ARAP3

ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3, the group of Ankyrin repeat domain containing|Pleckstrin homology domain containing|Sterile alpha motif domain containing|ArfGAPs

Basic information

Region (hg38): 5:141653400-141682230

Previous symbols: [ "CENTD3" ]

Links

ENSG00000120318 ∙ NCBI:64411 ∙ OMIM:606647 ∙ HGNC:24097 ∙ Uniprot:Q8WWN8 ∙ 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 ARAP3 gene.

• Inborn genetic diseases (72 variants)
• not provided (2 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARAP3 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				1		1
missense			72	2		74
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	72	3	0

Variants in ARAP3

This is a list of pathogenic ClinVar variants found in the ARAP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-141654027-G-T		not specified	Uncertain significance (Nov 15, 2021)
5-141654153-G-A		not specified	Uncertain significance (Jul 27, 2021)
5-141654161-G-A		not specified	Uncertain significance (Nov 08, 2022)
5-141654218-A-T		not specified	Uncertain significance (Sep 15, 2021)
5-141654302-G-A		not specified	Uncertain significance (Aug 23, 2021)
5-141654432-T-C		not specified	Uncertain significance (Feb 05, 2024)
5-141655385-G-A		not specified	Uncertain significance (Apr 21, 2022)
5-141655396-C-T		not specified	Likely benign (Aug 10, 2021)
5-141655658-T-C		not specified	Uncertain significance (Jan 09, 2024)
5-141655668-G-A		not specified	Uncertain significance (Sep 29, 2023)
5-141655913-C-T		not specified	Uncertain significance (Nov 12, 2021)
5-141656240-C-A		not specified	Uncertain significance (Jan 19, 2024)
5-141656242-C-T		not specified	Uncertain significance (Dec 14, 2022)
5-141656261-G-A			Uncertain significance (Aug 07, 2018)
5-141656601-C-T		not specified	Uncertain significance (Jan 30, 2024)
5-141656628-C-T		not specified	Uncertain significance (Mar 01, 2024)
5-141656737-T-A		not specified	Uncertain significance (May 27, 2022)
5-141656748-G-T		not specified	Uncertain significance (Sep 16, 2021)
5-141658437-G-T		not specified	Uncertain significance (Mar 01, 2023)
5-141658470-T-C		not specified	Uncertain significance (Jun 22, 2023)
5-141658595-T-C		not specified	Uncertain significance (Oct 17, 2023)
5-141658617-T-C		not specified	Uncertain significance (Oct 10, 2023)
5-141659473-C-T		not specified	Uncertain significance (Mar 16, 2022)
5-141659829-C-T		not specified	Uncertain significance (Jun 23, 2021)
5-141659835-C-T		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARAP3	protein_coding	protein_coding	ENST00000239440	32	28821

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000165	1.00	125675	0	73	125748	0.000290

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.82	769	925	0.832	0.0000578	9859
Missense in Polyphen		285	378.48	0.75301		3975
Synonymous	1.05	340	366	0.930	0.0000207	3292
Loss of Function	5.66	24	77.9	0.308	0.00000423	831

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000835	0.000796
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000326	0.000326
Finnish	0.000417	0.000416
European (Non-Finnish)	0.000267	0.000264
Middle Eastern	0.000326	0.000326
South Asian	0.000330	0.000327
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Phosphatidylinositol 3,4,5-trisphosphate-dependent GTPase-activating protein that modulates actin cytoskeleton remodeling by regulating ARF and RHO family members. Is activated by phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3) binding. Can be activated by phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4,5)P2) binding, albeit with lower efficiency. Acts on ARF6, RAC1, RHOA and CDC42. Plays a role in the internalization of anthrax toxin. {ECO:0000269|PubMed:11804589, ECO:0000269|PubMed:15569923}.
• Pathway: Endocytosis - Homo sapiens (human);cAMP signaling pathway - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases;Class I PI3K signaling events;Regulation of RhoA activity (Consensus)

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.566
• rvis_EVS: -0.71
• rvis_percentile_EVS: 14.41

Haploinsufficiency Scores

• pHI: 0.151
• hipred: Y
• hipred_score: 0.563
• ghis: 0.513

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.185

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arap3
• Phenotype: growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); 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); 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); 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); embryo phenotype

Gene ontology

• Biological process: cytoskeleton organization;signal transduction;regulation of cell shape;vesicle-mediated transport;negative regulation of cell migration;negative regulation of Rho protein signal transduction;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction
• Cellular component: ruffle;cytoplasm;cytosol;cytoskeleton;plasma membrane;lamellipodium
• Molecular function: GTPase activator activity;protein binding;phosphatidylinositol-3,4,5-trisphosphate binding;phosphatidylinositol-3,4-bisphosphate binding;metal ion binding