ARF4

ADP ribosylation factor 4, the group of ARF GTPase family

Basic information

Region (hg38): 3:57571363-57598220

Previous symbols: [ "ARF2" ]

Links

ENSG00000168374

∙ NCBI:378 ∙ OMIM:601177 ∙ HGNC:655 ∙ Uniprot:P18085 ∙ 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 ARF4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARF4 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			2 clinvar			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in ARF4

This is a list of pathogenic ClinVar variants found in the ARF4 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-57577356-C-T		not specified	Uncertain significance (Feb 22, 2023)	2462602
3-57577357-G-T		not specified	Uncertain significance (Feb 28, 2024)	3128326

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARF4	protein_coding	protein_coding	ENST00000303436	6	26858

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.960	0.0400	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.11	38	96.1	0.395	0.00000462	1175
Missense in Polyphen		5	34.67	0.14422		470
Synonymous	0.276	31	33.0	0.939	0.00000151	345
Loss of Function	2.94	0	10.0	0.00	4.29e-7	119

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Function: FUNCTION: GTP-binding protein that functions as an allosteric activator of the cholera toxin catalytic subunit, an ADP- ribosyltransferase. Involved in protein trafficking; may modulate vesicle budding and uncoating within the Golgi apparatus.;
Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;EGFR1;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;ErbB1 downstream signaling;COPI-dependent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;COPI-mediated anterograde transport;ER to Golgi Anterograde Transport;VxPx cargo-targeting to cilium;Cargo trafficking to the periciliary membrane;Intra-Golgi and retrograde Golgi-to-ER traffic;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

pRec: 0.363

Intolerance Scores

loftool
rvis_EVS: 0.06
rvis_percentile_EVS: 58

Haploinsufficiency Scores

pHI: 0.321
hipred: Y
hipred_score: 0.825
ghis: 0.637

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.955

Mouse Genome Informatics

Gene name: Arf4
Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype;

Gene ontology

Biological process: protein ADP-ribosylation;intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;Golgi to plasma membrane transport;epidermal growth factor receptor signaling pathway;brain development;learning;vesicle-mediated transport;cell migration;activation of phospholipase D activity;negative regulation of apoptotic process;apical protein localization;establishment or maintenance of epithelial cell apical/basal polarity;positive regulation of transcription by RNA polymerase II;response to axon injury;dendritic spine development;protein localization to cilium;regulation of postsynapse organization;regulation of reactive oxygen species metabolic process
Cellular component: cytoplasm;Golgi apparatus;cytosol;plasma membrane;membrane;ruffle membrane;dendritic spine;extracellular exosome;glutamatergic synapse
Molecular function: GTPase activity;ARF guanyl-nucleotide exchange factor activity;epidermal growth factor receptor binding;protein binding;GTP binding