ARHGAP40

protein-coding

Rho GTPase activating protein 40, the group of Rho GTPase activating proteins

Gene summary

Predicted to enable GTPase activator activity. Predicted to be involved in regulation of actin filament polymerization and regulation of small GTPase mediated signal transduction. Predicted to be located in cytosol. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C20orf95

MANE transcript

NM_001164431.3

Inheritance

—

ClinVar variants

U:109B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.53

Max pathogenic AF

—

Genomic locus

chr20:38,601,809-38,651,035

External References & Databases

Ensembl (ENSG00000124143)

Transcript & Mutation Effects

hg38 • Region Span ~49.2 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 ARHGAP40 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 108

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001164431.3. 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				1 clinvar		1
missense			108 clinvar	4 clinvar		112
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	109	5	0	114

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001164431.3	RefSeq	NP_001157903.2	15	MANE Select
ENST00000373345.9	Ensembl	ENSP00000362442.5	15	MANE Select
ENST00000243967.8	Ensembl	ENSP00000243967.4	14	Standard
ENST00000414158.1	Ensembl	ENSP00000414822.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Signal Transduction
Rho GTPase cycle
Signaling by Rho GTPases

Biological Process

signal transduction
regulation of actin filament polymerization
regulation of actin cytoskeleton organization
positive regulation of GTPase activity
regulation of small GTPase mediated signal transduction

Molecular Function

GTPase activator activity

Cellular Component

cytoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373345
Coding exons: 14
Length: 49102
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.53	258	337	0.765	0.0000182	4023
Missense (PolyPhen)		67	94.718	0.70736		1174
Synonymous	1.51	119	142	0.838	0.00000807	1259
Loss of Function	2.33	15	28.4	0.528	0.00000150	329

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound state. {ECO:0000250}.;

Recessive Scores

pRec: 0.109

Essentials

Essential (CRISPR2): S
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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