ARHGEF25

Rho guanine nucleotide exchange factor 25, the group of Dbl family Rho GEFs

Basic information

Region (hg38): 12:57610180-57617245

Links

ENSG00000240771 ∙ NCBI:115557 ∙ OMIM:610215 ∙ HGNC:30275 ∙ Uniprot:Q86VW2 ∙ 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 ARHGEF25 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGEF25 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			36			36
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	36	0	0

Variants in ARHGEF25

This is a list of pathogenic ClinVar variants found in the ARHGEF25 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-57610261-A-G		not specified	Uncertain significance (May 24, 2024)
12-57610277-G-T		not specified	Uncertain significance (Apr 25, 2023)
12-57610278-G-T		not specified	Uncertain significance (Jun 29, 2023)
12-57610299-T-C		not specified	Uncertain significance (Dec 20, 2023)
12-57610314-G-A		not specified	Uncertain significance (Feb 21, 2024)
12-57610606-G-A		not specified	Uncertain significance (Oct 27, 2021)
12-57610672-G-T		not specified	Uncertain significance (Jan 02, 2024)
12-57612983-G-A		not specified	Uncertain significance (Nov 14, 2023)
12-57612983-G-T		not specified	Uncertain significance (May 29, 2024)
12-57613023-C-G		not specified	Uncertain significance (Apr 18, 2023)
12-57613028-C-G		not specified	Uncertain significance (Jan 17, 2024)
12-57613047-C-A		not specified	Uncertain significance (Dec 09, 2023)
12-57613077-T-C		not specified	Uncertain significance (Dec 01, 2022)
12-57613095-G-A		not specified	Uncertain significance (Apr 23, 2024)
12-57613104-T-C		not specified	Uncertain significance (Mar 12, 2024)
12-57613338-G-A			Likely benign (Aug 01, 2024)
12-57613355-C-T		not specified	Uncertain significance (May 09, 2022)
12-57613357-C-A		not specified	Uncertain significance (Feb 28, 2023)
12-57613705-G-A		not specified	Uncertain significance (Aug 08, 2023)
12-57613749-C-A		not specified	Uncertain significance (Dec 31, 2023)
12-57614038-C-T		not specified	Uncertain significance (Mar 17, 2023)
12-57614118-G-A		not specified	Uncertain significance (Oct 12, 2021)
12-57614324-C-A		Malignant tumor of prostate	Uncertain significance (-)
12-57614546-T-C		not specified	Uncertain significance (Aug 04, 2023)
12-57614558-C-T		not specified	Uncertain significance (Jul 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGEF25	protein_coding	protein_coding	ENST00000333972	16	9200

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.95e-10	0.977	125678	0	70	125748	0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.933	302	351	0.860	0.0000189	3957
Missense in Polyphen		117	151.33	0.77314		1699
Synonymous	0.370	132	138	0.960	0.00000727	1261
Loss of Function	2.26	21	35.5	0.591	0.00000182	396

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000915	0.000789
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.000598	0.000489
Finnish	0.00	0.00
European (Non-Finnish)	0.000261	0.000255
Middle Eastern	0.000598	0.000489
South Asian	0.000425	0.000425
Other	0.000351	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in actin cytoskeleton reorganization in different tissues since its activation induces formation of actin stress fibers. It works as a guanine nucleotide exchange factor for Rho family of small GTPases. Links specifically G alpha q/11- coupled receptors to RHOA activation. May be an important regulator of processes involved in axon and dendrite formation. In neurons seems to be an exchange factor primarily for RAC1. Involved in skeletal myogenesis (By similarity). {ECO:0000250, ECO:0000269|PubMed:11861769, ECO:0000269|PubMed:12547822, ECO:0000269|PubMed:15069594, ECO:0000269|PubMed:15632174, ECO:0000269|PubMed:16314529, ECO:0000269|PubMed:17606614}.
• Pathway: Signaling by GPCR;Signal Transduction;Regulation of RAC1 activity;G alpha (q) signalling events;GPCR downstream signalling;Regulation of CDC42 activity;Regulation of RhoA activity (Consensus)

Intolerance Scores

• rvis_EVS: -0.02
• rvis_percentile_EVS: 52.15

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.538
• ghis: 0.512

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• 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: Arhgef25
• Phenotype: normal phenotype

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;regulation of Rho protein signal transduction
• Cellular component: cytosol;plasma membrane;myofibril;sarcomere
• Molecular function: Rho guanyl-nucleotide exchange factor activity