ARFIP2

ADP ribosylation factor interacting protein 2, the group of AH domain containing

Basic information

Region (hg38): 11:6474683-6481479

Links

ENSG00000132254 ∙ NCBI:23647 ∙ OMIM:601638 ∙ HGNC:17160 ∙ Uniprot:P53365 ∙ 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 ARFIP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARFIP2 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	13	1	0

Variants in ARFIP2

This is a list of pathogenic ClinVar variants found in the ARFIP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-6477156-C-T		not specified	Uncertain significance (Dec 08, 2023)
11-6477222-G-A		not specified	Uncertain significance (Nov 09, 2021)
11-6477234-T-C		not specified	Uncertain significance (Aug 02, 2023)
11-6477783-G-A		not specified	Uncertain significance (Jan 22, 2024)
11-6477809-C-T		not specified	Uncertain significance (Apr 05, 2023)
11-6477821-C-T		not specified	Uncertain significance (Mar 25, 2024)
11-6477891-G-C		not specified	Uncertain significance (Nov 07, 2022)
11-6478129-C-T		not specified	Uncertain significance (Nov 23, 2021)
11-6478832-C-T		not specified	Uncertain significance (Apr 20, 2024)
11-6478862-C-T		not specified	Uncertain significance (Jan 02, 2024)
11-6478911-C-T		not specified	Uncertain significance (Jun 11, 2021)
11-6479274-C-T		not specified	Uncertain significance (Oct 05, 2021)
11-6479345-G-A		not specified	Uncertain significance (Aug 02, 2022)
11-6479980-A-G		not specified	Uncertain significance (Aug 10, 2021)
11-6480015-C-T		not specified	Likely benign (Feb 28, 2024)
11-6480346-G-A		not specified	Uncertain significance (Mar 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARFIP2	protein_coding	protein_coding	ENST00000254584	7	5757

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.774	0.226	125741	0	5	125746	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.69	130	197	0.660	0.0000113	2188
Missense in Polyphen		63	96.118	0.65545		1110
Synonymous	-0.364	86	81.8	1.05	0.00000447	707
Loss of Function	3.29	3	18.1	0.166	0.00000108	187

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative target protein of ADP-ribosylation factor. Involved in membrane ruffling.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;Vesicle-mediated transport;Membrane Trafficking;rac1 cell motility signaling pathway;Arf1 pathway;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.146

Intolerance Scores

• loftool: 0.360
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

• pHI: 0.150
• hipred: Y
• hipred_score: 0.825
• ghis: 0.621

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.874

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arfip2

Gene ontology

• Biological process: intracellular protein transport;small GTPase mediated signal transduction;lamellipodium assembly;actin cytoskeleton organization;ruffle organization
• Cellular component: ruffle;cytoplasm;cytosol;plasma membrane;cell cortex;trans-Golgi network membrane
• Molecular function: protein binding;GTP binding;phospholipid binding;protein domain specific binding;GTP-dependent protein binding;identical protein binding;cadherin binding;Rac GTPase binding;phosphatidylinositol-4-phosphate binding