ARHGAP24

Rho GTPase activating protein 24, the group of Pleckstrin homology domain containing|MicroRNA protein coding host genes|Rho GTPase activating proteins

Basic information

Region (hg38): 4:85475149-86002668

Links

ENSG00000138639 ∙ NCBI:83478 ∙ OMIM:610586 ∙ HGNC:25361 ∙ Uniprot:Q8N264 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• familial idiopathic steroid-resistant nephrotic syndrome (Supportive), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ARHGAP24 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGAP24 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				25	5	30
missense			79	9	4	92
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	2	4	7
non coding			1	23	37	61
Total	0	0	82	57	46

Variants in ARHGAP24

This is a list of pathogenic ClinVar variants found in the ARHGAP24 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-85570281-T-C			Benign (Nov 11, 2018)
4-85570360-CTTTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT-C			Likely benign (May 25, 2021)
4-85570364-CTCTTTCTTTCTTTCTTTCTTTCTTTCTT-C			Benign (Jul 24, 2020)
4-85570364-CTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT-C			Benign (Jun 18, 2020)
4-85570364-CTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT-C			Likely benign (May 22, 2021)
4-85570386-CTTT-C			Benign (Mar 15, 2020)
4-85570431-C-CT			Benign (Dec 24, 2019)
4-85570437-T-C			Likely benign (Jun 07, 2020)
4-85570549-A-G			Uncertain significance (Oct 24, 2023)
4-85570561-C-T		not specified	Uncertain significance (Mar 19, 2024)
4-85570565-G-A			Likely benign (Dec 09, 2023)
4-85570590-C-T			Uncertain significance (Nov 28, 2023)
4-85570591-G-A			Uncertain significance (Nov 13, 2023)
4-85570657-G-A		not specified	Uncertain significance (Jun 11, 2021)
4-85570661-G-A			Uncertain significance (Apr 29, 2019)
4-85570665-G-C			Uncertain significance (Sep 20, 2023)
4-85570705-A-T		not specified	Uncertain significance (Dec 21, 2023)
4-85570706-T-C		ARHGAP24-related disorder	Likely benign (Jan 12, 2023)
4-85570708-A-G		not specified	Conflicting classifications of pathogenicity (Jan 17, 2024)
4-85570719-T-G			Uncertain significance (Aug 10, 2022)
4-85570815-G-A			Benign (Feb 24, 2020)
4-85570865-G-A			Benign (Dec 18, 2019)
4-85570908-A-G			Benign (May 04, 2020)
4-85721665-T-C			Benign (Apr 04, 2020)
4-85721703-G-A			Likely benign (Nov 02, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGAP24	protein_coding	protein_coding	ENST00000395184	9	527557

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.95e-10	0.984	125679	0	69	125748	0.000274

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.153	397	406	0.979	0.0000218	5030
Missense in Polyphen		93	115.43	0.80571		1400
Synonymous	-0.453	156	149	1.05	0.00000812	1355
Loss of Function	2.35	21	36.3	0.579	0.00000236	375

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000329	0.000329
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000272	0.000272
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000396	0.000396
Middle Eastern	0.000272	0.000272
South Asian	0.000229	0.000229
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Rho GTPase-activating protein involved in cell polarity, cell morphology and cytoskeletal organization. Acts as a GTPase activator for the Rac-type GTPase by converting it to an inactive GDP-bound state. Controls actin remodeling by inactivating Rac downstream of Rho leading to suppress leading edge protrusion and promotes cell retraction to achieve cellular polarity. Able to suppress RAC1 and CDC42 activity in vitro. Overexpression induces cell rounding with partial or complete disruption of actin stress fibers and formation of membrane ruffles, lamellipodia, and filopodia. Isoform 2 is a vascular cell-specific GAP involved in modulation of angiogenesis. {ECO:0000269|PubMed:15302923, ECO:0000269|PubMed:15611138, ECO:0000269|PubMed:16862148}.
• Pathway: Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases (Consensus)

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.783
• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.45

Haploinsufficiency Scores

• pHI: 0.393
• hipred: Y
• hipred_score: 0.540
• ghis: 0.518

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.486

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arhgap24
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: angiogenesis;signal transduction;cell differentiation;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction
• Cellular component: cytosol;cytoskeleton;focal adhesion;cell projection
• Molecular function: GTPase activator activity;protein binding