ARHGAP40

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

Basic information

Region (hg38): 20:38601809-38651035

Previous symbols: [ "C20orf95" ]

Links

ENSG00000124143 ∙ NCBI:343578 ∙ ∙ HGNC:16226 ∙ Uniprot:Q5TG30 ∙ 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 ARHGAP40 gene.

• Inborn genetic diseases (35 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGAP40 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				1		1
missense			33	2		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	3	0

Variants in ARHGAP40

This is a list of pathogenic ClinVar variants found in the ARHGAP40 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-38601952-C-T		not specified	Uncertain significance (May 31, 2023)
20-38602015-C-T		not specified	Uncertain significance (Nov 01, 2021)
20-38602025-C-T		not specified	Uncertain significance (Apr 16, 2024)
20-38602033-C-G		not specified	Uncertain significance (Sep 10, 2024)
20-38623424-C-T		not specified	Uncertain significance (Nov 09, 2023)
20-38623447-G-A		not specified	Uncertain significance (Sep 26, 2023)
20-38623457-G-A		not specified	Uncertain significance (Sep 13, 2023)
20-38623460-C-T		not specified	Uncertain significance (Dec 14, 2023)
20-38627085-T-C		not specified	Uncertain significance (Feb 28, 2023)
20-38627127-G-A		not specified	Uncertain significance (Apr 08, 2024)
20-38627144-C-T		not specified	Uncertain significance (May 17, 2023)
20-38627145-G-A		not specified	Uncertain significance (Sep 27, 2024)
20-38627171-C-T		not specified	Uncertain significance (Apr 06, 2024)
20-38628947-C-T			Likely benign (Sep 01, 2022)
20-38628951-T-G		not specified	Uncertain significance (Jan 19, 2025)
20-38628967-C-A		not specified	Uncertain significance (Nov 03, 2023)
20-38629540-G-C		not specified	Uncertain significance (Mar 19, 2024)
20-38629547-C-A		not specified	Uncertain significance (Feb 05, 2025)
20-38629613-G-C		not specified	Likely benign (Oct 26, 2021)
20-38629649-C-T		not specified	Uncertain significance (Jan 26, 2025)
20-38634629-G-A		not specified	Likely benign (Jul 05, 2023)
20-38634650-G-A		not specified	Uncertain significance (Feb 27, 2025)
20-38634650-G-T		not specified	Uncertain significance (Sep 03, 2024)
20-38634654-C-T		not specified	Uncertain significance (Nov 14, 2024)
20-38634737-C-T		not specified	Uncertain significance (Apr 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGAP40	protein_coding	protein_coding	ENST00000373345	14	49102

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.15e-7	0.989	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.53	258	337	0.765	0.0000182	4023
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound state. {ECO:0000250}.
• Pathway: Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases (Consensus)

Recessive Scores

• pRec: 0.109

Haploinsufficiency Scores

• pHI: 0.0888

Essentials

• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arhgap40

Gene ontology

• 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
• Cellular component: cytoplasm;cytosol
• Molecular function: GTPase activator activity