RBM19
protein-codingRNA binding motif protein 19, the group of RNA binding motif containing|SSU processome
Gene summary
This gene encodes a nucleolar protein that contains six RNA-binding motifs. The encoded protein may be involved in regulating ribosome biogenesis. Multiple alternatively spliced variants, encoding the same protein, have been identified.[provided by RefSeq, Apr 2009]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~149.6 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 RBM19 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_016196.4. 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 | 183 | 6 | 189 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 7 | 7 | ||||
| Total | 0 | 0 | 191 | 6 | 0 | 197 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_057280.2 | 24 | MANE Select | |
| Ensembl | ENSP00000261741.5 | 24 | MANE Select | |
| RefSeq | NP_001140170.1 | 24 | Standard | |
| RefSeq | NP_001140171.1 | 24 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| rbm19 | Danio rerio | Structure: anatomical system Quality: quality abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- miR-targeted genes in lymphocytes - TarBase
Biological Process
- regulation of alternative mRNA splicing, via spliceosome
- multicellular organism development
- positive regulation of embryonic development
- mRNA cis splicing, via spliceosome
Molecular Function
- RNA binding
Cellular Component
- nucleoplasm
- chromosome
- nucleolus
- cytoplasm
- membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000545145
- Coding exons
- 24
- Length
- 149634
- Individuals with no LoFs
- 125620
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 127
- Defined
- 125748
- p
- 0.000509
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.176 | 583 | 571 | 1.02 | 0.0000346 | 6307 |
| Missense (PolyPhen) | 187 | 201.58 | 0.92767 | 2044 | ||
| Synonymous | 0.541 | 234 | 245 | 0.956 | 0.0000168 | 1823 |
| Loss of Function | 3.14 | 28 | 52.6 | 0.532 | 0.00000267 | 623 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.00082 | 0.00081 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00076 | 0.00076 | rare |
| Finnish | 0.00024 | 0.00023 | rare |
| European (Non-Finnish) | 0.00044 | 0.00044 | rare |
| South Asian | 0.00088 | 0.00085 | rare |
| Other | 0.00066 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays a role in embryo pre-implantation development. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.168
Intolerance Scores
- LoFtool
- 0.924
- RVIS EVS
- 0.04
- RVIS percentile EVS
- 56.27
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.895
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | High | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |