ARHGAP17

Rho GTPase activating protein 17, the group of AH/BAR family Rho GTPase activating proteins|N-BAR domain containing

Basic information

Region (hg38): 16:24919389-25015666

Links

ENSG00000140750 ∙ NCBI:55114 ∙ OMIM:608293 ∙ HGNC:18239 ∙ Uniprot:Q68EM7 ∙ 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 ARHGAP17 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGAP17 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			44	2		46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	44	2	0

Variants in ARHGAP17

This is a list of pathogenic ClinVar variants found in the ARHGAP17 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-24920137-G-A		not specified	Uncertain significance (Dec 14, 2023)
16-24920176-C-T		not specified	Likely benign (Jul 20, 2022)
16-24920183-G-A		not specified	Uncertain significance (Aug 10, 2021)
16-24920230-C-T		not specified	Uncertain significance (May 31, 2023)
16-24930909-G-T		not specified	Uncertain significance (Nov 07, 2022)
16-24930915-G-A		not specified	Uncertain significance (Sep 01, 2021)
16-24931008-G-A		not specified	Uncertain significance (Nov 18, 2022)
16-24931024-T-C		not specified	Uncertain significance (May 30, 2023)
16-24931036-G-A		not specified	Uncertain significance (Sep 17, 2021)
16-24931043-G-C		not specified	Uncertain significance (May 05, 2023)
16-24931156-G-A		not specified	Uncertain significance (Jun 21, 2022)
16-24931203-C-T		not specified	Uncertain significance (Aug 28, 2023)
16-24931263-G-A		not specified	Uncertain significance (Oct 03, 2022)
16-24931386-G-A		not specified	Uncertain significance (Apr 12, 2024)
16-24931392-G-T		not specified	Uncertain significance (Jul 05, 2023)
16-24931402-C-T		not specified	Uncertain significance (Dec 17, 2023)
16-24935475-C-T		not specified	Uncertain significance (Jan 23, 2023)
16-24935481-G-A		not specified	Uncertain significance (Jan 04, 2022)
16-24935549-C-G		not specified	Uncertain significance (Feb 16, 2023)
16-24935583-T-C		not specified	Likely benign (Mar 02, 2023)
16-24935628-G-A		not specified	Uncertain significance (Nov 14, 2023)
16-24939388-T-C		not specified	Uncertain significance (Apr 15, 2024)
16-24939389-G-C		not specified	Uncertain significance (Dec 01, 2023)
16-24939434-T-C		not specified	Uncertain significance (Jul 25, 2023)
16-24939446-T-C		not specified	Uncertain significance (Jan 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGAP17	protein_coding	protein_coding	ENST00000289968	20	96282

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0197	0.980	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.57	402	501	0.802	0.0000278	5712
Missense in Polyphen		74	125.91	0.58773		1543
Synonymous	-0.129	204	202	1.01	0.0000127	1776
Loss of Function	4.47	12	44.0	0.273	0.00000230	515

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000295	0.000295
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000107	0.000105
Middle Eastern	0.0000544	0.0000544
South Asian	0.000138	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Rho GTPase-activating protein involved in the maintenance of tight junction by regulating the activity of CDC42, thereby playing a central role in apical polarity of epithelial cells. Specifically acts as a GTPase activator for the CDC42 GTPase by converting it to an inactive GDP-bound state. The complex formed with AMOT acts by regulating the uptake of polarity proteins at tight junctions, possibly by deciding whether tight junction transmembrane proteins are recycled back to the plasma membrane or sent elsewhere. Participates in the Ca(2+)-dependent regulation of exocytosis, possibly by catalyzing GTPase activity of Rho family proteins and by inducing the reorganization of the cortical actin filaments. Acts as a GTPase activator in vitro for RAC1. {ECO:0000269|PubMed:11431473, ECO:0000269|PubMed:16678097}.
• Pathway: Tight junction - Homo sapiens (human);Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases;Regulation of RAC1 activity;Regulation of CDC42 activity (Consensus)

Intolerance Scores

• loftool: 0.527
• rvis_EVS: -1.59
• rvis_percentile_EVS: 3.07

Haploinsufficiency Scores

• pHI: 0.218
• hipred: Y
• hipred_score: 0.792
• ghis: 0.581

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.796

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arhgap17
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: actin filament organization;signal transduction;calcium ion regulated exocytosis;regulation of actin cytoskeleton organization;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction
• Cellular component: nucleus;cytoplasm;cytosol;plasma membrane;bicellular tight junction
• Molecular function: GTPase activator activity;protein binding;SH3 domain binding;Rac GTPase binding