RABL2A
protein-codingRAB, member of RAS oncogene family like 2A, the group of RAB like GTPases
Gene summary
This gene is a member of the RAB gene family which belongs to the RAS GTPase superfamily. The proteins in the family of RAS-related signaling molecules are small GTP-binding proteins that play important roles in the regulation of exocytotic and endocytotic pathways. This gene maps to the site of an ancestral telomere fusion event and may be a subtelomeric gene. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Apr 2015]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~16.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0005047
Submitter: PanelApp Australia
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to RABL2A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001306158.2. 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 | 36 | 1 | 37 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 36 | 1 | 0 | 37 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001293087.1 | 8 | MANE Select | |
| Ensembl | ENSP00000507832.1 | 8 | MANE Select | |
| RefSeq | NP_001293088.1 | 8 | Standard | |
| RefSeq | NP_001293089.1 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- intracellular protein transport
- Rab protein signal transduction
Molecular Function
- GTPase activity
- GTP binding
Cellular Component
- cell
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000393167
- Coding exons
- 8
- Length
- 16168
- Individuals with no LoFs
- 118174
- Homozygous LoFs
- 295
- Heterozygous LoFs
- 7279
- Defined
- 125748
- p
- 0.0306
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.436 | 106 | 119 | 0.888 | 0.00000638 | 1530 |
| Missense (PolyPhen) | 43 | 43.095 | 0.99779 | 543 | ||
| Synonymous | 0.795 | 40 | 46.9 | 0.852 | 0.00000278 | 386 |
| Loss of Function | 0.0229 | 11 | 11.1 | 0.993 | 5.08e-7 | 138 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0041 | 0.0041 | notable |
| Latino/Admixed American | 0.027 | 0.026 | notable |
| Ashkenazi Jewish | 0.030 | 0.030 | notable |
| East Asian | 0.10 | 0.10 | notable |
| Finnish | 0.011 | 0.011 | notable |
| European (Non-Finnish) | 0.016 | 0.016 | notable |
| South Asian | 0.079 | 0.078 | notable |
| Other | 0.033 | 0.032 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays an essential role in male fertility, sperm intra- flagellar transport, and tail assembly. Binds, in a GTP-regulated manner, to a specific set of effector proteins including key proteins involved in cilia development and function and delivers them into the growing sperm tail. {ECO:0000250|UniProtKB:E9Q9D5}.;
Recessive Scores
- pRec
- 0.0982
Intolerance Scores
- LoFtool
- 0.669
- RVIS EVS
- 0.28
- RVIS percentile EVS
- 71.27
Essentials
- Essential (CRISPR)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.000365
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |