ARFIP1

ADP ribosylation factor interacting protein 1, the group of AH domain containing

Basic information

Region (hg38): 4:152779937-152918463

Links

ENSG00000164144 ∙ NCBI:27236 ∙ OMIM:605928 ∙ HGNC:21496 ∙ Uniprot:P53367 ∙ 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 ARFIP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARFIP1 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			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	0

Variants in ARFIP1

This is a list of pathogenic ClinVar variants found in the ARFIP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-152829682-A-G		not specified	Uncertain significance (Aug 16, 2022)
4-152829686-A-G		not specified	Uncertain significance (Dec 20, 2023)
4-152829707-G-A		not specified	Likely benign (Oct 12, 2022)
4-152863610-T-G		not specified	Uncertain significance (Sep 15, 2021)
4-152863673-A-G		not specified	Uncertain significance (Mar 22, 2022)
4-152863694-T-C		not specified	Uncertain significance (Dec 15, 2022)
4-152870765-C-T		not specified	Uncertain significance (Jan 03, 2024)
4-152872518-T-C		not specified	Uncertain significance (May 31, 2023)
4-152880997-G-A		not specified	Uncertain significance (Jun 09, 2022)
4-152881000-G-C		not specified	Uncertain significance (Dec 15, 2023)
4-152881042-T-C		not specified	Uncertain significance (Oct 16, 2023)
4-152881120-T-C		not specified	Uncertain significance (Mar 31, 2024)
4-152882810-A-G		not specified	Uncertain significance (Apr 22, 2024)
4-152882823-T-C		not specified	Uncertain significance (May 11, 2022)
4-152888135-T-C		not specified	Uncertain significance (Jun 13, 2024)
4-152888271-T-A		not specified	Uncertain significance (Feb 12, 2024)
4-152910098-A-G		not specified	Uncertain significance (Dec 12, 2022)
4-152910108-T-G		not specified	Uncertain significance (Dec 19, 2023)
4-152910112-G-T		not specified	Uncertain significance (Oct 05, 2023)
4-152910147-G-T		not specified	Uncertain significance (Aug 21, 2023)
4-152910196-C-A		not specified	Uncertain significance (Dec 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARFIP1	protein_coding	protein_coding	ENST00000451320	8	138527

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000308	0.943	125726	0	21	125747	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	149	191	0.779	0.00000939	2447
Missense in Polyphen		29	45.135	0.64252		610
Synonymous	-0.0129	69	68.9	1.00	0.00000329	708
Loss of Function	1.75	10	18.0	0.555	8.72e-7	231

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000271	0.000271
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000534	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.000131	0.000131
Other	0.000330	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative target protein of ADP-ribosylation factor.
• Pathway: miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in squamous cell - TarBase (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.491
• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.73

Haploinsufficiency Scores

• pHI: 0.372
• hipred: Y
• hipred_score: 0.676
• ghis: 0.611

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.521

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arfip1

Gene ontology

• Biological process: intracellular protein transport;regulation of protein secretion
• Cellular component: Golgi membrane;cytoplasm;cytosol;trans-Golgi network membrane
• Molecular function: phospholipid binding;protein domain specific binding;phosphatidylinositol-4-phosphate binding