ARHGAP20

protein-coding

Rho GTPase activating protein 20, the group of Rho GTPase activating proteins

Gene summary

The protein encoded by this gene is an activator of RHO-type GTPases, transducing a signal from RAP1 to RHO and impacting neurite outgrowth. [provided by RefSeq, Sep 2016]

MANE transcript

NM_001384657.1

Inheritance

—

ClinVar variants

U:139B:8

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 0.27

Max pathogenic AF

—

Genomic locus

chr11:110,577,042-110,713,189

External References & Databases

Ensembl (ENSG00000137727)

Transcript & Mutation Effects

hg38 • Region Span ~136.1 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 ARHGAP20 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 143

Prostate cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001384657.1. 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			137 clinvar	7 clinvar		144
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	139	8	0	147

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001384657.1	RefSeq	NP_001371586.1	15	MANE Select
ENST00000683387.1	Ensembl	ENSP00000507405.1	15	MANE Select
NM_001258415.2	RefSeq	NP_001245344.1	15	Standard
NM_001258416.2	RefSeq	NP_001245345.1	15	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
positive regulation of GTPase activity
regulation of small GTPase mediated signal transduction

Molecular Function

GTPase activator activity

Cellular Component

cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000260283
Coding exons: 15
Length: 136147
Individuals with no LoFs: 125719
Homozygous LoFs: 0
Heterozygous LoFs: 29
Defined: 125748
p: 0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.14	533	612	0.870	0.0000308	7810
Missense (PolyPhen)		108	180.25	0.59916		2446
Synonymous	-0.100	229	227	1.01	0.0000112	2317
Loss of Function	4.57	12	45.1	0.266	0.00000233	575

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0.00011	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.00012	rare
South Asian	0	0.0	absent
Other	0.00016	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. {ECO:0000250}.;
Disease: DISEASE: Note=A chromosomal aberration involving ARHGAP20 may be a cause of B-cell chronic lymphocytic leukemia (B-CLL) (PubMed:15543602). Translocation t(X;11)(q21;q23) with BRWD3 does not result in fusion transcripts but disrupts both genes (PubMed:15543602). {ECO:0000269|PubMed:15543602}.;

Recessive Scores

pRec: 0.133

Intolerance Scores

LoFtool: 0.752
RVIS EVS: -0.39
RVIS percentile EVS: 27.05

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.813

Gene Damage Prediction

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