ARFGAP3

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

Basic information

Region (hg38): 22:42796502-42858106

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.

• not_specified (74 variants)
• not_provided (1 variants)

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. These statistics are base on transcript: NM_000014570.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			71	2	1	74
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	71	3	1

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