RBM23
protein-codingRNA binding motif protein 23, the group of RNA binding motif containing
Gene summary
This gene encodes a member of the U2AF-like family of RNA binding proteins. This protein interacts with some steroid nuclear receptors, localizes to the promoter of a steroid- responsive gene, and increases transcription of steroid-responsive transcriptional reporters in a hormone-dependent manner. It is also implicated in the steroid receptor-dependent regulation of alternative splicing. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
- RNPC4
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~26.0 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 RBM23 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001077351.2. 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 | 3 | 3 | ||||
| missense | 83 | 3 | 86 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 7 | 7 | ||||
| Total | 0 | 0 | 93 | 3 | 0 | 96 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001070819.1 | 13 | MANE Select | |
| Ensembl | ENSP00000352956.3 | 13 | MANE Select | |
| RefSeq | NP_001070820.1 | 11 | Standard | |
| RefSeq | NP_001294973.1 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- mRNA processing
- 3'-UTR-mediated mRNA destabilization
Molecular Function
- RNA binding
- mRNA binding
- protein binding
- U1 snRNP binding
Cellular Component
- nucleus
- cytoplasmic stress granule
- membrane
- ribonucleoprotein complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000359890
- Coding exons
- 13
- Length
- 18540
- Individuals with no LoFs
- 124618
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 198
- Defined
- 124816
- p
- 0.000793
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.471 | 310 | 288 | 1.08 | 0.0000190 | 2862 |
| Missense (PolyPhen) | 57 | 49.785 | 1.1449 | 530 | ||
| Synonymous | 0.00965 | 91 | 91.1 | 0.999 | 0.00000455 | 885 |
| Loss of Function | 1.36 | 20 | 27.7 | 0.722 | 0.00000187 | 262 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00097 | 0.00097 | rare |
| Latino/Admixed American | 0.00064 | 0.00064 | rare |
| Ashkenazi Jewish | 0.00079 | 0.00079 | rare |
| East Asian | 0.00039 | 0.00039 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00058 | 0.00057 | rare |
| South Asian | 0.0043 | 0.0025 | notable |
| Other | 0.00083 | 0.00082 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Probable RNA-binding protein. May be involved in pre- mRNA splicing process.;
Recessive Scores
- pRec
- 0.103
Intolerance Scores
- LoFtool
- 0.960
- RVIS EVS
- -0.13
- RVIS percentile EVS
- 43.91
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.000281
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |