16, 2018)
10-5800687-T-C		not specified	Uncertain significance (Feb 11, 2022)
10-5813237-T-C		not specified	Uncertain significance (Aug 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GDI2	protein_coding	protein_coding	ENST00000380191	11	76910

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.849	0.151	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.72	171	247	0.692	0.0000126	2933
Missense in Polyphen		18	63.332	0.28422		780
Synonymous	1.70	65	84.9	0.765	0.00000450	817
Loss of Function	3.76	4	23.8	0.168	0.00000121	305

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000678	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates the GDP/GTP exchange reaction of most Rab proteins by inhibiting the dissociation of GDP from them, and the subsequent binding of GTP to them.
• Pathway: Neutrophil degranulation;Signal Transduction;Vesicle-mediated transport;Membrane Trafficking;TCR;Innate Immune System;Immune System;Rho GTPase cycle;Signaling by Rho GTPases;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs (Consensus)

Recessive Scores

• pRec: 0.209

Intolerance Scores

• loftool: 0.0651
• rvis_EVS: -0.12
• rvis_percentile_EVS: 45.13

Haploinsufficiency Scores

• pHI: 0.349
• hipred: Y
• hipred_score: 0.814
• ghis: 0.646

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.992

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gdi2
• Phenotype: hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype

Gene ontology

• Biological process: signal transduction;small GTPase mediated signal transduction;protein transport;neutrophil degranulation;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction
• Cellular component: extracellular region;cytoplasm;Golgi apparatus;cytosol;focal adhesion;membrane;vesicle;secretory granule lumen;azurophil granule lumen;myelin sheath;synapse;extracellular exosome
• Molecular function: RNA binding;Rab GDP-dissociation inhibitor activity;GTPase activator activity;protein binding;small GTPase binding