ARHGAP28

Rho GTPase activating protein 28, the group of Rho GTPase activating proteins

Basic information

Region (hg38): 18:6729715-6915716

Links

ENSG00000088756 ∙ NCBI:79822 ∙ OMIM:610592 ∙ HGNC:25509 ∙ Uniprot:Q9P2N2 ∙ 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 ARHGAP28 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGAP28 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		2
missense			28	1	1	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	28	4	1

Variants in ARHGAP28

This is a list of pathogenic ClinVar variants found in the ARHGAP28 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-6824816-C-G			Likely benign (Jun 01, 2022)
18-6851055-C-T		not specified	Uncertain significance (Sep 16, 2021)
18-6851070-G-T		not specified	Uncertain significance (Aug 04, 2023)
18-6851091-G-A		not specified	Uncertain significance (Mar 08, 2024)
18-6868203-G-C		not specified	Likely benign (Oct 10, 2023)
18-6868226-C-T		not specified	Uncertain significance (Feb 13, 2023)
18-6870607-A-G		not specified	Uncertain significance (Apr 07, 2022)
18-6870608-A-G		not specified	Uncertain significance (Jun 29, 2023)
18-6870625-G-A		not specified	Uncertain significance (Apr 22, 2024)
18-6870663-G-A		not specified	Uncertain significance (Jun 22, 2023)
18-6873461-C-T		not specified	Uncertain significance (May 27, 2022)
18-6873501-T-G		not specified	Uncertain significance (Oct 03, 2022)
18-6873562-G-C		not specified	Uncertain significance (Jul 12, 2022)
18-6873731-C-G		not specified	Uncertain significance (Feb 22, 2023)
18-6882174-A-G		not specified	Uncertain significance (Dec 28, 2023)
18-6887171-A-G		not specified	Uncertain significance (Jun 24, 2022)
18-6887208-C-T		not specified	Uncertain significance (Dec 20, 2023)
18-6887226-G-C		not specified	Uncertain significance (Aug 04, 2021)
18-6889958-C-A		not specified	Uncertain significance (May 27, 2022)
18-6889996-A-G		not specified	Uncertain significance (Apr 22, 2022)
18-6890013-A-C		not specified	Uncertain significance (Nov 09, 2021)
18-6890030-A-G		not specified	Uncertain significance (Aug 02, 2021)
18-6890050-C-T		not specified	Uncertain significance (May 14, 2024)
18-6890131-C-G		ARHGAP28-related disorder	Likely benign (Jul 14, 2021)
18-6890476-C-T		not specified	Uncertain significance (Dec 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGAP28	protein_coding	protein_coding	ENST00000419673	16	185999

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.63e-9	0.975	125714	0	34	125748	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.785	266	305	0.873	0.0000156	3745
Missense in Polyphen		65	80.092	0.81157		1059
Synonymous	0.219	107	110	0.973	0.00000605	1059
Loss of Function	2.20	19	32.6	0.583	0.00000181	399

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000339	0.000337
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.000176	0.000176
Middle Eastern	0.000109	0.000109
South Asian	0.0000657	0.0000653
Other	0.000165	0.000163

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: 0.113

Intolerance Scores

• loftool: 0.859
• rvis_EVS: -0.35
• rvis_percentile_EVS: 29.49

Haploinsufficiency Scores

• pHI: 0.110
• hipred: N
• hipred_score: 0.422
• ghis: 0.430

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0302

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arhgap28
• Phenotype: normal phenotype

Gene ontology

• Biological process: signal transduction;regulation of actin filament polymerization;regulation of actin cytoskeleton organization;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction;negative regulation of stress fiber assembly;negative regulation of GTP binding
• Cellular component: cytoplasm;cytosol
• Molecular function: GTPase activator activity