ARFGAP3

ADP ribosylation factor GTPase activating protein 3, the group of ArfGAPs

Basic information

Region (hg38): 22:42796501-42858106

Previous symbols: [ "ARFGAP1" ]

Links

ENSG00000242247 ∙ NCBI:26286 ∙ OMIM:612439 ∙ HGNC:661 ∙ Uniprot:Q9NP61 ∙ 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 ARFGAP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARFGAP3 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						0
missense			30	1	1	32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	1	1

Variants in ARFGAP3

This is a list of pathogenic ClinVar variants found in the ARFGAP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-42797592-G-C		not specified	Uncertain significance (Jul 20, 2022)
22-42799044-T-C		not specified	Uncertain significance (Aug 08, 2023)
22-42799061-T-C		not specified	Uncertain significance (Aug 13, 2021)
22-42799122-C-T		not specified	Uncertain significance (Sep 17, 2021)
22-42807111-G-A		not specified	Uncertain significance (Jun 11, 2021)
22-42807147-C-T		not specified	Uncertain significance (Feb 03, 2022)
22-42808795-A-G			Benign (Apr 01, 2022)
22-42808822-C-A		not specified	Uncertain significance (Mar 31, 2024)
22-42808828-T-G		not specified	Uncertain significance (Feb 27, 2023)
22-42808877-G-A		not specified	Uncertain significance (Jun 27, 2023)
22-42808877-G-C		not specified	Uncertain significance (Feb 15, 2023)
22-42808879-C-G		not specified	Uncertain significance (May 03, 2023)
22-42808879-C-T		not specified	Uncertain significance (May 12, 2024)
22-42808886-T-A		not specified	Uncertain significance (Oct 02, 2023)
22-42810914-G-C		not specified	Uncertain significance (Mar 22, 2023)
22-42817167-C-T		not specified	Uncertain significance (Jul 09, 2021)
22-42817209-T-G		not specified	Uncertain significance (Nov 08, 2022)
22-42817211-G-A		not specified	Uncertain significance (Nov 01, 2022)
22-42817212-G-A		not specified	Uncertain significance (Aug 12, 2021)
22-42817244-G-A		not specified	Uncertain significance (Apr 07, 2022)
22-42817774-T-C		not specified	Uncertain significance (May 25, 2022)
22-42817834-T-C		not specified	Uncertain significance (Apr 17, 2024)
22-42822327-G-A		not specified	Likely benign (Nov 17, 2022)
22-42822338-T-A		not specified	Uncertain significance (Mar 17, 2023)
22-42823671-A-T		not specified	Uncertain significance (May 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARFGAP3	protein_coding	protein_coding	ENST00000263245	16	61605

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.02e-11	0.864	125692	0	56	125748	0.000223

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.468	255	277	0.921	0.0000147	3356
Missense in Polyphen		98	100.49	0.97525		1170
Synonymous	-0.0512	101	100	1.01	0.00000590	930
Loss of Function	1.81	21	32.0	0.656	0.00000160	402

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000426	0.000425
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000299	0.000299
Middle Eastern	0.000164	0.000163
South Asian	0.000230	0.000229
Other	0.000330	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase-activating protein (GAP) for ADP ribosylation factor 1 (ARF1). Hydrolysis of ARF1-bound GTP may lead to dissociation of coatomer from Golgi-derived membranes to allow fusion with target membranes. {ECO:0000269|PubMed:11172815}.
• Pathway: Endocytosis - Homo sapiens (human);Vesicle-mediated transport;rho cell motility signaling pathway;t cell receptor signaling pathway;Membrane Trafficking;rac1 cell motility signaling pathway;Post-translational protein modification;Metabolism of proteins;adp-ribosylation factor;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPI-dependent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;COPI-mediated anterograde transport;ER to Golgi Anterograde Transport;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.949
• rvis_EVS: 1.07
• rvis_percentile_EVS: 91.67

Haploinsufficiency Scores

• pHI: 0.128
• hipred: N
• hipred_score: 0.207
• ghis: 0.403

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.105

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arfgap3

Gene ontology

• Biological process: intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;protein secretion;vesicle-mediated transport;positive regulation of GTPase activity;COPI coating of Golgi vesicle
• Cellular component: Golgi membrane;Golgi apparatus;trans-Golgi network;cytosol;membrane;COPI vesicle coat
• Molecular function: GTPase activator activity;protein binding;protein transporter activity;metal ion binding