ARHGAP10

Rho GTPase activating protein 10, the group of MicroRNA protein coding host genes|AH/BAR family Rho GTPase activating proteins

Basic information

Region (hg38): 4:147732062-148072776

Links

ENSG00000071205 ∙ NCBI:79658 ∙ OMIM:609746 ∙ HGNC:26099 ∙ Uniprot:A1A4S6 ∙ 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 ARHGAP10 gene.

• Inborn genetic diseases (33 variants)
• not provided (13 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGAP10 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	4	6
missense			33	1		34
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	33	3	4

Variants in ARHGAP10

This is a list of pathogenic ClinVar variants found in the ARHGAP10 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-147732435-A-G		not specified	Uncertain significance (Dec 01, 2022)
4-147822741-C-A		not specified	Uncertain significance (Jan 23, 2023)
4-147822769-A-G		not specified	Uncertain significance (Dec 19, 2022)
4-147822893-C-T			Likely benign (May 01, 2022)
4-147847160-G-A		not specified	Uncertain significance (Oct 04, 2022)
4-147847166-G-A		not specified	Uncertain significance (Mar 07, 2023)
4-147847186-G-T		not specified	Uncertain significance (Feb 16, 2023)
4-147864870-C-T		not specified	Uncertain significance (Dec 04, 2023)
4-147864955-C-T		not specified	Uncertain significance (Apr 05, 2023)
4-147866778-A-G		not specified	Uncertain significance (Apr 19, 2023)
4-147866779-A-G		Epidermolysis bullosa simplex with nail dystrophy	Uncertain significance (-)
4-147875031-G-T		not specified	Uncertain significance (Nov 27, 2023)
4-147875034-T-A			not provided (-)
4-147875047-G-A			Benign (Jan 30, 2018)
4-147875140-C-T			not provided (-)
4-147879258-G-A		not specified	Uncertain significance (Nov 14, 2023)
4-147879280-G-A		not specified	Uncertain significance (Sep 06, 2022)
4-147879334-A-T		not specified	Uncertain significance (Sep 06, 2022)
4-147881844-G-A		not specified	Uncertain significance (Jul 09, 2021)
4-147881876-G-A			Likely benign (May 01, 2022)
4-147881893-T-C		not specified	Uncertain significance (Apr 05, 2023)
4-147906642-G-A		not specified	Uncertain significance (May 25, 2022)
4-147906644-C-T			Likely benign (Nov 01, 2022)
4-147906645-G-A		not specified	Uncertain significance (Oct 12, 2021)
4-147906672-G-A		not specified	Uncertain significance (Apr 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGAP10	protein_coding	protein_coding	ENST00000336498	23	340718

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.31e-17	0.675	125628	0	120	125748	0.000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.194	418	429	0.974	0.0000227	5178
Missense in Polyphen		160	168.75	0.94816		1962
Synonymous	-0.218	164	160	1.02	0.00000915	1433
Loss of Function	1.94	34	48.6	0.700	0.00000263	577

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000941	0.000938
Ashkenazi Jewish	0.00	0.00
East Asian	0.00101	0.000979
Finnish	0.00	0.00
European (Non-Finnish)	0.000576	0.000571
Middle Eastern	0.00101	0.000979
South Asian	0.000396	0.000392
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase activator for the small GTPases RhoA and Cdc42 by converting them to an inactive GDP-bound state. Essential for PTKB2 regulation of cytoskeletal organization via Rho family GTPases. Inhibits PAK2 proteolytic fragment PAK-2p34 kinase activity and changes its localization from the nucleus to the perinuclear region. Stabilizes PAK-2p34 thereby increasing stimulation of cell death (By similarity). {ECO:0000250, ECO:0000269|PubMed:11432776}.
• Pathway: Bacterial invasion of epithelial cells - Homo sapiens (human);Ectoderm Differentiation;Signal Transduction;Regulation of PAK-2p34 activity by PS-GAP/RHG10;Regulation of Apoptosis;Apoptosis;Programmed Cell Death;Rho GTPase cycle;Signaling by Rho GTPases;Arf1 pathway (Consensus)

Recessive Scores

• pRec: 0.123

Intolerance Scores

• loftool: 0.972
• rvis_EVS: 1.09
• rvis_percentile_EVS: 91.91

Haploinsufficiency Scores

• pHI: 0.153
• hipred: Y
• hipred_score: 0.706
• ghis: 0.435

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.680

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arhgap10
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: cytoskeleton organization;signal transduction;negative regulation of apoptotic process;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction
• Cellular component: cytosol;plasma membrane;perinuclear region of cytoplasm
• Molecular function: GTPase activator activity;protein binding