ARFGAP2

ADP ribosylation factor GTPase activating protein 2, the group of ArfGAPs

Basic information

Region (hg38): 11:47164298-47177125

Previous symbols: [ "ZNF289" ]

Links

ENSG00000149182 ∙ NCBI:84364 ∙ OMIM:606908 ∙ HGNC:13504 ∙ Uniprot:Q8N6H7 ∙ 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 ARFGAP2 gene.

• Inborn genetic diseases (20 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARFGAP2 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	0

Variants in ARFGAP2

This is a list of pathogenic ClinVar variants found in the ARFGAP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-47165478-C-T		ARFGAP2-related disorder	Benign (Oct 28, 2019)
11-47165493-C-T		ARFGAP2-related disorder	Likely benign (Feb 23, 2022)
11-47166368-T-A		not specified	Uncertain significance (Jul 20, 2021)
11-47166777-G-A		not specified	Uncertain significance (Jan 26, 2023)
11-47166830-G-A		not specified	Uncertain significance (Aug 17, 2022)
11-47166843-C-T		not specified	Uncertain significance (Feb 17, 2022)
11-47166858-G-A		not specified	Uncertain significance (Dec 16, 2023)
11-47166875-C-T		not specified	Uncertain significance (Nov 04, 2023)
11-47166876-G-A		ARFGAP2-related disorder	Benign (Oct 04, 2019)
11-47166879-T-G		not specified	Uncertain significance (Dec 19, 2022)
11-47167924-C-T		not specified	Uncertain significance (May 31, 2023)
11-47167946-C-G		not specified	Uncertain significance (Oct 06, 2023)
11-47167955-T-C		not specified	Uncertain significance (Aug 22, 2023)
11-47168012-T-C		not specified	Uncertain significance (Aug 22, 2023)
11-47168017-C-T		not specified	Uncertain significance (Sep 27, 2022)
11-47168147-C-T		not specified	Uncertain significance (Feb 03, 2022)
11-47168177-C-A		ARFGAP2-related disorder	Likely benign (Dec 18, 2019)
11-47168177-C-T		ARFGAP2-related disorder	Benign (Jul 12, 2019)
11-47168184-A-C		not specified	Uncertain significance (Apr 18, 2023)
11-47171501-T-C		not specified	Uncertain significance (Dec 21, 2023)
11-47171510-T-A		not specified	Uncertain significance (Jul 09, 2021)
11-47171513-C-A		not specified	Uncertain significance (May 22, 2023)
11-47171547-T-C		not specified	Uncertain significance (Sep 25, 2023)
11-47171658-A-G		ARFGAP2-related disorder	Benign (Jul 12, 2019)
11-47171675-C-T		ARFGAP2-related disorder	Benign (Oct 04, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARFGAP2	protein_coding	protein_coding	ENST00000524782	16	12829

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00489	0.995	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.697	275	309	0.889	0.0000175	3397
Missense in Polyphen		74	105.79	0.69947		1143
Synonymous	-0.101	119	118	1.01	0.00000687	991
Loss of Function	3.54	10	31.4	0.318	0.00000159	348

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase-activating protein (GAP) for ADP ribosylation factor 1 (ARF1). Implicated in coatomer-mediated protein transport between the Golgi complex and the endoplasmic reticulum. Hydrolysis of ARF1-bound GTP may lead to dissociation of coatomer from Golgi-derived membranes to allow fusion with target membranes. {ECO:0000269|PubMed:17760859}.
• Pathway: Endocytosis - Homo sapiens (human);Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;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: 0.129

Intolerance Scores

• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.88

Haploinsufficiency Scores

• pHI: 0.454
• hipred: N
• hipred_score: 0.426
• ghis: 0.483

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.486

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arfgap2

Gene ontology

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