ARL13A
protein-codingADP ribosylation factor like GTPase 13A, the group of ARF GTPase family
Gene summary
Predicted to enable GTP binding activity and GTPase activity. Predicted to be involved in non-motile cilium assembly and receptor localization to non-motile cilium. Predicted to be located in cilium. Predicted to be active in ciliary membrane; motile cilium; and non-motile cilium. [provided by Alliance of Genome Resources, Jun 2026]
- ARL13
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~21.1 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 ARL13A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001162491.2. 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 | 1 | 1 | ||||
| missense | 5 | 5 | ||||
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| 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_001155963.1 | 7 | MANE Select | |
| Ensembl | ENSP00000398637.2 | 7 | MANE Select | |
| Ensembl | ENSP00000362044.5 | 5 | Standard | |
| Ensembl | ENSP00000414757.2 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- receptor localization to non-motile cilium
- non-motile cilium assembly
Molecular Function
- GTP binding
Cellular Component
- cilium
- ciliary membrane
- non-motile cilium
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000450049
- Coding exons
- 7
- Length
- 21122
- Individuals with no LoFs
- 124624
- Homozygous LoFs
- 6
- Heterozygous LoFs
- 7
- Defined
- 124637
- p
- 0.0000522
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.05 | 61 | 88.8 | 0.687 | 0.00000662 | 1635 |
| Missense (PolyPhen) | 11 | 24.297 | 0.45272 | 465 | ||
| Synonymous | 0.209 | 32 | 33.5 | 0.954 | 0.00000239 | 501 |
| Loss of Function | 0.917 | 6 | 8.96 | 0.669 | 7.08e-7 | 173 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000081 | 0.000065 | rare |
| 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) | 0.00012 | 0.000080 | rare |
| South Asian | 0.00017 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- LoFtool
- 0.622
- RVIS EVS
- 0.06
- RVIS percentile EVS
- 58.26
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.257
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |