RANBP3L
protein-codingRAN binding protein 3 like
Gene summary
Enables SMAD binding activity. Predicted to be involved in several processes, including mesenchymal cell differentiation involved in bone development; negative regulation of osteoblast differentiation; and protein export from nucleus. Predicted to be located in cytoplasm and nucleus. Predicted to be part of nuclear pore. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~55.2 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 RANBP3L variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_145000.5. 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 | 53 | 3 | 56 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 55 | 3 | 0 | 58 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_659437.3 | 14 | MANE Select | |
| Ensembl | ENSP00000296604.3 | 14 | MANE Select | |
| RefSeq | NP_001154901.1 | 15 | Standard | |
| RefSeq | NP_001310202.1 | 14 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- protein export from nucleus
- positive regulation of GTPase activity
- positive regulation of myoblast differentiation
- negative regulation of osteoblast differentiation
- mesenchymal cell differentiation involved in bone development
Molecular Function
- GTPase activator activity
- Ran GTPase binding
- SMAD binding
Cellular Component
- nucleus
- nuclear pore
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000502994
- Coding exons
- 15
- Length
- 53681
- Individuals with no LoFs
- 125678
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 68
- Defined
- 125747
- p
- 0.000274
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.426 | 224 | 243 | 0.923 | 0.0000119 | 3196 |
| Missense (PolyPhen) | 56 | 61.377 | 0.91239 | 841 | ||
| Synonymous | 0.588 | 78 | 84.9 | 0.919 | 0.00000400 | 891 |
| Loss of Function | 0.780 | 26 | 30.7 | 0.848 | 0.00000165 | 373 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.00022 | 0.00020 | rare |
| Ashkenazi Jewish | 0.00011 | 0.000099 | rare |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00014 | 0.00014 | rare |
| South Asian | 0.0013 | 0.0012 | notable |
| Other | 0.00018 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Nuclear export factor for BMP-specific SMAD1/5/8 that plays a critical role in terminating BMP signaling and regulating mesenchymal stem cell differentiation by blocking osteoblast differentiation to promote myogenic differention. Directly recognizes dephosphorylated SMAD1/5/8 and mediates their nuclear export in a Ran-dependent manner. {ECO:0000250|UniProtKB:Q6PDH4, ECO:0000269|PubMed:25755279}.;
Intolerance Scores
- LoFtool
- 0.988
- RVIS EVS
- 0.11
- RVIS percentile EVS
- 61.91
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |