ARHGAP5

Rho GTPase activating protein 5, the group of Rho GTPase activating proteins

Basic information

Region (hg38): 14:32076113-32159728

Previous symbols: [ "GFI2" ]

Links

ENSG00000100852 ∙ NCBI:394 ∙ OMIM:602680 ∙ HGNC:675 ∙ Uniprot:Q13017 ∙ 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 ARHGAP5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGAP5 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					5	5
missense			60	1	1	62
nonsense						0
start loss						0
frameshift		1	3			4
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	63	1	6

Variants in ARHGAP5

This is a list of pathogenic ClinVar variants found in the ARHGAP5 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-32090727-C-T		not specified	Uncertain significance (Aug 16, 2022)
14-32090778-T-G		ARHGAP5-related disorder	Uncertain significance (Jul 27, 2023)
14-32090813-A-T		not specified	Uncertain significance (May 24, 2023)
14-32091147-T-G		not specified	Uncertain significance (Jan 10, 2022)
14-32091157-T-C		not specified	Uncertain significance (Jan 25, 2023)
14-32091178-A-G		not specified	Uncertain significance (Jun 03, 2024)
14-32091184-A-C		not specified	Uncertain significance (Feb 28, 2023)
14-32091310-C-T		not specified	Uncertain significance (Oct 06, 2021)
14-32091349-CAT-C		ARHGAP5-related disorder	Uncertain significance (Apr 03, 2023)
14-32091391-C-T		not specified	Uncertain significance (Oct 25, 2023)
14-32091426-C-T		not specified	Uncertain significance (Nov 07, 2022)
14-32091525-T-C		not specified	Uncertain significance (Dec 26, 2023)
14-32091540-A-G		not specified	Uncertain significance (Jul 09, 2021)
14-32091622-C-G		not specified	Uncertain significance (Nov 14, 2023)
14-32091661-T-C		not specified	Uncertain significance (Dec 15, 2022)
14-32091695-A-G			Benign (Jul 26, 2018)
14-32091742-A-G		not specified	Uncertain significance (Feb 13, 2024)
14-32091771-A-G		not specified	Uncertain significance (Oct 20, 2021)
14-32091784-C-T		not specified	Uncertain significance (Mar 25, 2024)
14-32091923-A-G			Benign (May 18, 2018)
14-32091949-G-T		not specified	Uncertain significance (Mar 23, 2022)
14-32092031-G-A		not specified	Uncertain significance (Jan 23, 2024)
14-32092090-T-C		Pulmonary artery atresia	Pathogenic (-)
14-32092167-CT-C		Martsolf syndrome 1	Uncertain significance (Apr 01, 2022)
14-32092352-A-T		not specified	Uncertain significance (Nov 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGAP5	protein_coding	protein_coding	ENST00000345122	6	83615

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00138	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.21	611	785	0.778	0.0000393	10001
Missense in Polyphen		135	268.13	0.50349		3414
Synonymous	-0.816	289	272	1.06	0.0000135	2780
Loss of Function	5.64	7	50.0	0.140	0.00000251	722

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000244	0.000243
Ashkenazi Jewish	0.0000999	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase-activating protein for Rho family members (PubMed:8537347). {ECO:0000269|PubMed:8537347}.
• Pathway: Focal adhesion - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);Focal Adhesion;Signal Transduction;erk and pi-3 kinase are necessary for collagen binding in corneal epithelia;pkc-catalyzed phosphorylation of inhibitory phosphoprotein of myosin phosphatase;rho cell motility signaling pathway;t cell receptor signaling pathway;rac1 cell motility signaling pathway;Rho GTPase cycle;adp-ribosylation factor;Signaling by Rho GTPases;EGFR1;d4gdi signaling pathway;RAC1 signaling pathway;Regulation of RhoA activity (Consensus)

Recessive Scores

• pRec: 0.164

Intolerance Scores

• loftool: 0.319
• rvis_EVS: -0.55
• rvis_percentile_EVS: 20.02

Haploinsufficiency Scores

• pHI: 0.237
• hipred: Y
• hipred_score: 0.745
• ghis: 0.600

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.932

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arhgap5
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); 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); respiratory system phenotype; immune system phenotype

Gene ontology

• Biological process: cell adhesion;Rho protein signal transduction;mammary gland development;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction
• Cellular component: cytoplasm;endoplasmic reticulum;cytosol;plasma membrane
• Molecular function: GTPase activity;GTPase activator activity;protein binding;GTP binding;SH2 domain binding