ARL4C
protein-codingADP ribosylation factor like GTPase 4C, the group of ARF GTPase family
Gene summary
ADP-ribosylation factor-like 4C is a member of the ADP-ribosylation factor family of GTP-binding proteins. ARL4C is closely similar to ARL4A and ARL4D and each has a nuclear localization signal and an unusually high guanine nucleotide exchange rate. This protein may play a role in cholesterol transport. [provided by RefSeq, Jul 2008]
- ARL7
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~4.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ARL4C variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001282431.2. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 11 | 11 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 11 | 0 | 0 | 11 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001269360.1 | 2 | MANE Select | |
| Ensembl | ENSP00000339754.3 | 2 | MANE Select | |
| RefSeq | NP_005728.2 | 1 | Standard | |
| Ensembl | ENSP00000375057.2 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- intracellular protein transport
- vesicle-mediated transport
- endocytic recycling
Molecular Function
- GTPase activity
- protein binding
- GTP binding
- alpha-tubulin binding
Cellular Component
- nucleus
- cytoplasm
- cytosol
- plasma membrane
- filopodium
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000390645
- Coding exons
- 1
- Length
- 4013
- Individuals with no LoFs
- 0
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 0
- Defined
- 0
- p
- 0.00
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.45 | 39 | 112 | 0.348 | 0.00000507 | 1243 |
| Missense (PolyPhen) | 8 | 52.937 | 0.15112 | 578 | ||
| Synonymous | -0.199 | 54 | 52.2 | 1.04 | 0.00000256 | 396 |
| Loss of Function | 2.02 | 0 | 4.74 | 0.00 | 2.03e-7 | 56 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Small GTP-binding protein which cycles between an inactive GDP-bound and an active GTP-bound form, and the rate of cycling is regulated by guanine nucleotide exchange factors (GEF) and GTPase-activating proteins (GAP). GTP-binding protein that does not act as an allosteric activator of the cholera toxin catalytic subunit. May be involved in transport between a perinuclear compartment and the plasma membrane, apparently linked to the ABCA1-mediated cholesterol secretion pathway. Recruits CYTH1, CYTH2, CYTH3 and CYTH4 to the plasma membrane in the GDP- bound form. Regulates the microtubule-dependent intracellular vesicular transport from early endosome to recycling endosome process. {ECO:0000269|PubMed:15147902, ECO:0000269|PubMed:17398095, ECO:0000269|PubMed:19409876}.;
Recessive Scores
- pRec
- 0.129
Intolerance Scores
- LoFtool
- 0.0900
- RVIS EVS
- 0.04
- RVIS percentile EVS
- 56.25
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.307
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |