ARHGAP20

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

Basic information

Region (hg38): 11:110577041-110713189

Links

ENSG00000137727 ∙ NCBI:57569 ∙ OMIM:609568 ∙ HGNC:18357 ∙ Uniprot:Q9P2F6 ∙ 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 ARHGAP20 gene.

• Inborn genetic diseases (48 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGAP20 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			47	1		48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	47	1	0

Variants in ARHGAP20

This is a list of pathogenic ClinVar variants found in the ARHGAP20 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-110579393-T-C		not specified	Uncertain significance (Feb 06, 2024)
11-110579420-G-A		not specified	Uncertain significance (Feb 27, 2023)
11-110579542-A-T		not specified	Uncertain significance (Jun 11, 2021)
11-110579573-G-T		not specified	Uncertain significance (Nov 01, 2022)
11-110579680-T-C		not specified	Uncertain significance (Aug 02, 2023)
11-110579725-G-T		not specified	Uncertain significance (Dec 14, 2021)
11-110579765-C-T		not specified	Uncertain significance (Aug 10, 2021)
11-110579794-T-C		not specified	Uncertain significance (Dec 06, 2021)
11-110579809-T-C		not specified	Uncertain significance (Sep 12, 2023)
11-110579911-C-T		not specified	Likely benign (Feb 06, 2024)
11-110579948-C-T		not specified	Uncertain significance (Oct 25, 2022)
11-110579954-C-A		not specified	Uncertain significance (Jun 06, 2023)
11-110580052-A-C		not specified	Uncertain significance (Dec 27, 2023)
11-110580161-G-A		not specified	Uncertain significance (Aug 22, 2023)
11-110580292-A-T		not specified	Uncertain significance (Jul 25, 2023)
11-110580317-G-A		not specified	Uncertain significance (Dec 15, 2022)
11-110580382-C-A		not specified	Uncertain significance (Jul 15, 2021)
11-110580382-C-T		not specified	Uncertain significance (Jul 21, 2022)
11-110580396-T-C		not specified	Uncertain significance (Jun 29, 2023)
11-110580397-A-G		not specified	Uncertain significance (Jan 04, 2024)
11-110580418-C-T		not specified	Uncertain significance (Jun 11, 2021)
11-110580559-G-C		not specified	Uncertain significance (Oct 26, 2022)
11-110580578-C-T		not specified	Likely benign (Feb 01, 2023)
11-110580667-C-T		not specified	Uncertain significance (Jun 06, 2023)
11-110580821-C-T		not specified	Uncertain significance (Feb 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGAP20	protein_coding	protein_coding	ENST00000260283	15	136147

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0292	0.971	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.14	533	612	0.870	0.0000308	7810
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000419	0.000419
Ashkenazi Jewish	0.000111	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

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

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.752
• rvis_EVS: -0.39
• rvis_percentile_EVS: 27.05

Haploinsufficiency Scores

• pHI: 0.266
• hipred: Y
• hipred_score: 0.571
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.813

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arhgap20

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