ARFRP1
protein-codingADP ribosylation factor related protein 1, the group of ARF GTPase family
Gene summary
The protein encoded by this gene is a membrane-associated GTP-ase which localizes to the plasma membrane and is related to the ADP-ribosylation factor (ARF) and ARF-like (ARL) proteins. This gene plays a role in membrane trafficking between the trans-Golgi network and endosomes. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, May 2012]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~9.4 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 ARFRP1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001267547.3. 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 | 1 | 1 | 2 | |||
| missense | 35 | 1 | 36 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 36 | 1 | 1 | 38 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001254476.1 | 7 | MANE Select | |
| Ensembl | ENSP00000483486.1 | 7 | MANE Select | |
| RefSeq | NP_001128230.1 | 6 | Standard | |
| RefSeq | NP_001254473.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Vesicle-mediated transport
- Membrane Trafficking
- Retrograde transport at the Trans-Golgi-Network
- Intra-Golgi and retrograde Golgi-to-ER traffic
Biological Process
- intracellular protein transport
- signal transduction
- gastrulation
- protein localization to organelle
- protein localization to Golgi apparatus
Molecular Function
- GTPase activity
- protein binding
- GTP binding
Cellular Component
- Golgi apparatus
- trans-Golgi network
- cytosol
- membrane
- trans-Golgi network membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000359715
- Coding exons
- 7
- Length
- 9382
- Individuals with no LoFs
- 124972
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 28
- Defined
- 125000
- p
- 0.000112
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.852 | 103 | 130 | 0.790 | 0.00000854 | 1296 |
| Missense (PolyPhen) | 27 | 49.133 | 0.54953 | 548 | ||
| Synonymous | -0.955 | 69 | 59.6 | 1.16 | 0.00000444 | 386 |
| Loss of Function | 2.52 | 4 | 14.3 | 0.280 | 7.77e-7 | 150 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0.00010 | 0.00010 | rare |
| East Asian | 0.000055 | 0.000054 | rare |
| Finnish | 0.00099 | 0.00097 | rare |
| European (Non-Finnish) | 0.000036 | 0.000036 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Trans-Golgi-associated GTPase that regulates protein sorting. Controls the targeting of ARL1 and its effector to the trans-Golgi. Required for the lipidation of chylomicrons in the intestine and required for VLDL lipidation in the liver. {ECO:0000250|UniProtKB:Q8BXL7}.;
Recessive Scores
- pRec
- 0.235
Intolerance Scores
- LoFtool
- 0.247
- RVIS EVS
- -0.14
- RVIS percentile EVS
- 43.29
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- E
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.934
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |