ARHGAP22

Rho GTPase activating protein 22, the group of Pleckstrin homology domain containing|Rho GTPase activating proteins

Basic information

Region (hg38): 10:48446035-48656265

Links

ENSG00000128805 ∙ NCBI:58504 ∙ OMIM:610585 ∙ HGNC:30320 ∙ Uniprot:Q7Z5H3 ∙ 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 ARHGAP22 gene.

• Inborn genetic diseases (38 variants)
• not provided (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGAP22 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				2	1	3
missense			36	6	1	43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	37	8	2

Variants in ARHGAP22

This is a list of pathogenic ClinVar variants found in the ARHGAP22 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-48446401-G-A		not specified	Uncertain significance (Mar 01, 2024)
10-48446419-C-T		not specified	Uncertain significance (Jun 18, 2021)
10-48446502-C-T			Benign (Jun 27, 2018)
10-48446506-C-T		not specified	Uncertain significance (Dec 26, 2023)
10-48446537-T-C		not specified	Uncertain significance (Jul 25, 2023)
10-48446537-T-G		not specified	Uncertain significance (Mar 01, 2024)
10-48446578-C-T		not specified	Likely benign (May 11, 2022)
10-48446579-G-A		not specified	Uncertain significance (Oct 07, 2022)
10-48446599-T-C		not specified	Uncertain significance (Dec 14, 2023)
10-48450277-C-T		not specified	Uncertain significance (Jun 01, 2023)
10-48450295-G-A			Benign (Aug 20, 2018)
10-48450380-G-T		not specified	Uncertain significance (Dec 19, 2022)
10-48450406-C-T		not specified	Likely benign (Apr 26, 2023)
10-48450411-G-T		not specified	Uncertain significance (Nov 03, 2022)
10-48450438-A-G		not specified	Likely benign (May 05, 2022)
10-48450493-C-G		not specified	Uncertain significance (Dec 15, 2023)
10-48450538-C-A		not specified	Uncertain significance (Jan 29, 2024)
10-48450549-C-T		not specified	Uncertain significance (Mar 29, 2022)
10-48450621-C-A		not specified	Uncertain significance (Aug 15, 2023)
10-48450635-C-T			Likely benign (Jun 01, 2022)
10-48450694-G-A		not specified	Uncertain significance (Oct 20, 2023)
10-48450712-G-A		not specified	Uncertain significance (Jan 17, 2023)
10-48450715-G-A		not specified	Uncertain significance (Aug 30, 2021)
10-48450795-C-T		not specified	Uncertain significance (Jun 28, 2022)
10-48450801-T-A		not specified	Uncertain significance (Nov 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGAP22	protein_coding	protein_coding	ENST00000417912	10	210234

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.40e-9	0.926	125687	0	61	125748	0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.597	413	449	0.921	0.0000309	4541
Missense in Polyphen		108	134.82	0.8011		1496
Synonymous	0.474	193	202	0.958	0.0000150	1486
Loss of Function	1.89	18	29.0	0.621	0.00000143	312

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000364	0.000362
Ashkenazi Jewish	0.00	0.00
East Asian	0.000602	0.000598
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000211	0.000202
Middle Eastern	0.000602	0.000598
South Asian	0.000532	0.000523
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Rho GTPase-activating protein involved in the signal transduction pathway that regulates endothelial cell capillary tube formation during angiogenesis. Acts as a GTPase activator for the RAC1 by converting it to an inactive GDP-bound state. Inhibits RAC1-dependent lamellipodia formation. May also play a role in transcription regulation via its interaction with VEZF1, by regulating activity of the endothelin-1 (EDN1) promoter (By similarity). {ECO:0000250}.
• Pathway: Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases (Consensus)

Recessive Scores

• pRec: 0.135

Intolerance Scores

• loftool: 0.731
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.98

Haploinsufficiency Scores

• pHI: 0.122
• hipred: N
• hipred_score: 0.285
• ghis: 0.496

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.925

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arhgap22
• Phenotype: hematopoietic system phenotype; immune system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: angiogenesis;signal transduction;cell differentiation;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction;regulation of postsynapse organization
• Cellular component: nucleus;cytosol;focal adhesion;glutamatergic synapse
• Molecular function: GTPase activator activity;protein binding