ARF1
ADP ribosylation factor 1, the group of Receptor ligands|ARF GTPase family|MicroRNA protein coding host genes
Basic information
Region (hg38): 1:228082708-228099212
Links
Phenotypes
GenCC
Source:
- periventricular nodular heterotopia 8 (Definitive), mode of inheritance: AD
- periventricular nodular heterotopia (Supportive), mode of inheritance: AD
- periventricular nodular heterotopia 8 (Moderate), mode of inheritance: AD
- periventricular nodular heterotopia 8 (Strong), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Periventricular nodular heterotopia 8 | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Neurologic | 28868155 |
ClinVar
This is a list of variants' phenotypes submitted to
- Periventricular nodular heterotopia 8 (5 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARF1 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 | 4 | |||||
| missense | 14 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 2 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 5 | 4 | 7 | 2 | 2 |
Variants in ARF1
This is a list of pathogenic ClinVar variants found in the ARF1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-228097169-C-T | Periventricular nodular heterotopia 8 | Likely pathogenic (Mar 12, 2022) | ||
| 1-228097217-T-C | Periventricular nodular heterotopia 8 | Pathogenic (Nov 13, 2018) | ||
| 1-228097217-T-G | Periventricular nodular heterotopia 8 | Pathogenic (Mar 12, 2022) | ||
| 1-228097257-C-T | Periventricular nodular heterotopia 8 | Likely pathogenic (Mar 22, 2019) | ||
| 1-228097344-T-C | Periventricular nodular heterotopia 8 | Pathogenic (Mar 12, 2022) | ||
| 1-228097346-C-A | Periventricular nodular heterotopia 8 | Pathogenic (Mar 12, 2022) | ||
| 1-228097358-C-A | ARF1-related disorder | Likely benign (Jun 27, 2024) | ||
| 1-228097389-T-A | Uncertain significance (Dec 01, 2020) | |||
| 1-228097394-C-G | Periventricular nodular heterotopia 8 | Uncertain significance (Sep 05, 2022) | ||
| 1-228097395-G-A | Pathogenic (Feb 15, 2024) | |||
| 1-228097405-AG-A | Periventricular nodular heterotopia 8 | Uncertain significance (Mar 01, 2022) | ||
| 1-228097431-C-T | Periventricular nodular heterotopia 8 | Uncertain significance (-) | ||
| 1-228097609-A-G | Periventricular nodular heterotopia 8 | Conflicting classifications of pathogenicity (Mar 12, 2022) | ||
| 1-228097614-A-C | not specified | Uncertain significance (Oct 10, 2023) | ||
| 1-228097624-A-C | Charcot-Marie-Tooth disease | Uncertain significance (-) | ||
| 1-228097624-A-G | Charcot-Marie-Tooth disease | Uncertain significance (-) | ||
| 1-228097626-C-T | Periventricular nodular heterotopia 8 | Likely pathogenic (Mar 12, 2022) | ||
| 1-228097627-G-A | Periventricular nodular heterotopia 8 | Pathogenic/Likely pathogenic (Sep 22, 2024) | ||
| 1-228097631-G-A | ARF1-related disorder | Benign (Mar 29, 2024) | ||
| 1-228097656-AGGATGCTGGCCGAGGACGAGCTCCG-A | Uncertain significance (Nov 29, 2022) | |||
| 1-228097710-A-G | Periventricular nodular heterotopia 8 | Pathogenic (Mar 12, 2022) | ||
| 1-228097717-T-C | not specified | Uncertain significance (Jun 10, 2024) | ||
| 1-228097859-C-G | Periventricular nodular heterotopia 8 | Pathogenic (Mar 12, 2022) | ||
| 1-228097859-C-T | Periventricular nodular heterotopia 8 | Conflicting classifications of pathogenicity (Mar 01, 2024) | ||
| 1-228097878-C-T | ARF1-related disorder | Likely benign (Apr 01, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ARF1 | protein_coding | protein_coding | ENST00000541182 | 4 | 16552 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.900 | 0.0995 | 125585 | 0 | 4 | 125589 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.39 | 17 | 122 | 0.139 | 0.00000807 | 1199 |
| Missense in Polyphen | 1 | 29.103 | 0.034361 | 378 | ||
| Synonymous | -0.370 | 53 | 49.7 | 1.07 | 0.00000352 | 348 |
| Loss of Function | 2.53 | 0 | 7.44 | 0.00 | 3.16e-7 | 84 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000913 | 0.0000905 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000881 | 0.00000881 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000342 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: GTP-binding protein that functions as an allosteric activator of the cholera toxin catalytic subunit, an ADP- ribosyltransferase. Involved in protein trafficking among different compartments. Modulates vesicle budding and uncoating within the Golgi complex. Deactivation induces the redistribution of the entire Golgi complex to the endoplasmic reticulum, suggesting a crucial role in protein trafficking. In its GTP-bound form, its triggers the association with coat proteins with the Golgi membrane. The hydrolysis of ARF1-bound GTP, which is mediated by ARFGAPs proteins, is required for dissociation of coat proteins from Golgi membranes and vesicles. The GTP-bound form interacts with PICK1 to limit PICK1-mediated inhibition of Arp2/3 complex activity; the function is linked to AMPA receptor (AMPAR) trafficking, regulation of synaptic plasicity of excitatory synapses and spine shrinkage during long-term depression (LTD).;
- Pathway
- Legionellosis - Homo sapiens (human);Endocytosis - Homo sapiens (human);Vibrio cholerae infection - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Cell Cycle;Integrated Lung Cancer Pathway;Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation;Insulin Signaling;Golgi Associated Vesicle Biogenesis;Lysosome Vesicle Biogenesis;Clathrin derived vesicle budding;Disease;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;phosphoinositides and their downstream targets;Membrane Trafficking;Metabolism of lipids;Host Interactions of HIV factors;HIV Infection;Post-translational protein modification;Metabolism of proteins;MHC class II antigen presentation;Infectious disease;Immune System;Metabolism;Adaptive Immune System;adp-ribosylation factor;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Nef Mediated CD4 Down-regulation;Nef-mediates down modulation of cell surface receptors by recruiting them to clathrin adapters;The role of Nef in HIV-1 replication and disease pathogenesis;Synthesis of PIPs at the Golgi membrane;Arf1 pathway;COPI-dependent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;Synthesis of PIPs at the plasma membrane;Class I PI3K signaling events;Intra-Golgi traffic;COPI-mediated anterograde transport;PI Metabolism;Phospholipid metabolism;ER to Golgi Anterograde Transport;Arf6 downstream pathway;Signaling events mediated by VEGFR1 and VEGFR2;Intra-Golgi and retrograde Golgi-to-ER traffic
(Consensus)
Recessive Scores
- pRec
- 0.221
Intolerance Scores
- loftool
- rvis_EVS
- -0.14
- rvis_percentile_EVS
- 42.88
Haploinsufficiency Scores
- pHI
- 0.381
- hipred
- Y
- hipred_score
- 0.664
- ghis
- 0.649
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Arf1
- 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);
Zebrafish Information Network
- Gene name
- arf1
- Affected structure
- post-vent region
- Phenotype tag
- abnormal
- Phenotype quality
- increased curvature
Gene ontology
- Biological process
- regulation of receptor internalization;phosphatidylinositol biosynthetic process;cellular copper ion homeostasis;intracellular protein transport;Golgi to plasma membrane transport;actin filament organization;vesicle-mediated transport;antigen processing and presentation of exogenous peptide antigen via MHC class II;regulation of Arp2/3 complex-mediated actin nucleation;very-low-density lipoprotein particle assembly;interleukin-12-mediated signaling pathway;positive regulation of catalytic activity;positive regulation of endocytosis;positive regulation of calcium ion-dependent exocytosis;regulation of defense response to virus by virus;positive regulation of protein secretion;Golgi to transport vesicle transport;long-term synaptic depression;positive regulation of dendritic spine development;synaptic vesicle budding;dendritic spine organization;lysosomal membrane organization;cellular response to virus;postsynaptic actin cytoskeleton organization;positive regulation of sodium ion transmembrane transport;positive regulation of late endosome to lysosome transport;positive regulation of ER to Golgi vesicle-mediated transport;regulation of phospholipid metabolic process;mitotic cleavage furrow ingression
- Cellular component
- Golgi membrane;cytoplasm;late endosome;peroxisomal membrane;Golgi apparatus;trans-Golgi network;cytosol;plasma membrane;focal adhesion;postsynaptic density;sarcomere;COPI-coated vesicle;cell leading edge;protein-containing complex;neuron projection;postsynaptic membrane;perinuclear region of cytoplasm;extracellular exosome;glutamatergic synapse
- Molecular function
- magnesium ion binding;RNA binding;GTPase activity;protein binding;GTP binding;GDP binding;protein domain specific binding;protein heterodimerization activity;phospholipase D activator activity