RBM4B

RNA binding motif protein 4B, the group of RNA binding motif containing|Zinc fingers CCHC-type

Basic information

Region (hg38): 11:66664998-66677887

Previous symbols: [ "RBM30" ]

Links

ENSG00000173914 ∙ NCBI:83759 ∙ ∙ HGNC:28842 ∙ Uniprot:Q9BQ04 ∙ 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 RBM4B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBM4B 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			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	28	1	0

Variants in RBM4B

This is a list of pathogenic ClinVar variants found in the RBM4B region.

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

Position	Type	Phenotype	Significance	ClinVar
11-66665910-A-G		not specified	Uncertain significance (Nov 12, 2021)
11-66665934-T-C		not specified	Uncertain significance (Oct 12, 2021)
11-66668640-C-T		not specified	Uncertain significance (Jan 10, 2022)
11-66668641-G-A		not specified	Uncertain significance (Mar 19, 2024)
11-66668664-C-T		not specified	Uncertain significance (May 31, 2023)
11-66668665-G-A		not specified	Uncertain significance (Mar 23, 2022)
11-66668673-C-T		not specified	Uncertain significance (Jan 18, 2022)
11-66668700-G-A		not specified	Uncertain significance (Jul 13, 2022)
11-66668707-C-T		not specified	Uncertain significance (Dec 18, 2023)
11-66668727-C-T		not specified	Uncertain significance (Mar 29, 2022)
11-66668743-C-T		not specified	Uncertain significance (Sep 14, 2022)
11-66668781-C-A		not specified	Uncertain significance (Nov 07, 2022)
11-66668808-T-C		not specified	Uncertain significance (Jun 16, 2023)
11-66668877-A-G		not specified	Uncertain significance (Jul 12, 2023)
11-66668897-A-T		not specified	Uncertain significance (Apr 26, 2024)
11-66668918-G-C		not specified	Uncertain significance (Dec 03, 2021)
11-66668932-T-C		not specified	Likely benign (Nov 08, 2022)
11-66668941-G-C		not specified	Uncertain significance (Sep 14, 2022)
11-66668980-T-C		not specified	Uncertain significance (Feb 26, 2024)
11-66669000-G-A		not specified	Uncertain significance (Feb 07, 2023)
11-66669012-G-A		not specified	Uncertain significance (Jan 03, 2024)
11-66669019-A-G		not specified	Uncertain significance (Jul 06, 2022)
11-66669042-T-C		not specified	Uncertain significance (Sep 14, 2022)
11-66669096-A-G		not specified	Uncertain significance (Jul 14, 2021)
11-66669133-T-C		not specified	Uncertain significance (Dec 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBM4B	protein_coding	protein_coding	ENST00000525754	2	12924

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0236	0.964	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.671	195	223	0.874	0.0000147	2323
Missense in Polyphen		23	41.733	0.55112		494
Synonymous	-1.34	100	84.3	1.19	0.00000539	740
Loss of Function	2.17	5	13.7	0.366	9.04e-7	158

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000239	0.000239
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000794	0.0000791
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for the translational activation of PER1 mRNA in response to circadian clock. Binds directly to the 3'-UTR of the PER1 mRNA (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.259
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.54

Haploinsufficiency Scores

• pHI: 0.351
• hipred: Y
• hipred_score: 0.675
• ghis: 0.620

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rbm4b
• Phenotype: endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: regulation of alternative mRNA splicing, via spliceosome;regulation of translation;circadian rhythm;positive regulation of gene expression;circadian regulation of gene expression;entrainment of circadian clock by photoperiod;mRNA cis splicing, via spliceosome
• Cellular component: nucleoplasm;nucleolus;cytosol;nuclear speck;protein-containing complex
• Molecular function: RNA binding;protein binding;zinc ion binding