ARHGAP12

Rho GTPase activating protein 12, the group of Pleckstrin homology domain containing|Rho GTPase activating proteins

Basic information

Region (hg38): 10:31805398-31928876

Links

ENSG00000165322 ∙ NCBI:94134 ∙ OMIM:610577 ∙ HGNC:16348 ∙ Uniprot:Q8IWW6 ∙ 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 ARHGAP12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGAP12 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			36	2		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	2	1

Variants in ARHGAP12

This is a list of pathogenic ClinVar variants found in the ARHGAP12 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-31807663-G-A		not specified	Uncertain significance (Jan 22, 2024)
10-31807757-T-A		not specified	Uncertain significance (Mar 05, 2024)
10-31807791-C-T		not specified	Uncertain significance (Nov 18, 2022)
10-31807797-T-A		not specified	Uncertain significance (Jun 02, 2024)
10-31807827-A-G		not specified	Uncertain significance (Jun 10, 2024)
10-31808718-T-A		not specified	Uncertain significance (Jan 22, 2024)
10-31808733-C-T		not specified	Uncertain significance (Mar 15, 2024)
10-31809014-T-A		not specified	Uncertain significance (Jul 14, 2021)
10-31810672-C-G		not specified	Uncertain significance (Apr 22, 2024)
10-31810729-T-C		not specified	Uncertain significance (Jun 22, 2024)
10-31812769-A-G		not specified	Uncertain significance (Feb 12, 2024)
10-31814310-T-C		not specified	Uncertain significance (Jun 29, 2023)
10-31817799-T-C		not specified	Uncertain significance (May 13, 2024)
10-31817811-G-A		not specified	Uncertain significance (May 23, 2023)
10-31817841-C-T		not specified	Uncertain significance (Mar 11, 2024)
10-31817843-T-C		not specified	Uncertain significance (Sep 14, 2023)
10-31817876-C-T		not specified	Uncertain significance (Feb 21, 2024)
10-31817877-G-A		not specified	Uncertain significance (Apr 28, 2022)
10-31820479-T-G		not specified	Uncertain significance (Sep 28, 2021)
10-31826362-G-A		not specified	Uncertain significance (Jun 09, 2022)
10-31839318-G-A		not specified	Uncertain significance (Apr 26, 2023)
10-31839319-C-A		not specified	Uncertain significance (Nov 08, 2022)
10-31843552-A-G		not specified	Uncertain significance (Sep 15, 2021)
10-31843579-G-A		not specified	Uncertain significance (Jan 17, 2023)
10-31852528-C-T		not specified	Uncertain significance (Mar 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGAP12	protein_coding	protein_coding	ENST00000344936	18	123378

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.51e-7	1.00	125701	0	47	125748	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	387	449	0.862	0.0000231	5603
Missense in Polyphen		78	131.54	0.59297		1599
Synonymous	0.115	154	156	0.988	0.00000811	1525
Loss of Function	3.77	19	46.8	0.406	0.00000231	577

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000459	0.000452
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000942	0.0000924
European (Non-Finnish)	0.000117	0.000114
Middle Eastern	0.000109	0.000109
South Asian	0.000783	0.000653
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: 0.135

Intolerance Scores

• loftool: 0.667
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.94

Haploinsufficiency Scores

• pHI: 0.592
• hipred: N
• hipred_score: 0.414
• ghis: 0.584

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.121

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arhgap12
• Phenotype: normal phenotype

Gene ontology

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