ARHGAP25

Rho GTPase activating protein 25, the group of Pleckstrin homology domain containing|Rho GTPase activating proteins

Basic information

Region (hg38): 2:68679600-68826833

Links

ENSG00000163219 ∙ NCBI:9938 ∙ OMIM:610587 ∙ HGNC:28951 ∙ Uniprot:P42331 ∙ 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 ARHGAP25 gene.

• Inborn genetic diseases (19 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGAP25 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					2	2
missense			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	19	0	2

Variants in ARHGAP25

This is a list of pathogenic ClinVar variants found in the ARHGAP25 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-68775259-G-A		not specified	Uncertain significance (Nov 21, 2023)
2-68775272-C-T		not specified	Uncertain significance (Oct 29, 2021)
2-68775388-T-C		not specified	Uncertain significance (Nov 09, 2023)
2-68782248-C-G		not specified	Uncertain significance (Feb 03, 2022)
2-68782272-G-A		not specified	Uncertain significance (Jan 08, 2024)
2-68807288-G-A		not specified	Uncertain significance (Mar 17, 2023)
2-68807350-G-A		not specified	Uncertain significance (Dec 17, 2023)
2-68807464-C-T		not specified	Uncertain significance (Apr 26, 2023)
2-68813279-T-C			Benign (Dec 28, 2017)
2-68813348-C-T		not specified	Uncertain significance (Jun 13, 2023)
2-68813375-G-A		not specified	Uncertain significance (Mar 22, 2023)
2-68813413-G-C		not specified	Uncertain significance (Oct 22, 2021)
2-68816319-A-G		not specified	Uncertain significance (Jul 05, 2023)
2-68816329-G-A		not specified	Uncertain significance (Jun 13, 2022)
2-68819153-T-G		not specified	Uncertain significance (Jan 30, 2024)
2-68819200-C-A		not specified	Uncertain significance (May 25, 2022)
2-68819238-A-T		not specified	Uncertain significance (Dec 21, 2023)
2-68822390-G-A			Benign (Dec 28, 2017)
2-68822406-A-G		not specified	Uncertain significance (Dec 02, 2022)
2-68822554-C-T		not specified	Uncertain significance (Sep 26, 2023)
2-68822597-G-A			Benign (Dec 28, 2017)
2-68822626-A-T		not specified	Uncertain significance (Oct 17, 2023)
2-68822634-C-T		not specified	Uncertain significance (Apr 25, 2022)
2-68822635-G-A		not specified	Uncertain significance (Apr 08, 2022)
2-68822739-A-C		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGAP25	protein_coding	protein_coding	ENST00000409202	11	147233

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.946	0.0536	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.619	334	367	0.909	0.0000211	4287
Missense in Polyphen		80	118.6	0.67454		1444
Synonymous	0.604	133	142	0.936	0.00000857	1203
Loss of Function	4.35	5	31.3	0.160	0.00000160	350

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000182	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000795	0.0000703
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: 0.120

Intolerance Scores

• loftool: 0.657
• rvis_EVS: 0.76
• rvis_percentile_EVS: 86.82

Haploinsufficiency Scores

• pHI: 0.826
• hipred: N
• hipred_score: 0.462
• ghis: 0.467

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.452

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arhgap25
• Phenotype: growth/size/body region phenotype; cellular phenotype; immune system phenotype; pigmentation phenotype; hematopoietic system phenotype; vision/eye phenotype

Gene ontology

• Biological process: phagocytosis, engulfment;actin filament organization;signal transduction;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction;negative regulation of small GTPase mediated signal transduction
• Cellular component: phagocytic cup;cytosol
• Molecular function: GTPase activator activity