RBM11
protein-codingRNA binding motif protein 11, the group of RNA binding motif containing
Gene summary
Enables poly(U) RNA binding activity and protein homodimerization activity. Acts upstream of or within cellular response to oxidative stress and regulation of alternative mRNA splicing, via spliceosome. Located in nuclear speck. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~12.2 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 RBM11 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_144770.5. 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 | 2 | 2 | ||||
| missense | 43 | 4 | 47 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 45 | 4 | 0 | 49 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_658983.3 | 5 | MANE Select | |
| Ensembl | ENSP00000383421.3 | 5 | MANE Select | |
| RefSeq | NP_001307531.1 | 5 | Standard | |
| Ensembl | ENSP00000570888.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- regulation of alternative mRNA splicing, via spliceosome
- mRNA processing
- multicellular organism development
- RNA splicing
- cell differentiation
Molecular Function
- single-stranded RNA binding
- protein binding
- poly(U) RNA binding
- protein homodimerization activity
Cellular Component
- nucleus
- nucleoplasm
- nuclear speck
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000400577
- Coding exons
- 5
- Length
- 12243
- Individuals with no LoFs
- 124627
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 27
- Defined
- 124654
- p
- 0.000108
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.380 | 126 | 139 | 0.909 | 0.00000665 | 1831 |
| Missense (PolyPhen) | 47 | 42.825 | 1.0975 | 554 | ||
| Synonymous | 0.769 | 44 | 51.0 | 0.863 | 0.00000265 | 511 |
| Loss of Function | 1.11 | 9 | 13.4 | 0.672 | 7.29e-7 | 161 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000065 | 0.000065 | rare |
| Latino/Admixed American | 0.00021 | 0.00020 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00017 | 0.00017 | rare |
| Finnish | 0.00029 | 0.00028 | rare |
| European (Non-Finnish) | 0.000045 | 0.000044 | rare |
| South Asian | 0.00017 | 0.00016 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Tissue-specific splicing factor with potential implication in the regulation of alternative splicing during neuron and germ cell differentiation. Antagonizes SRSF1-mediated BCL-X splicing. May affect the choice of alternative 5' splice sites by binding to specific sequences in exons and antagonizing the SR protein SRSF1. {ECO:0000269|PubMed:21984414}.;
Recessive Scores
- pRec
- 0.0845
Intolerance Scores
- LoFtool
- 0.787
- RVIS EVS
- 1.62
- RVIS percentile EVS
- 95.96
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.737
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |