RBM5
Basic information
Region (hg38): 3:50088919-50119021
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (61 variants)
- Male_infertility_with_azoospermia_or_oligozoospermia_due_to_single_gene_mutation (1 variants)
- See_cases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBM5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005778.4. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 0 | |||||
missense | 61 | 62 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 1 | 61 | 0 | 0 |
Highest pathogenic variant AF is 0.00000123936
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RBM5 | protein_coding | protein_coding | ENST00000347869 | 24 | 30114 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 1.17e-7 | 125734 | 0 | 14 | 125748 | 0.0000557 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 4.17 | 224 | 481 | 0.465 | 0.0000278 | 5370 |
Missense in Polyphen | 68 | 198.67 | 0.34228 | 2164 | ||
Synonymous | 1.80 | 143 | 173 | 0.826 | 0.0000103 | 1503 |
Loss of Function | 6.66 | 3 | 57.5 | 0.0522 | 0.00000320 | 625 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000231 | 0.000231 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000264 | 0.0000264 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000653 | 0.0000653 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the spliceosome A complex. Regulates alternative splicing of a number of mRNAs. May modulate splice site pairing after recruitment of the U1 and U2 snRNPs to the 5' and 3' splice sites of the intron. May both positively and negatively regulate apoptosis by regulating the alternative splicing of several genes involved in this process, including FAS and CASP2/caspase-2. In the case of FAS, promotes exclusion of exon 6 thereby producing a soluble form of FAS that inhibits apoptosis. In the case of CASP2/caspase-2, promotes exclusion of exon 9 thereby producing a catalytically active form of CASP2/Caspase-2 that induces apoptosis. {ECO:0000269|PubMed:10949932, ECO:0000269|PubMed:12207175, ECO:0000269|PubMed:12581154, ECO:0000269|PubMed:15192330, ECO:0000269|PubMed:16585163, ECO:0000269|PubMed:18840686, ECO:0000269|PubMed:18851835}.;
- Pathway
- mRNA Processing;Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Recessive Scores
- pRec
- 0.117
Intolerance Scores
- loftool
- 0.287
- rvis_EVS
- -1.11
- rvis_percentile_EVS
- 6.72
Haploinsufficiency Scores
- pHI
- 0.499
- hipred
- Y
- hipred_score
- 0.816
- ghis
- 0.647
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.710
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rbm5
- Phenotype
- reproductive system phenotype; cellular phenotype; endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- spliceosomal complex assembly;regulation of alternative mRNA splicing, via spliceosome;mRNA splicing, via spliceosome;RNA processing;apoptotic process;negative regulation of cell population proliferation;positive regulation of apoptotic process
- Cellular component
- nucleus;nucleoplasm;spliceosomal complex
- Molecular function
- DNA binding;RNA binding;mRNA binding;protein binding;metal ion binding