ARHGAP4

Rho GTPase activating protein 4, the group of AH/BAR family Rho GTPase activating proteins|F-BAR domain containing

Basic information

Region (hg38): X:153907366-153934999

Links

ENSG00000089820 ∙ NCBI:393 ∙ OMIM:300023 ∙ HGNC:674 ∙ Uniprot:P98171 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability (Limited), mode of inheritance: XL

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ARHGAP4 gene.

• Inborn genetic diseases (47 variants)
• not provided (26 variants)
• not specified (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGAP4 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				8	4	12
missense			47	6		53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	3	5
non coding					3	3
Total	0	0	47	14	7

Variants in ARHGAP4

This is a list of pathogenic ClinVar variants found in the ARHGAP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-153907745-G-A		not specified	Conflicting classifications of pathogenicity (Mar 01, 2023)
X-153907748-G-A			Likely benign (Sep 01, 2023)
X-153907751-T-G		not specified	Uncertain significance (Sep 16, 2021)
X-153907769-G-A			Uncertain significance (Aug 01, 2023)
X-153907802-C-T		not specified	Uncertain significance (May 27, 2022)
X-153907841-G-A		not specified	Uncertain significance (Feb 07, 2023)
X-153907884-A-G		not specified	Uncertain significance (Apr 07, 2022)
X-153907892-C-T		not specified	Uncertain significance (Apr 21, 2022)
X-153907904-C-T		not specified	Uncertain significance (Apr 08, 2022)
X-153907905-G-A		not specified	Uncertain significance (Jan 04, 2024)
X-153907959-C-T		not specified	Uncertain significance (Jan 23, 2024)
X-153907968-G-A		not specified	Benign (Mar 28, 2016)
X-153909117-G-A			Likely benign (Jan 01, 2023)
X-153909144-C-T			Uncertain significance (Apr 01, 2022)
X-153909156-T-G		not specified	Uncertain significance (Jul 25, 2023)
X-153909168-G-C		not specified	Uncertain significance (May 04, 2023)
X-153909461-G-C		not specified	Uncertain significance (Jan 23, 2023)
X-153909492-C-G		not specified	Uncertain significance (Dec 16, 2023)
X-153909513-C-T		not specified	Uncertain significance (Jan 06, 2023)
X-153909533-G-A		not specified	Uncertain significance (Jan 09, 2024)
X-153909539-C-T			Benign (Dec 31, 2019)
X-153909540-G-A			Likely benign (Dec 01, 2023)
X-153909743-G-T			Likely benign (Apr 01, 2023)
X-153909744-G-T		not specified	Uncertain significance (Dec 22, 2023)
X-153909746-G-A			Likely benign (Jun 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGAP4	protein_coding	protein_coding	ENST00000370028	23	27632

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.977	0.0231	125605	4	4	125613	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.687	394	434	0.907	0.0000406	6256
Missense in Polyphen		97	147.08	0.65949		2079
Synonymous	-2.33	231	190	1.22	0.0000176	2057
Loss of Function	4.57	5	33.6	0.149	0.00000238	557

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000365	0.0000365
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000764	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000623	0.0000440
Middle Eastern	0.0000764	0.0000544
South Asian	0.00	0.00
Other	0.000223	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibitory effect on stress fiber organization. May down-regulate Rho-like GTPase in hematopoietic cells.
• Pathway: Signal Transduction;rho cell motility signaling pathway;t cell receptor signaling pathway;rac1 cell motility signaling pathway;Rho GTPase cycle;adp-ribosylation factor;Signaling by Rho GTPases;Regulation of RhoA activity (Consensus)

Recessive Scores

• pRec: 0.233

Intolerance Scores

• loftool: 0.0857
• rvis_EVS: 0.16
• rvis_percentile_EVS: 64.92

Haploinsufficiency Scores

• pHI: 0.127
• hipred: Y
• hipred_score: 0.536
• ghis: 0.537

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.508

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arhgap4

Gene ontology

• Biological process: cytoskeleton organization;Rho protein signal transduction;positive regulation of signal transduction;negative regulation of fibroblast migration;negative regulation of cell migration;negative regulation of axon extension;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction
• Cellular component: cytoplasm;Golgi apparatus;cytosol;microtubule;growth cone
• Molecular function: SH3/SH2 adaptor activity;GTPase activator activity;protein binding;Rac GTPase binding