RBPMS2
protein-codingRNA binding protein, mRNA processing factor 2, the group of RNA binding motif containing|MicroRNA protein coding host genes
Gene summary
The protein encoded by this gene is a member of the RNA recognition motif (RRM)-containing protein family and is involved in the development and dedifferentiation of digestive smooth muscle cells. The encoded protein functions as a homodimer and indirectly inhibits the bone morphogenetic protein pathway. [provided by RefSeq, Aug 2016]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~35.7 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 RBPMS2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_194272.3. 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 | 29 | 29 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 30 | 0 | 0 | 30 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_919248.1 | 7 | MANE Select | |
| Ensembl | ENSP00000300069.4 | 7 | MANE Select | |
| Ensembl | ENSP00000456720.1 | 3 | Standard | |
| Ensembl | ENSP00000456720.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- mRNA splicing, via spliceosome
- negative regulation of BMP signaling pathway
- embryonic digestive tract morphogenesis
- positive regulation of smooth muscle cell proliferation
- negative regulation of smooth muscle cell differentiation
Molecular Function
- mRNA binding
- protein binding
- snRNA stem-loop binding
- protein homodimerization activity
Cellular Component
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000300069
- Coding exons
- 7
- Length
- 35696
- Individuals with no LoFs
- 125737
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 2
- Defined
- 125739
- p
- 0.00000795
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.937 | 91 | 120 | 0.759 | 0.00000720 | 1325 |
| Missense (PolyPhen) | 21 | 38.799 | 0.54125 | 425 | ||
| Synonymous | -0.706 | 56 | 49.7 | 1.13 | 0.00000332 | 433 |
| Loss of Function | 2.83 | 1 | 11.2 | 0.0892 | 5.75e-7 | 128 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.0000088 | 0.0000088 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Contributes to the regulation of smooth muscle cell differentiation and proliferation in the gastrointestinal system. Binds NOG mRNA. Mediates an increase of NOG mRNA levels, and thereby contributes to the negative regulation of the BMP signaling pathway. This promotes reversible dedifferentiation of smooth muscle cells and promotes smooth muscle cell proliferation. {ECO:0000250|UniProtKB:Q9W6I1}.;
Recessive Scores
- pRec
- 0.0991
Intolerance Scores
- LoFtool
- 0.251
- RVIS EVS
- 0.31
- RVIS percentile EVS
- 72.23
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.795
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |