ARHGAP15

protein-coding

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

Gene summary

RHO GTPases (see ARHA; MIM 165390) regulate diverse biologic processes, and their activity is regulated by RHO GTPase-activating proteins (GAPs), such as ARHGAP15 (Seoh et al., 2003 [PubMed 12650940]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_018460.4

Inheritance

—

ClinVar variants

U:79B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.6

Max pathogenic AF

—

Genomic locus

chr2:143,091,362-143,768,352

External References & Databases

Ensembl (ENSG00000075884)

Transcript & Mutation Effects

hg38 • Region Span ~677.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ARHGAP15 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 72

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018460.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			73 clinvar	2 clinvar		75
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	79	2	0	81

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 31 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018460.4	RefSeq	NP_060930.3	13	MANE Select
ENST00000295095.11	Ensembl	ENSP00000295095.6	13	MANE Select
ENST00000409869.5	Ensembl	ENSP00000386560.1	5	Standard
ENST00000906468.1	Ensembl	ENSP00000576527.1	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ectoderm Differentiation
Signal Transduction
Rho GTPase cycle
Signaling by Rho GTPases

Biological Process

signal transduction
regulation of cell shape
regulation of GTPase activity
positive regulation of GTPase activity
regulation of small GTPase mediated signal transduction

Molecular Function

GTPase activator activity

Cellular Component

cytoplasm
cytosol
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000295095
Coding exons: 13
Length: 676991
Individuals with no LoFs: 125695
Homozygous LoFs: 0
Heterozygous LoFs: 49
Defined: 125744
p: 0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.136	246	252	0.976	0.0000133	3162
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.000059	0.000058	rare
Ashkenazi Jewish	0.00080	0.00079	rare
East Asian	0.00022	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00022	0.00021	rare
South Asian	0.00020	0.00020	rare
Other	0.00018	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.127

Intolerance Scores

LoFtool: 0.794
RVIS EVS: -0.62
RVIS percentile EVS: 17.16

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.504

Gene Damage Prediction

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