RBM24
RNA binding motif protein 24, the group of RNA binding motif containing
Basic information
Region (hg38): 6:17281361-17293871
Previous symbols: [ "RNPC6" ]
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 RBM24 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 | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 0 | 0 |
Variants in RBM24
This is a list of pathogenic ClinVar variants found in the RBM24 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-17282837-G-T | not specified | Uncertain significance (Jan 08, 2024) | ||
| 6-17282854-A-G | not specified | Uncertain significance (Dec 20, 2022) | ||
| 6-17291760-C-G | not specified | Uncertain significance (Apr 18, 2023) | ||
| 6-17291880-G-A | not specified | Uncertain significance (Sep 20, 2023) | ||
| 6-17291994-G-A | not specified | Uncertain significance (Aug 20, 2023) | ||
| 6-17292003-C-G | not specified | Uncertain significance (Aug 14, 2023) | ||
| 6-17292057-G-A | not specified | Uncertain significance (Nov 17, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RBM24 | protein_coding | protein_coding | ENST00000379052 | 4 | 12530 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0864 | 0.875 | 125318 | 0 | 13 | 125331 | 0.0000519 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.50 | 93 | 144 | 0.648 | 0.00000799 | 1485 |
| Missense in Polyphen | 13 | 32.362 | 0.40171 | 347 | ||
| Synonymous | 0.355 | 60 | 63.6 | 0.943 | 0.00000440 | 514 |
| Loss of Function | 1.77 | 3 | 8.59 | 0.349 | 3.63e-7 | 105 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000644 | 0.0000627 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.000523 | 0.000418 |
| European (Non-Finnish) | 0.0000270 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000170 | 0.000164 |
dbNSFP
Source:
- Function
- FUNCTION: Multifunctional RNA-binding protein involved in the regulation of pre-mRNA splicing, mRNA stability and mRNA translation important for cell fate decision and differentiation (PubMed:20977548, PubMed:24375645, PubMed:29358667, PubMed:29104163). Plays a major role in pre-mRNA alternative splicing regulation (PubMed:26990106, PubMed:29104163). Mediates preferentially muscle-specific exon inclusion in numerous mRNAs important for striated cardiac and skeletal muscle cell differentiation (PubMed:29104163). Binds to intronic splicing enhancer (ISE) composed of stretches of GU-rich motifs localized in flanking intron of exon that will be included by alternative splicing (By similarity). Involved in embryonic stem cell (ESC) transition to cardiac cell differentiation by promoting pre-mRNA alternative splicing events of several pluripotency and/or differentiation genes (PubMed:26990106). Plays a role in the regulation of mRNA stability (PubMed:20977548, PubMed:24356969, PubMed:24375645, PubMed:29104163). Binds to 3'-untranslated region (UTR) AU-rich elements in target transcripts, such as CDKN1A and MYOG, leading to maintain their stabilities (PubMed:20977548, PubMed:24356969). Involved in myogenic differentiation by regulating MYOG levels (PubMed:20977548). Binds to multiple regions in the mRNA 3'-UTR of TP63 isoform 2, hence inducing its destabilization (PubMed:24375645). Promotes also the destabilization of the CHRM2 mRNA via its binding to a region in the coding sequence (PubMed:29104163). Plays a role in the regulation of mRNA translation (PubMed:29358667). Mediates repression of p53/TP53 mRNA translation through its binding to U- rich element in the 3'-UTR, hence preventing EIF4E from binding to p53/TP53 mRNA and translation initiation (PubMed:29358667). Binds to a huge amount of mRNAs (PubMed:29104163). Required for embryonic heart development, sarcomer and M-band formation in striated muscles (By similarity). {ECO:0000250|UniProtKB:D3Z4I3, ECO:0000269|PubMed:20977548, ECO:0000269|PubMed:24356969, ECO:0000269|PubMed:24375645, ECO:0000269|PubMed:26990106, ECO:0000269|PubMed:29104163, ECO:0000269|PubMed:29358667}.;
Recessive Scores
- pRec
- 0.0772
Intolerance Scores
- loftool
- 0.447
- rvis_EVS
- 0.06
- rvis_percentile_EVS
- 58.26
Haploinsufficiency Scores
- pHI
- 0.256
- hipred
- Y
- hipred_score
- 0.589
- ghis
- 0.492
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.307
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rbm24
- Phenotype
- embryo phenotype; growth/size/body region phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); muscle phenotype; cellular phenotype;
Zebrafish Information Network
- Gene name
- rbm24b
- Affected structure
- skeletal muscle cell
- Phenotype tag
- abnormal
- Phenotype quality
- loose
Gene ontology
- Biological process
- regulation of alternative mRNA splicing, via spliceosome;endocardial cushion development;mRNA processing;cellular response to DNA damage stimulus;RNA splicing;regulation of myotube differentiation;positive regulation of myotube differentiation;cell differentiation;regulation of mRNA stability;positive regulation of myoblast differentiation;mRNA stabilization;mRNA destabilization;3'-UTR-mediated mRNA destabilization;positive regulation of skeletal muscle fiber differentiation;positive regulation of 3'-UTR-mediated mRNA stabilization;positive regulation of stem cell differentiation;negative regulation of cytoplasmic translation
- Cellular component
- nucleus;nucleoplasm;cytosol;ribonucleoprotein complex
- Molecular function
- RNA binding;mRNA binding;mRNA 3'-UTR binding;protein binding;mRNA 3'-UTR AU-rich region binding;pre-mRNA intronic binding;mRNA CDS binding;sequence-specific mRNA binding