ARHGAP1

Rho GTPase activating protein 1, the group of Rho GTPase activating proteins|BCH domain containing

Basic information

Region (hg38): 11:46677080-46700619

Links

ENSG00000175220 ∙ NCBI:392 ∙ OMIM:602732 ∙ HGNC:673 ∙ Uniprot:Q07960 ∙ 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 ARHGAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGAP1 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				3	2	5
missense			21	1	1	23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	4	3

Variants in ARHGAP1

This is a list of pathogenic ClinVar variants found in the ARHGAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-46679056-G-A		not specified	Uncertain significance (Dec 20, 2023)
11-46679098-G-A		not specified	Uncertain significance (Jan 08, 2024)
11-46679165-G-A		not specified	Uncertain significance (Dec 31, 2023)
11-46679207-G-C		not specified	Uncertain significance (Jan 23, 2024)
11-46679215-T-C		not specified	Uncertain significance (Aug 26, 2022)
11-46679391-G-A			Likely benign (May 09, 2018)
11-46679412-C-T		not specified	Uncertain significance (Feb 14, 2023)
11-46679666-G-A		not specified	Uncertain significance (Nov 07, 2022)
11-46679760-G-A			Likely benign (Jun 11, 2018)
11-46680520-G-A			Benign (Jul 02, 2018)
11-46680539-C-T			Likely benign (Jun 01, 2020)
11-46680547-G-T		not specified	Uncertain significance (Nov 27, 2023)
11-46680549-T-A		not specified	Uncertain significance (Feb 13, 2024)
11-46680675-G-T			Benign (Jun 18, 2018)
11-46680679-G-T		not specified	Uncertain significance (May 23, 2023)
11-46680710-C-A		not specified	Uncertain significance (Dec 08, 2023)
11-46680720-C-G		not specified	Uncertain significance (Jun 18, 2021)
11-46680741-G-A			Likely benign (Apr 16, 2018)
11-46681083-T-C		not specified	Uncertain significance (Aug 17, 2021)
11-46681303-G-C		not specified	Uncertain significance (Jul 12, 2023)
11-46682088-T-A		not specified	Uncertain significance (Mar 11, 2022)
11-46682106-C-T		not specified	Uncertain significance (Aug 16, 2021)
11-46688192-C-T		not specified	Uncertain significance (Dec 15, 2022)
11-46688206-G-A		not specified	Uncertain significance (Dec 08, 2023)
11-46688234-T-C		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGAP1	protein_coding	protein_coding	ENST00000311956	12	23536

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.768	0.232	125738	0	9	125747	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.25	207	264	0.783	0.0000157	2896
Missense in Polyphen		61	92.884	0.65673		1045
Synonymous	0.817	102	113	0.902	0.00000727	837
Loss of Function	3.60	4	22.4	0.179	9.52e-7	265

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000618	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase activator for the Rho, Rac and Cdc42 proteins, converting them to the putatively inactive GDP-bound state. Cdc42 seems to be the preferred substrate.
• Pathway: Signal Transduction;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;Regulation of RAC1 activity;Regulation of CDC42 activity (Consensus)

Recessive Scores

• pRec: 0.308

Intolerance Scores

• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.57

Haploinsufficiency Scores

• pHI: 0.382
• hipred: Y
• hipred_score: 0.792
• ghis: 0.632

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.944

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arhgap1
• Phenotype: liver/biliary system phenotype; embryo 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); reproductive system phenotype; 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); renal/urinary system phenotype; skeleton phenotype; homeostasis/metabolism phenotype; immune system phenotype; cellular 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); muscle phenotype

Gene ontology

• Biological process: small GTPase mediated signal transduction;Rho protein signal transduction;positive regulation of signal transduction;endosomal transport;transferrin transport;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction;negative regulation of endocytic recycling
• Cellular component: cytoplasm;cytosol;endosome membrane;perinuclear region of cytoplasm;extracellular exosome;sorting endosome
• Molecular function: SH3/SH2 adaptor activity;GTPase activator activity;protein binding;SH3 domain binding;Rab GTPase binding;cadherin binding