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

ENSG00000003756

∙ NCBI:10181 ∙ OMIM:606884 ∙ HGNC:9902 ∙ Uniprot:P52756 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
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

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: 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

	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