ARF6
ADP ribosylation factor 6, the group of ARF GTPase family
Basic information
Region (hg38): 14:49893079-49897054
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARF6 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 | 2 | |||||
| missense | 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 | 2 |
Variants in ARF6
This is a list of pathogenic ClinVar variants found in the ARF6 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 14-49893787-C-T | Benign (Dec 31, 2019) | |||
| 14-49893923-G-A | Uncertain significance (Aug 06, 2019) | |||
| 14-49893955-C-T | Benign (Dec 31, 2019) | |||
| 14-49894208-T-A | not specified | Uncertain significance (Mar 30, 2024) | ||
| 14-49894224-A-G | not specified | Uncertain significance (Feb 16, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ARF6 | protein_coding | protein_coding | ENST00000298316 | 1 | 1681 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.715 | 0.272 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.78 | 23 | 102 | 0.226 | 0.00000462 | 1142 |
| Missense in Polyphen | 7 | 47.258 | 0.14812 | 534 | ||
| Synonymous | -2.05 | 60 | 42.9 | 1.40 | 0.00000201 | 355 |
| Loss of Function | 1.89 | 0 | 4.14 | 0.00 | 1.79e-7 | 50 |
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:
- Function
- FUNCTION: GTP-binding protein involved in protein trafficking that regulates endocytic recycling and cytoskeleton remodeling (PubMed:11266366, PubMed:21170023, PubMed:16737952, PubMed:7589240, PubMed:18400762). Required for normal completion of mitotic cytokinesis (By similarity). Plays a role in the reorganization of the actin cytoskeleton and the formation of stress fibers (By similarity). Involved in the regulation of dendritic spine development, contributing to the regulation of dendritic branching and filopodia extension (PubMed:14978216). Plays an important role in membrane trafficking, during junctional remodeling and epithelial polarization. Regulates surface levels of adherens junction proteins such as CDH1 (By similarity). {ECO:0000250|UniProtKB:P62331, ECO:0000269|PubMed:11266366, ECO:0000269|PubMed:14978216, ECO:0000269|PubMed:16099990, ECO:0000269|PubMed:16737952, ECO:0000269|PubMed:18400762, ECO:0000269|PubMed:21170023, ECO:0000269|PubMed:7589240}.;
- Pathway
- Fc gamma R-mediated phagocytosis - Homo sapiens (human);Endocytosis - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Integrated Lung Cancer Pathway;VEGFA-VEGFR2 Signaling Pathway;Ras Signaling;EGF-EGFR Signaling Pathway;Insulin Signaling;Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Clathrin-mediated endocytosis;Rab regulation of trafficking;Posttranslational regulation of adherens junction stability and dissassembly;Class I PI3K signaling events;Arf6 trafficking events;Plexin-D1 Signaling;Stabilization and expansion of the E-cadherin adherens junction;Signaling events mediated by Hepatocyte Growth Factor Receptor (c-Met);Arf6 signaling events;Arf6 downstream pathway;Alpha4 beta1 integrin signaling events;E-cadherin signaling in the nascent adherens junction
(Consensus)
Recessive Scores
- pRec
- 0.413
Intolerance Scores
- loftool
- rvis_EVS
- -0.14
- rvis_percentile_EVS
- 42.88
Haploinsufficiency Scores
- pHI
- 0.438
- hipred
- Y
- hipred_score
- 0.804
- ghis
- 0.631
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.782
Mouse Genome Informatics
- Gene name
- Arf6
- Phenotype
- homeostasis/metabolism phenotype; liver/biliary system 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype;
Zebrafish Information Network
- Gene name
- arf6b
- Affected structure
- intrahepatic bile duct
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- liver development;intracellular protein transport;cell cycle;cell adhesion;vesicle-mediated transport;positive regulation of actin filament polymerization;cortical actin cytoskeleton organization;endocytic recycling;myeloid cell apoptotic process;protein localization to cell surface;regulation of Rac protein signal transduction;protein localization to endosome;negative regulation of receptor-mediated endocytosis;synaptic vesicle endocytosis;cell division;regulation of filopodium assembly;positive regulation of keratinocyte migration;regulation of dendritic spine development;establishment of epithelial cell polarity;ruffle assembly;hepatocyte apoptotic process;maintenance of postsynaptic density structure;positive regulation of protein localization to plasma membrane;positive regulation of adherens junction organization;regulation of presynapse assembly;cellular response to nerve growth factor stimulus;negative regulation of protein localization to cell surface;negative regulation of dendrite development
- Cellular component
- ruffle;cytoplasm;endosome;early endosome;cytosol;plasma membrane;focal adhesion;cell cortex;membrane;endocytic vesicle;filopodium membrane;cleavage furrow;myelin sheath;recycling endosome membrane;extracellular exosome;Flemming body;presynapse;glutamatergic synapse
- Molecular function
- GTPase activity;protein binding;GTP binding;thioesterase binding;protein N-terminus binding