RBM5

RNA binding motif protein 5, the group of Spliceosomal A complex|RNA binding motif containing|G-patch domain containing|Zinc fingers RANBP2-type

Basic information

Region (hg38): 3:50088919-50119021

Links

ENSG00000003756NCBI:10181OMIM:606884HGNC:9902Uniprot:P52756AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RBM5 gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
0
missense
1
clinvar
61
clinvar
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

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RBM5protein_codingprotein_codingENST00000347869 2430114
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.001.17e-71257340141257480.0000557
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense4.172244810.4650.00002785370
Missense in Polyphen68198.670.342282164
Synonymous1.801431730.8260.00001031503
Loss of Function6.66357.50.05220.00000320625

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002310.000231
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00002640.0000264
Middle Eastern0.000.00
South Asian0.00006530.0000653
Other0.0001630.000163

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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