RBM4
RNA binding motif protein 4, the group of RNA binding motif containing|Zinc fingers CCHC-type
Basic information
Region (hg38): 11:66638667-66668374
Links
Phenotypes
GenCC
Source:
No genCC data.
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 RBM4 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 | 1 | |||||
| missense | 4 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 4 | 1 | 0 |
Variants in RBM4
This is a list of pathogenic ClinVar variants found in the RBM4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 11-66639778-G-A | not specified | Uncertain significance (Oct 12, 2024) | ||
| 11-66639845-A-G | not specified | Uncertain significance (Oct 09, 2024) | ||
| 11-66639962-A-G | not specified | Uncertain significance (Jan 23, 2025) | ||
| 11-66643528-G-A | not specified | Uncertain significance (Jun 05, 2024) | ||
| 11-66643713-C-G | not specified | Uncertain significance (Feb 20, 2025) | ||
| 11-66643749-G-A | not specified | Uncertain significance (Oct 25, 2022) | ||
| 11-66643913-C-T | Likely benign (Oct 01, 2023) | |||
| 11-66643936-C-T | Myoepithelial tumor | Uncertain significance (Nov 01, 2022) | ||
| 11-66665910-A-G | not specified | Uncertain significance (Nov 12, 2021) | ||
| 11-66665934-T-C | not specified | Uncertain significance (Oct 12, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RBM4 | protein_coding | protein_coding | ENST00000409406 | 2 | 50057 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.990 | 0.00994 | 125738 | 0 | 10 | 125748 | 0.0000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.98 | 161 | 249 | 0.647 | 0.0000174 | 2338 |
| Missense in Polyphen | 33 | 58.368 | 0.56538 | 580 | ||
| Synonymous | -0.405 | 113 | 108 | 1.05 | 0.00000799 | 766 |
| Loss of Function | 3.45 | 0 | 13.9 | 0.00 | 7.58e-7 | 162 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000555 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000354 | 0.0000352 |
| Middle Eastern | 0.0000555 | 0.0000544 |
| South Asian | 0.000163 | 0.000163 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: RNA-binding factor involved in multiple aspects of cellular processes like alternative splicing of pre-mRNA and translation regulation. Modulates alternative 5'-splice site and exon selection. Acts as a muscle cell differentiation-promoting factor. Activates exon skipping of the PTB pre-mRNA during muscle cell differentiation. Antagonizes the activity of the splicing factor PTBP1 to modulate muscle cell-specific exon selection of alpha tropomyosin. Binds to intronic pyrimidine-rich sequence of the TPM1 and MAPT pre-mRNAs. Required for the translational activation of PER1 mRNA in response to circadian clock. Binds directly to the 3'-UTR of the PER1 mRNA. Exerts a suppressive activity on Cap-dependent translation via binding to CU-rich responsive elements within the 3'UTR of mRNAs, a process increased under stress conditions or during myocytes differentiation. Recruits EIF4A1 to stimulate IRES-dependent translation initiation in respons to cellular stress. Associates to internal ribosome entry segment (IRES) in target mRNA species under stress conditions. Plays a role for miRNA-guided RNA cleavage and translation suppression by promoting association of AGO2- containing miRNPs with their cognate target mRNAs. Associates with miRNAs during muscle cell differentiation. Binds preferentially to 5'-CGCGCG[GCA]-3' motif in vitro. {ECO:0000269|PubMed:12628928, ECO:0000269|PubMed:16260624, ECO:0000269|PubMed:16777844, ECO:0000269|PubMed:16934801, ECO:0000269|PubMed:17284590, ECO:0000269|PubMed:17932509, ECO:0000269|PubMed:19801630, ECO:0000269|PubMed:21343338, ECO:0000269|PubMed:21518792}.;
Recessive Scores
- pRec
- 0.147
Intolerance Scores
- loftool
- rvis_EVS
- -0.52
- rvis_percentile_EVS
- 21.2
Haploinsufficiency Scores
- pHI
- 0.617
- hipred
- Y
- hipred_score
- 0.743
- ghis
- 0.501
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.955
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Rbm4
- Phenotype
- homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; hematopoietic system phenotype; growth/size/body region phenotype; immune system phenotype;
Gene ontology
- Biological process
- regulation of alternative mRNA splicing, via spliceosome;cap-independent translational initiation;IRES-dependent translational initiation of linear mRNA;RNA processing;negative regulation of translation;cell differentiation;negative regulation of translation in response to stress;miRNA mediated inhibition of translation;entrainment of circadian clock by photoperiod;mRNA cis splicing, via spliceosome;negative regulation of translational initiation;response to arsenic-containing substance;regulation of nucleocytoplasmic transport;positive regulation of muscle cell differentiation;circadian regulation of translation
- Cellular component
- nucleus;nucleoplasm;nucleolus;cytoplasm;cytosol;cytoplasmic stress granule;nuclear speck
- Molecular function
- RNA binding;mRNA binding;mRNA 3'-UTR binding;protein binding;zinc ion binding;cyclin binding;miRNA binding;pre-mRNA intronic binding;pre-mRNA intronic pyrimidine-rich binding