RBM3

RNA binding motif protein 3, the group of RNA binding motif containing

Basic information

Region (hg38): X:48574448-48581162

Links

ENSG00000102317 ∙ NCBI:5935 ∙ OMIM:300027 ∙ HGNC:9900 ∙ Uniprot:P98179 ∙ 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 RBM3 gene.

• Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBM3 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in RBM3

This is a list of pathogenic ClinVar variants found in the RBM3 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-48576371-A-G		not specified	Uncertain significance (Apr 04, 2023)
X-48576387-G-C		not specified	Uncertain significance (Mar 31, 2023)
X-48576410-T-C		not specified	Uncertain significance (May 18, 2022)
X-48576577-A-G		not specified	Uncertain significance (Oct 06, 2022)
X-48577075-T-C		not specified	Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBM3	protein_coding	protein_coding	ENST00000376759	5	4618

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.826	0.170	119397	0	3	119400	0.0000126

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.32	37	67.5	0.548	0.00000551	1003
Missense in Polyphen		6	14.172	0.42338		252
Synonymous	-0.153	23	22.1	1.04	0.00000157	309
Loss of Function	2.23	0	5.77	0.00	4.15e-7	110

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000739	0.0000560
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000739	0.0000560
South Asian	0.0000630	0.0000352
Other	0.000253	0.000171

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cold-inducible mRNA binding protein that enhances global protein synthesis at both physiological and mild hypothermic temperatures. Reduces the relative abundance of microRNAs, when overexpressed. Enhances phosphorylation of translation initiation factors and active polysome formation (By similarity). {ECO:0000250}.
• Pathway: EGFR1 (Consensus)

Intolerance Scores

• loftool: 0.378
• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.2

Haploinsufficiency Scores

• pHI: 0.348
• hipred: N
• hipred_score: 0.278
• ghis: 0.501

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.991

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rbm3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; cellular phenotype

Gene ontology

• Biological process: RNA processing;regulation of translation;response to cold;negative regulation of translation;positive regulation of translation;positive regulation of mRNA splicing, via spliceosome
• Cellular component: nucleus;nucleoplasm;spliceosomal complex;nucleolus;cytoplasm;large ribosomal subunit;dendrite;ribonucleoprotein complex
• Molecular function: RNA binding;mRNA 3'-UTR binding;protein binding;poly(U) RNA binding;translation repressor activity;ribosomal large subunit binding;small ribosomal subunit rRNA binding