ARHGDIG

Rho GDP dissociation inhibitor gamma

Basic information

Region (hg38): 16:280449-283010

Links

ENSG00000242173 ∙ NCBI:398 ∙ OMIM:602844 ∙ HGNC:680 ∙ Uniprot:Q99819 ∙ 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 ARHGDIG gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGDIG 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					1	1
missense			17	2		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	2	1

Variants in ARHGDIG

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

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

Position	Type	Phenotype	Significance	ClinVar
16-280697-C-G		not specified	Uncertain significance (Dec 09, 2023)
16-280702-G-A		not specified	Uncertain significance (May 26, 2023)
16-281760-A-G		not specified	Uncertain significance (Sep 27, 2021)
16-281777-G-A			Benign (Dec 31, 2019)
16-281787-G-A		not specified	Uncertain significance (Nov 17, 2022)
16-281799-G-A		not specified	Uncertain significance (May 26, 2022)
16-281867-C-A		not specified	Likely benign (Oct 22, 2021)
16-281917-C-T		not specified	Uncertain significance (Jun 12, 2023)
16-282070-C-T		not specified	Uncertain significance (May 20, 2024)
16-282082-C-T		not specified	Uncertain significance (Jan 08, 2024)
16-282093-G-A		not specified	Uncertain significance (Sep 20, 2023)
16-282106-C-G		not specified	Uncertain significance (Feb 07, 2023)
16-282500-C-G		not specified	Uncertain significance (Feb 26, 2024)
16-282519-G-A		not specified	Uncertain significance (Aug 04, 2021)
16-282615-T-C		not specified	Uncertain significance (Dec 16, 2022)
16-282655-C-G		not specified	Likely benign (Aug 09, 2021)
16-282660-A-G		not specified	Uncertain significance (Oct 26, 2022)
16-282663-A-C		not specified	Uncertain significance (Oct 26, 2021)
16-282705-C-T		not specified	Uncertain significance (Jun 02, 2024)
16-282714-G-A		not specified	Uncertain significance (Nov 03, 2023)
16-282732-T-C		not specified	Uncertain significance (Mar 07, 2024)
16-282782-G-A		not specified	Uncertain significance (Aug 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGDIG	protein_coding	protein_coding	ENST00000219409	6	14278

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.922	0.0780	125506	0	4	125510	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00349	128	128	0.999	0.00000826	1405
Missense in Polyphen		34	46.911	0.72477		610
Synonymous	-2.59	87	61.2	1.42	0.00000431	473
Loss of Function	2.65	0	8.15	0.00	3.47e-7	112

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	0.00	0.00
European (Non-Finnish)	0.0000273	0.0000265
Middle Eastern	0.00	0.00
South Asian	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits GDP/GTP exchange reaction of RhoB. Interacts specifically with the GDP- and GTP-bound forms of post- translationally processed Rhob and Rhog proteins, both of which show a growth-regulated expression in mammalian cells. Stimulates the release of the GDP-bound but not the GTP-bound RhoB protein. Also inhibits the GDP/GTP exchange of RhoB but shows less ability to inhibit the dissociation of prebound GTP.
• Pathway: Neurotrophin signaling pathway - Homo sapiens (human);Vasopressin-regulated water reabsorption - Homo sapiens (human);Ectoderm Differentiation;G13 Signaling Pathway;Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases;Regulation of RhoA activity (Consensus)

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.0871
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.91

Haploinsufficiency Scores

• pHI: 0.147
• hipred: Y
• hipred_score: 0.523
• ghis: 0.574

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.850

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arhgdig
• Phenotype: normal phenotype

Gene ontology

• Biological process: blastocyst hatching;negative regulation of cell adhesion;Rho protein signal transduction;regulation of protein localization;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction
• Cellular component: cytosol;plasma membrane;membrane;cytoplasmic vesicle
• Molecular function: Rho GDP-dissociation inhibitor activity;GTPase activator activity;protein binding;Rac GTPase binding