RBM15B

RNA binding motif protein 15B, the group of RNA binding motif containing

Basic information

Region (hg38): 3:51391285-51397908

Links

ENSG00000259956 ∙ NCBI:29890 ∙ OMIM:612602 ∙ HGNC:24303 ∙ Uniprot:Q8NDT2 ∙ 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 RBM15B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBM15B 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				1		1
missense			47	1		48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	47	2	0

Variants in RBM15B

This is a list of pathogenic ClinVar variants found in the RBM15B region.

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

Position	Type	Phenotype	Significance	ClinVar
3-51391434-G-C		not specified	Uncertain significance (Jun 22, 2021)
3-51391488-C-T		not specified	Uncertain significance (Mar 15, 2024)
3-51391509-C-T		not specified	Uncertain significance (Jan 23, 2024)
3-51391529-G-A		not specified	Uncertain significance (May 17, 2023)
3-51391624-C-A		not specified	Uncertain significance (May 05, 2023)
3-51391625-G-A		not specified	Uncertain significance (Jan 05, 2022)
3-51391638-C-T		not specified	Uncertain significance (Dec 19, 2022)
3-51391670-G-A		not specified	Uncertain significance (Feb 10, 2023)
3-51391688-G-T		not specified	Uncertain significance (Jun 24, 2022)
3-51391700-G-A		not specified	Uncertain significance (May 29, 2024)
3-51391710-G-T		not specified	Uncertain significance (Dec 05, 2022)
3-51391725-C-T		not specified	Uncertain significance (May 30, 2024)
3-51391734-C-G		not specified	Uncertain significance (Mar 17, 2023)
3-51392063-G-A		not specified	Uncertain significance (Apr 01, 2024)
3-51392067-G-C		not specified	Uncertain significance (Dec 27, 2023)
3-51392122-A-G			Likely benign (Jul 01, 2022)
3-51392145-C-T		not specified	Uncertain significance (Dec 13, 2023)
3-51392147-C-T		not specified	Uncertain significance (Oct 05, 2021)
3-51392171-G-A		not specified	Uncertain significance (Dec 19, 2022)
3-51392253-C-T		not specified	Uncertain significance (Nov 21, 2023)
3-51392271-C-G		not specified	Uncertain significance (Jan 02, 2024)
3-51392309-C-G		not specified	Uncertain significance (Jan 02, 2024)
3-51392310-T-A		not specified	Uncertain significance (Jun 03, 2024)
3-51392349-A-G		not specified	Uncertain significance (Oct 26, 2021)
3-51392397-A-G		not specified	Uncertain significance (Jul 15, 2021)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-binding protein that acts as a key regulator of N6- methyladenosine (m6A) methylation of RNAs, thereby regulating different processes, such as alternative splicing of mRNAs and X chromosome inactivation mediated by Xist RNA (PubMed:16129689, PubMed:27602518). Associated component of the WMM complex, a complex that mediates N6-methyladenosine (m6A) methylation of RNAs, a modification that plays a role in the efficiency of mRNA splicing and RNA processing (PubMed:27602518). Plays a key role in m6A methylation, possibly by binding target RNAs and recruiting the WMM complex (PubMed:27602518). Involved in random X inactivation mediated by Xist RNA: acts by binding Xist RNA and recruiting the WMM complex, which mediates m6A methylation, leading to target YTHDC1 reader on Xist RNA and promoting transcription repression activity of Xist (PubMed:27602518). Functions in the regulation of alternative or illicit splicing, possibly by regulating m6A methylation (PubMed:16129689). Inhibits pre-mRNA splicing (PubMed:21044963). Also functions as a mRNA export factor by acting as a cofactor for the nuclear export receptor NXF1 (PubMed:19586903). {ECO:0000269|PubMed:19586903, ECO:0000269|PubMed:21044963, ECO:0000269|PubMed:27602518, ECO:0000305|PubMed:16129689}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.125
• rvis_EVS: -1.18
• rvis_percentile_EVS: 5.94

Haploinsufficiency Scores

• pHI: 0.379
• hipred: Y
• hipred_score: 0.673
• ghis: 0.396

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.924

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rbm15b

Gene ontology

• Biological process: regulation of alternative mRNA splicing, via spliceosome;RNA methylation;mRNA processing;mRNA export from nucleus;nucleocytoplasmic transport;RNA splicing;dosage compensation by inactivation of X chromosome;viral process;negative regulation of transcription, DNA-templated
• Cellular component: nucleus;nuclear envelope;nucleoplasm;nucleolus;nuclear speck;RNA N6-methyladenosine methyltransferase complex
• Molecular function: RNA binding;protein binding