RBPMS
Basic information
Region (hg38): 8:30384511-30572256
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBPMS gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 11 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 11 | 1 | 0 |
Variants in RBPMS
This is a list of pathogenic ClinVar variants found in the RBPMS region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-30385129-C-T | not specified | Uncertain significance (Nov 06, 2023) | ||
| 8-30504298-G-A | not specified | Uncertain significance (Jan 25, 2023) | ||
| 8-30504365-A-G | not specified | Uncertain significance (Nov 09, 2023) | ||
| 8-30544527-G-T | not specified | Uncertain significance (Jan 18, 2022) | ||
| 8-30544554-T-C | not specified | Uncertain significance (Apr 17, 2023) | ||
| 8-30544563-C-T | not specified | Uncertain significance (Feb 21, 2024) | ||
| 8-30544589-C-G | not specified | Uncertain significance (Jan 22, 2024) | ||
| 8-30544592-G-A | not specified | Uncertain significance (Jun 24, 2022) | ||
| 8-30544733-A-C | Likely benign (Apr 01, 2022) | |||
| 8-30547397-G-A | not specified | Uncertain significance (Aug 09, 2021) | ||
| 8-30547416-C-T | not specified | Uncertain significance (Jun 27, 2022) | ||
| 8-30549543-C-G | not specified | Uncertain significance (Feb 13, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RBPMS | protein_coding | protein_coding | ENST00000339877 | 7 | 187835 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.972 | 0.0282 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.72 | 67 | 120 | 0.559 | 0.00000651 | 1410 |
| Missense in Polyphen | 10 | 35.101 | 0.28489 | 398 | ||
| Synonymous | 0.0954 | 46 | 46.8 | 0.982 | 0.00000269 | 446 |
| Loss of Function | 3.08 | 0 | 11.0 | 0.00 | 5.67e-7 | 133 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Acts as a coactivator of transcriptional activity. Required to increase TGFB1/Smad-mediated transactivation. Acts through SMAD2, SMAD3 and SMAD4 to increase transcriptional activity. Increases phosphorylation of SMAD2 and SMAD3 on their C- terminal SSXS motif, possibly through recruitment of TGFBR1. Promotes the nuclear accumulation of SMAD2, SMAD3 and SMAD4 proteins (PubMed:26347403). Binds to poly(A) RNA (PubMed:17099224, PubMed:26347403). {ECO:0000269|PubMed:17099224, ECO:0000269|PubMed:26347403}.;
- Pathway
- Exercise-induced Circadian Regulation
(Consensus)
Recessive Scores
- pRec
- 0.186
Intolerance Scores
- loftool
- 0.326
- rvis_EVS
- 0.13
- rvis_percentile_EVS
- 63
Haploinsufficiency Scores
- pHI
- 0.395
- hipred
- Y
- hipred_score
- 0.794
- ghis
- 0.529
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.973
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rbpms
- Phenotype
Zebrafish Information Network
- Gene name
- rbpms
- Affected structure
- nucleate erythrocyte
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- mRNA splicing, via spliceosome;RNA processing;response to oxidative stress;positive regulation of pathway-restricted SMAD protein phosphorylation;positive regulation of SMAD protein signal transduction;positive regulation of nucleic acid-templated transcription
- Cellular component
- P-body;nucleoplasm;cytosol;cytoplasmic stress granule
- Molecular function
- transcription coactivator activity;RNA binding;protein binding;poly(A) binding;snRNA stem-loop binding;protein homodimerization activity