RBM15B

protein-coding

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

Gene summary

Members of the SPEN (Split-end) family of proteins, including RBM15B, have repressor function in several signaling pathways and may bind to RNA through interaction with spliceosome components (Hiriart et al., 2005 [PubMed 16129689]).[supplied by OMIM, Feb 2009]

MANE transcript

NM_013286.5

Inheritance

—

ClinVar variants

U:120B:2

Top phenotype

—

Max pathogenic AF

—

Genomic locus

chr3:51,391,285-51,397,908

External References & Databases

Ensembl (ENSG00000259956)

Transcript & Mutation Effects

hg38 • Region Span ~6.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RBM15B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 120

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_013286.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			119 clinvar	1 clinvar		120
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	120	2	0	122

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_013286.5	RefSeq	NP_037418.3	1	MANE Select
ENST00000563281.2	Ensembl	ENSP00000454545.1	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of alternative mRNA splicing, via spliceosome
RNA methylation
mRNA processing
mRNA export from nucleus
nucleocytoplasmic transport

Molecular Function

RNA binding
protein binding

Cellular Component

nucleus
nuclear envelope
nucleoplasm
nucleolus
nuclear speck

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.924

Gene Damage Prediction

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