ARHGAP33

Rho GTPase activating protein 33, the group of Rho GTPase activating proteins

Basic information

Region (hg38): 19:35774532-35788822

Previous symbols: [ "SNX26" ]

Links

ENSG00000004777 ∙ NCBI:115703 ∙ OMIM:614902 ∙ HGNC:23085 ∙ Uniprot:O14559 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ARHGAP33 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGAP33 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				3	4	7
missense			105	3		108
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				3		3
non coding						0
Total	0	0	105	6	4

Variants in ARHGAP33

This is a list of pathogenic ClinVar variants found in the ARHGAP33 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-35777684-T-A		not specified	Uncertain significance (Sep 30, 2024)
19-35777732-C-G		not specified	Uncertain significance (Nov 24, 2024)
19-35778304-G-A		not specified	Uncertain significance (Jun 17, 2024)
19-35778307-C-T		not specified	Uncertain significance (Dec 04, 2024)
19-35778343-G-T		not specified	Uncertain significance (May 13, 2024)
19-35778467-C-T		not specified	Uncertain significance (Dec 12, 2024)
19-35778468-G-A		not specified	Uncertain significance (Aug 20, 2024)
19-35778504-G-A		not specified	Uncertain significance (Feb 25, 2025)
19-35778533-A-C		not specified	Uncertain significance (Nov 08, 2024)
19-35778541-C-T			Benign (Apr 10, 2018)
19-35779086-A-G		not specified	Uncertain significance (Dec 16, 2023)
19-35780230-G-A		not specified	Uncertain significance (Aug 15, 2023)
19-35780296-G-A		not specified	Uncertain significance (Jun 26, 2024)
19-35780431-T-C		not specified	Uncertain significance (Aug 21, 2024)
19-35780603-T-C		not specified	Uncertain significance (Oct 27, 2023)
19-35780634-C-A		not specified	Uncertain significance (Oct 14, 2023)
19-35780637-G-T		not specified	Uncertain significance (Jan 17, 2024)
19-35780750-C-T			Likely benign (Dec 04, 2017)
19-35780762-G-A		not specified	Uncertain significance (Mar 27, 2023)
19-35780770-C-T			Likely benign (Sep 01, 2022)
19-35780772-C-G		not specified	Uncertain significance (Nov 15, 2021)
19-35780781-T-G		not specified	Uncertain significance (Mar 11, 2022)
19-35780821-T-C		not specified	Likely benign (Sep 19, 2016)
19-35780929-G-A		not specified	Uncertain significance (Sep 17, 2021)
19-35780935-G-A		not specified	Uncertain significance (Jan 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGAP33	protein_coding	protein_coding	ENST00000314737	21	14291

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0286	0.971	125701	0	46	125747	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.80	576	711	0.810	0.0000468	7016
Missense in Polyphen		171	193.49	0.88375		2036
Synonymous	-0.276	310	304	1.02	0.0000198	2532
Loss of Function	5.03	14	53.9	0.260	0.00000310	529

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000589	0.000565
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000170	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000173	0.000167
Middle Eastern	0.000170	0.000163
South Asian	0.000131	0.000131
Other	0.000497	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in several stages of intracellular trafficking. Could play an important role in the regulation of glucose transport by insulin. May act as a downstream effector of RHOQ/TC10 in the regulation of insulin-stimulated glucose transport (By similarity). {ECO:0000250}.
• Pathway: Insulin Signaling;Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases (Consensus)

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.678
• rvis_EVS: -1.46
• rvis_percentile_EVS: 3.86

Haploinsufficiency Scores

• pHI: 0.402
• hipred: Y
• hipred_score: 0.595
• ghis: 0.671

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arhgap33
• Phenotype: embryo 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); pigmentation phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: small GTPase mediated signal transduction;response to toxic substance;protein transport;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction;regulation of dendritic spine morphogenesis
• Cellular component: cytoplasm;cytosol;plasma membrane;protein-containing complex;dendritic spine
• Molecular function: GTPase activator activity;protein binding;protein kinase binding;phosphatidylinositol binding