ARHGAP21

Rho GTPase activating protein 21, the group of Rho GTPase activating proteins|Pleckstrin homology domain containing|PDZ domain containing

Basic information

Region (hg38): 10:24583608-24723887

Links

ENSG00000107863 ∙ NCBI:57584 ∙ OMIM:609870 ∙ HGNC:23725 ∙ Uniprot:Q5T5U3 ∙ 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 ARHGAP21 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGAP21 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				12	5	17
missense		1	102	9	3	115
nonsense						0
start loss						0
frameshift			1	1		2
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	103	22	9

Variants in ARHGAP21

This is a list of pathogenic ClinVar variants found in the ARHGAP21 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-24584429-ACT-A			Likely benign (Dec 31, 2019)
10-24584440-C-G			Benign (Dec 31, 2019)
10-24584454-A-T			Likely benign (Mar 01, 2023)
10-24584467-G-C		not specified	Uncertain significance (Dec 22, 2023)
10-24584468-G-T		not specified	Uncertain significance (Sep 22, 2023)
10-24584504-C-T			Likely benign (Sep 14, 2018)
10-24584509-T-G		not specified	Uncertain significance (Mar 21, 2023)
10-24584531-G-T		not specified	Uncertain significance (May 18, 2022)
10-24584545-G-A		not specified	Uncertain significance (Mar 01, 2023)
10-24584689-C-T		not specified	Uncertain significance (Aug 22, 2023)
10-24584714-G-A		not specified	Uncertain significance (Jan 25, 2023)
10-24584720-G-A		not specified	Uncertain significance (Sep 26, 2023)
10-24584722-T-C		not specified	Uncertain significance (Aug 04, 2023)
10-24584786-C-A		not specified	Uncertain significance (Nov 21, 2023)
10-24584810-C-T		not specified	Uncertain significance (Oct 17, 2023)
10-24584831-T-C		not specified	Uncertain significance (Apr 16, 2024)
10-24584855-C-T		not specified	Uncertain significance (Mar 24, 2023)
10-24584894-G-T			Likely benign (Mar 29, 2018)
10-24584927-C-G		not specified	Uncertain significance (Feb 05, 2024)
10-24584927-C-T		not specified	Uncertain significance (Aug 03, 2022)
10-24584985-C-A			Likely benign (Apr 10, 2018)
10-24585035-C-T		not specified	Likely benign (Oct 05, 2023)
10-24585075-T-C			Likely benign (Feb 01, 2023)
10-24585091-A-G		not specified	Uncertain significance (Dec 03, 2021)
10-24585103-G-A		not specified	Uncertain significance (Feb 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGAP21	protein_coding	protein_coding	ENST00000396432	25	140060

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	7.20e-7	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.955	969	1.06e+3	0.917	0.0000576	12776
Missense in Polyphen		291	422.96	0.68801		5110
Synonymous	-2.03	447	396	1.13	0.0000227	3865
Loss of Function	7.45	10	83.5	0.120	0.00000495	983

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000937	0.0000908
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000142	0.000139
European (Non-Finnish)	0.000124	0.000114
Middle Eastern	0.00	0.00
South Asian	0.000107	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a GTPase-activating protein (GAP) for RHOA and CDC42. Downstream partner of ARF1 which may control Golgi apparatus structure and function. Also required for CTNNA1 recruitment to adherens junctions. {ECO:0000269|PubMed:15793564, ECO:0000269|PubMed:16184169}.
• Pathway: Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases (Consensus)

Recessive Scores

• pRec: 0.155

Intolerance Scores

• loftool: 0.464
• rvis_EVS: -0.78
• rvis_percentile_EVS: 12.78

Haploinsufficiency Scores

• pHI: 0.342
• hipred: Y
• hipred_score: 0.575
• ghis: 0.561

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.748

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arhgap21
• Phenotype: homeostasis/metabolism phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); immune system phenotype

Gene ontology

• Biological process: Golgi organization;signal transduction;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction;establishment of Golgi localization;maintenance of Golgi location;organelle transport along microtubule
• Cellular component: Golgi membrane;Golgi apparatus;cytosol;plasma membrane;actin cytoskeleton;cell junction;cytoplasmic vesicle membrane
• Molecular function: GTPase activator activity;protein binding