ARFGAP1

ADP ribosylation factor GTPase activating protein 1, the group of ArfGAPs|MicroRNA protein coding host genes

Basic information

Region (hg38): 20:63272785-63289790

Previous symbols: [ "ARF1GAP" ]

Links

ENSG00000101199 ∙ NCBI:55738 ∙ OMIM:608377 ∙ HGNC:15852 ∙ Uniprot:Q8N6T3 ∙ 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 ARFGAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARFGAP1 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			33	3		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	4	0

Variants in ARFGAP1

This is a list of pathogenic ClinVar variants found in the ARFGAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-63275615-A-C		not specified	Uncertain significance (Aug 16, 2021)
20-63276116-A-G		not specified	Uncertain significance (Feb 23, 2023)
20-63276517-A-G		not specified	Likely benign (May 23, 2023)
20-63276551-C-T		not specified	Uncertain significance (Sep 28, 2022)
20-63277289-C-T		not specified	Uncertain significance (Mar 24, 2023)
20-63277298-G-T		not specified	Uncertain significance (Sep 01, 2021)
20-63278146-C-T		not specified	Uncertain significance (Oct 30, 2023)
20-63278924-T-A		not specified	Uncertain significance (Jun 29, 2022)
20-63278940-C-T		not specified	Uncertain significance (Aug 08, 2023)
20-63278966-C-T		not specified	Uncertain significance (Jun 18, 2021)
20-63278982-C-T		not specified	Uncertain significance (Aug 12, 2021)
20-63281321-C-T		not specified	Uncertain significance (Dec 11, 2023)
20-63281322-G-A		not specified	Uncertain significance (Oct 20, 2023)
20-63282841-C-T		not specified	Uncertain significance (Jul 26, 2021)
20-63284867-C-T		not specified	Uncertain significance (Jul 06, 2021)
20-63284882-A-G		not specified	Uncertain significance (Aug 08, 2022)
20-63284912-C-T		not specified	Uncertain significance (Sep 17, 2021)
20-63285688-G-A		not specified	Uncertain significance (Nov 22, 2023)
20-63285697-C-A		not specified	Uncertain significance (Sep 27, 2022)
20-63285709-C-T		not specified	Uncertain significance (Mar 23, 2023)
20-63285711-A-G		not specified	Uncertain significance (Nov 08, 2021)
20-63286399-G-A		not specified	Uncertain significance (Aug 16, 2022)
20-63286429-G-A		not specified	Uncertain significance (Aug 10, 2021)
20-63287565-C-T		not specified	Uncertain significance (Aug 28, 2023)
20-63287620-A-G		not specified	Uncertain significance (Jun 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARFGAP1	protein_coding	protein_coding	ENST00000353546	13	17006

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00154	0.998	125685	0	23	125708	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.423	238	257	0.926	0.0000158	2736
Missense in Polyphen		65	91.782	0.7082		998
Synonymous	-1.82	138	113	1.22	0.00000877	738
Loss of Function	3.19	10	28.3	0.353	0.00000148	281

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000530	0.0000528
Middle Eastern	0.000164	0.000163
South Asian	0.000393	0.000392
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase-activating protein (GAP) for the ADP ribosylation factor 1 (ARF1). Involved in membrane trafficking and /or vesicle transport. Promotes hydrolysis of the ARF1-bound GTP and thus, is required for the dissociation of coat proteins from Golgi-derived membranes and vesicles, a prerequisite for vesicle's fusion with target compartment. Probably regulates ARF1-mediated transport via its interaction with the KDELR proteins and TMED2. Overexpression induces the redistribution of the entire Golgi complex to the endoplasmic reticulum, as when ARF1 is deactivated. Its activity is stimulated by phosphoinosides and inhibited by phosphatidylcholine (By similarity). {ECO:0000250}.
• Pathway: Endocytosis - Homo sapiens (human);XBP1(S) activates chaperone genes;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;Clathrin-mediated endocytosis;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Arf1 pathway;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: 0.630
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.49

Haploinsufficiency Scores

• pHI: 0.306
• hipred: Y
• hipred_score: 0.557
• ghis: 0.554

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.637

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arfgap1

Gene ontology

• Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;protein transport;regulation of endocytosis;regulation of ARF protein signal transduction;IRE1-mediated unfolded protein response;positive regulation of GTPase activity
• Cellular component: Golgi membrane;cytosol;postsynaptic density;synapse
• Molecular function: GTPase activator activity;protein binding;metal ion binding