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): 3:50088918-50119021

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.

• Inborn genetic diseases (9 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.

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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in RBM5

This is a list of pathogenic ClinVar variants found in the RBM5 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-50092185-T-C		not specified	Uncertain significance (Dec 21, 2022)
3-50093726-C-T		not specified	Uncertain significance (Mar 07, 2023)
3-50093753-G-A		Male infertility with azoospermia or oligozoospermia due to single gene mutation	Likely pathogenic (Sep 01, 2023)
3-50100005-C-A		not specified	Uncertain significance (Feb 02, 2024)
3-50105707-A-G		See cases	Uncertain significance (-)
3-50106839-G-A		not specified	Uncertain significance (Feb 21, 2024)
3-50109603-G-T		not specified	Uncertain significance (Nov 30, 2021)
3-50109627-C-T		not specified	Uncertain significance (Mar 07, 2023)
3-50109687-C-T		not specified	Uncertain significance (Feb 16, 2023)
3-50110458-A-G		not specified	Uncertain significance (Nov 29, 2023)
3-50110713-A-C		not specified	Uncertain significance (Aug 02, 2021)
3-50113461-A-G		not specified	Uncertain significance (Mar 01, 2024)
3-50113488-C-T		not specified	Uncertain significance (Dec 16, 2023)
3-50114190-C-T		not specified	Uncertain significance (Sep 17, 2021)
3-50117157-T-A		not specified	Uncertain significance (Jan 03, 2024)
3-50117348-G-A		not specified	Uncertain significance (Jun 01, 2023)
3-50118340-C-T		not specified	Uncertain significance (Jan 08, 2024)
3-50118365-C-T		not specified	Uncertain significance (Jun 26, 2023)

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