ARF3
Basic information
Region (hg38): 12:48935723-48957487
Links
Phenotypes
GenCC
Source:
- complex neurodevelopmental disorder (Strong), mode of inheritance: AD
- neurodevelopmental disorder (Moderate), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (12 variants)
- Intellectual_disability (6 variants)
- Inborn_genetic_diseases (6 variants)
- Atrophy/Degeneration_affecting_the_central_nervous_system (6 variants)
- Microcephaly (4 variants)
- Scoliosis (3 variants)
- Hypotonia (2 variants)
- Seizure (2 variants)
- Dystonic_disorder (2 variants)
- Kyphosis (1 variants)
- Motor_delay (1 variants)
- Long_ear (1 variants)
- Abnormality_of_the_dentition (1 variants)
- Bifid_uvula (1 variants)
- Delayed_early-childhood_social_milestone_development (1 variants)
- Delayed_speech_and_language_development (1 variants)
- Myopathic_facies (1 variants)
- Self-injurious_behavior (1 variants)
- Global_developmental_delay (1 variants)
- Neurodevelopmental_delay (1 variants)
- See_cases (1 variants)
- Long_neck (1 variants)
- Autism (1 variants)
- Pectus_excavatum (1 variants)
- Clinodactyly (1 variants)
- Heart,_malformation_of (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARF3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001659.3. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 13 | 21 | ||||
| nonsense | 0 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 4 | 4 | 14 | 0 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ARF3 | protein_coding | protein_coding | ENST00000256682 | 4 | 21829 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.353 | 0.636 | 125738 | 0 | 2 | 125740 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.82 | 28 | 112 | 0.250 | 0.00000664 | 1193 |
| Missense in Polyphen | 3 | 30.769 | 0.097499 | 381 | ||
| Synonymous | 1.19 | 34 | 44.1 | 0.771 | 0.00000269 | 351 |
| Loss of Function | 2.12 | 2 | 8.79 | 0.227 | 5.25e-7 | 87 |
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) | 0.0000180 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| 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; may modulate vesicle budding and uncoating within the Golgi apparatus.;
- Pathway
- Endocytosis - Homo sapiens (human);Vesicle-mediated transport;Membrane Trafficking;Metabolism of lipids;Post-translational protein modification;Metabolism of proteins;Metabolism;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Synthesis of PIPs at the Golgi membrane;COPI-dependent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;COPI-mediated anterograde transport;PI Metabolism;Phospholipid metabolism;ER to Golgi Anterograde Transport;Intra-Golgi and retrograde Golgi-to-ER traffic
(Consensus)
Intolerance Scores
- loftool
- 0.297
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.04
Haploinsufficiency Scores
- pHI
- 0.874
- hipred
- Y
- hipred_score
- 0.694
- ghis
- 0.652
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.955
Mouse Genome Informatics
- Gene name
- Arf3
- Phenotype
- immune system phenotype; vision/eye phenotype;
Gene ontology
- Biological process
- phosphatidylinositol biosynthetic process;intracellular protein transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;Golgi to plasma membrane transport;vesicle-mediated transport
- Cellular component
- Golgi membrane;cytoplasm;Golgi apparatus;plasma membrane;perinuclear region of cytoplasm;extracellular exosome
- Molecular function
- GTPase activity;GTP binding