ARHGAP11A

Rho GTPase activating protein 11A, the group of Rho GTPase activating proteins

Basic information

Region (hg38): 15:32615143-32639941

Links

ENSG00000198826 ∙ NCBI:9824 ∙ OMIM:610589 ∙ HGNC:15783 ∙ Uniprot:Q6P4F7 ∙ 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 ARHGAP11A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGAP11A 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	5	7
missense			42	4	2	48
nonsense						0
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	1	42	6	7

Variants in ARHGAP11A

This is a list of pathogenic ClinVar variants found in the ARHGAP11A region.

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

Position	Type	Phenotype	Significance	ClinVar
15-32616270-G-T		not specified	Uncertain significance (Jul 12, 2023)
15-32616326-G-A		not specified	Uncertain significance (Dec 28, 2023)
15-32620132-A-C		not specified	Uncertain significance (Mar 18, 2024)
15-32623540-A-T		not specified	Uncertain significance (Nov 10, 2023)
15-32624183-A-G		not specified	Uncertain significance (Mar 07, 2024)
15-32624186-A-G		not specified	Likely benign (Jun 14, 2023)
15-32624202-A-G			Benign (Jun 18, 2018)
15-32624213-C-T		not specified	Likely benign (Nov 22, 2023)
15-32624215-C-G		not specified	Uncertain significance (Jun 11, 2024)
15-32624234-T-A		not specified	Uncertain significance (Dec 09, 2023)
15-32625169-C-T		not specified	Uncertain significance (Oct 03, 2022)
15-32625519-C-A		not specified	Uncertain significance (Dec 07, 2021)
15-32625523-C-T		not specified	Uncertain significance (Oct 29, 2021)
15-32625541-G-T		not specified	Uncertain significance (Dec 14, 2023)
15-32625561-C-T			Likely benign (Oct 31, 2018)
15-32625568-G-A		not specified	Uncertain significance (Jun 21, 2022)
15-32628772-C-A		not specified	Uncertain significance (May 02, 2024)
15-32628797-G-T		-	no classification for the single variant (-)
15-32629621-C-T		not specified	Uncertain significance (Jun 12, 2023)
15-32629634-C-A		not specified	Uncertain significance (Jan 23, 2024)
15-32629642-A-G			Benign (Dec 31, 2019)
15-32629647-G-T		not specified	Uncertain significance (Jan 11, 2023)
15-32629654-G-C			Benign (Oct 17, 2018)
15-32629755-G-A			Benign (Jul 06, 2018)
15-32633000-A-G		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGAP11A	protein_coding	protein_coding	ENST00000361627	12	24806

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.11e-9	0.999	125544	1	203	125748	0.000811

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00549	522	522	0.999	0.0000254	6697
Missense in Polyphen		88	113.02	0.77862		1479
Synonymous	0.270	183	188	0.975	0.00000940	1960
Loss of Function	2.87	21	40.7	0.515	0.00000212	569

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00128	0.00127
Ashkenazi Jewish	0.000110	0.0000992
East Asian	0.000816	0.000816
Finnish	0.00273	0.00268
European (Non-Finnish)	0.000630	0.000624
Middle Eastern	0.000816	0.000816
South Asian	0.000948	0.000948
Other	0.000659	0.000652

dbNSFP

Source: dbNSFP

• Pathway: Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases (Consensus)

Recessive Scores

• pRec: 0.0806

Intolerance Scores

• loftool: 0.426
• rvis_EVS: -0.21
• rvis_percentile_EVS: 37.74

Haploinsufficiency Scores

• pHI: 0.238
• hipred: N
• hipred_score: 0.373
• ghis: 0.601

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.750

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arhgap11a

Gene ontology

• Biological process: signal transduction;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction
• Cellular component: cytosol
• Molecular function: GTPase activator activity