RBM38
protein-codingRNA binding motif protein 38, the group of RNA binding motif containing
Gene summary
Enables mRNA 3'-UTR binding activity. Involved in several processes, including DNA damage response, signal transduction by p53 class mediator; negative regulation of cell population proliferation; and regulation of gene expression. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]
- RNPC1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~17.9 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 RBM38 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_017495.6. 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 | 33 | 2 | 1 | 36 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 33 | 2 | 2 | 37 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_059965.2 | 4 | MANE Select | |
| Ensembl | ENSP00000348538.5 | 4 | MANE Select | |
| RefSeq | NP_001278709.1 | 5 | Standard | |
| RefSeq | NP_906270.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- mRNA processing
- cell cycle
- RNA splicing
- regulation of myotube differentiation
- cell differentiation
Molecular Function
- RNA binding
- mRNA binding
- mRNA 3'-UTR binding
Cellular Component
- nucleus
- cytosol
- ribonucleoprotein complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000356208
- Coding exons
- 4
- Length
- 17927
- Individuals with no LoFs
- 124518
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 2
- Defined
- 124520
- p
- 0.00000803
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.03 | 113 | 148 | 0.762 | 0.00000985 | 1492 |
| Missense (PolyPhen) | 17 | 44.627 | 0.38094 | 438 | ||
| Synonymous | 0.0297 | 72 | 72.3 | 0.996 | 0.00000574 | 510 |
| Loss of Function | 2.38 | 1 | 8.46 | 0.118 | 3.72e-7 | 97 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| 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) | 0.000018 | 0.000018 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: RNA-binding protein that specifically bind the 3'-UTR of CDKN1A transcripts, leading to maintain the stability of CDKN1A transcripts, thereby acting as a mediator of the p53/TP53 family to regulate CDKN1A. CDKN1A is a cyclin-dependent kinase inhibitor transcriptionally regulated by the p53/TP53 family to induce cell cycle arrest. Isoform 1, but not isoform 2, has the ability to induce cell cycle arrest in G1 and maintain the stability of CDKN1A transcripts induced by p53/TP53. Also acts as a mRNA splicing factor. Specifically regulates the expression of FGFR2- IIIb, an epithelial cell-specific isoform of FGFR2. Plays a role in myogenic differentiation. {ECO:0000269|PubMed:17050675, ECO:0000269|PubMed:19285943}.;
Recessive Scores
- pRec
- 0.111
Intolerance Scores
- RVIS EVS
- 0.44
- RVIS percentile EVS
- 77.57
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.842
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |