ARHGAP15

Rho GTPase activating protein 15, the group of Pleckstrin homology domain containing|Rho GTPase activating proteins

Basic information

Region (hg38): 2:143091361-143768352

Links

ENSG00000075884 ∙ NCBI:55843 ∙ OMIM:610578 ∙ HGNC:21030 ∙ Uniprot:Q53QZ3 ∙ 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 ARHGAP15 gene.

• Inborn genetic diseases (21 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGAP15 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						0
missense			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region				1		1
non coding						0
Total	0	0	22	0	0

Variants in ARHGAP15

This is a list of pathogenic ClinVar variants found in the ARHGAP15 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-143155542-C-T		not specified	Uncertain significance (Nov 18, 2022)
2-143155653-C-A		not specified	Uncertain significance (Oct 12, 2022)
2-143216432-G-A		not specified	Uncertain significance (Feb 15, 2023)
2-143228594-A-G		not specified	Uncertain significance (Nov 18, 2022)
2-143250601-G-A			Uncertain significance (Jan 01, 2023)
2-143435597-G-T			Likely benign (Dec 31, 2019)
2-143435623-A-G		not specified	Uncertain significance (Nov 18, 2022)
2-143435625-T-C		not specified	Uncertain significance (Aug 24, 2022)
2-143435660-G-C		not specified	Uncertain significance (Sep 06, 2022)
2-143436939-A-T		not specified	Uncertain significance (Jan 06, 2023)
2-143436976-A-G		not specified	Uncertain significance (Aug 12, 2022)
2-143487418-G-A		not specified	Uncertain significance (May 03, 2023)
2-143487421-T-C		not specified	Uncertain significance (Jan 26, 2022)
2-143487451-G-A		not specified	Uncertain significance (Dec 26, 2023)
2-143519295-G-A		not specified	Uncertain significance (Dec 27, 2022)
2-143519305-G-A		not specified	Uncertain significance (Apr 07, 2022)
2-143556474-T-C		not specified	Uncertain significance (Dec 17, 2023)
2-143624177-G-A		not specified	Uncertain significance (Apr 13, 2022)
2-143703439-A-G		not specified	Uncertain significance (Aug 02, 2022)
2-143703479-C-T		not specified	Uncertain significance (Dec 19, 2022)
2-143703488-G-A		not specified	Uncertain significance (Dec 06, 2023)
2-143703505-C-T		not specified	Uncertain significance (Mar 22, 2023)
2-143768024-C-T		not specified	Uncertain significance (Aug 12, 2022)
2-143768063-G-A		not specified	Uncertain significance (May 18, 2022)
2-143768098-A-G		not specified	Uncertain significance (Sep 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGAP15	protein_coding	protein_coding	ENST00000295095	13	676991

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.37e-8	0.948	125695	0	49	125744	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.136	246	252	0.976	0.0000133	3162
Missense in Polyphen		73	94.7	0.77085		1169
Synonymous	-0.391	96	91.2	1.05	0.00000517	848
Loss of Function	1.96	17	28.2	0.602	0.00000157	322

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000309	0.000305
Ashkenazi Jewish	0.000798	0.000794
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000216	0.000211
Middle Eastern	0.000218	0.000217
South Asian	0.000197	0.000196
Other	0.000179	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound state. Has activity toward RAC1. Overexpression results in an increase in actin stress fibers and cell contraction. {ECO:0000269|PubMed:12650940}.
• Pathway: Ectoderm Differentiation;Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.794
• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.16

Haploinsufficiency Scores

• pHI: 0.774
• hipred: Y
• hipred_score: 0.715
• ghis: 0.603

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.504

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arhgap15
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

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