RBPMS2
Basic information
Region (hg38): 15:64739891-64775589
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 RBPMS2 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 | 20 | 20 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 20 | 0 | 0 |
Variants in RBPMS2
This is a list of pathogenic ClinVar variants found in the RBPMS2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
15-64741194-G-T | not specified | Uncertain significance (Mar 23, 2022) | ||
15-64741214-G-A | not specified | Uncertain significance (Mar 01, 2024) | ||
15-64748424-C-T | not specified | Uncertain significance (Nov 06, 2023) | ||
15-64748442-C-T | not specified | Uncertain significance (Oct 26, 2021) | ||
15-64748483-G-A | not specified | Uncertain significance (Sep 13, 2023) | ||
15-64748502-T-C | not specified | Uncertain significance (Apr 20, 2024) | ||
15-64748517-G-T | not specified | Uncertain significance (Aug 21, 2023) | ||
15-64748547-G-C | not specified | Uncertain significance (Apr 20, 2023) | ||
15-64748553-C-A | not specified | Uncertain significance (Mar 07, 2024) | ||
15-64748555-C-T | not specified | Uncertain significance (Sep 26, 2024) | ||
15-64749012-C-T | not specified | Uncertain significance (Dec 12, 2023) | ||
15-64749014-A-G | not specified | Uncertain significance (Sep 25, 2023) | ||
15-64749042-C-T | not specified | Uncertain significance (Aug 03, 2022) | ||
15-64749059-G-A | not specified | Uncertain significance (Feb 21, 2024) | ||
15-64749069-G-T | not specified | Uncertain significance (Jan 25, 2024) | ||
15-64749143-C-T | not specified | Uncertain significance (Mar 12, 2024) | ||
15-64750351-C-T | not specified | Uncertain significance (Sep 20, 2024) | ||
15-64751572-G-A | not specified | Uncertain significance (Dec 15, 2022) | ||
15-64751635-G-A | not specified | Uncertain significance (Aug 08, 2023) | ||
15-64775312-T-C | not specified | Uncertain significance (May 20, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RBPMS2 | protein_coding | protein_coding | ENST00000300069 | 7 | 35696 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.877 | 0.123 | 125737 | 0 | 2 | 125739 | 0.00000795 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.937 | 91 | 120 | 0.759 | 0.00000720 | 1325 |
Missense in 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 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000289 | 0.0000289 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.00000879 | 0.00000879 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
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
Haploinsufficiency Scores
- pHI
- 0.770
- hipred
- N
- hipred_score
- 0.441
- ghis
- 0.402
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.795
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rbpms2
- Phenotype
Gene ontology
- 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
- Cellular component
- cytoplasm
- Molecular function
- mRNA binding;protein binding;snRNA stem-loop binding;protein homodimerization activity