RBM4

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

Basic information

Region (hg38): 11:66638667-66668374

Links

ENSG00000173933

∙ NCBI:5936 ∙ OMIM:602571 ∙ HGNC:9901 ∙ Uniprot:Q9BWF3 ∙ 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 RBM4 gene.

not_specified (10 variants)
not_provided (1 variants)
Myoepithelial_tumor (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBM4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002896.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			11 clinvar			11
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	11	1	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBM4	protein_coding	protein_coding	ENST00000409406	2	50057

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.990	0.00994	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.98	161	249	0.647	0.0000174	2338
Missense in Polyphen		33	58.368	0.56538		580
Synonymous	-0.405	113	108	1.05	0.00000799	766
Loss of Function	3.45	0	13.9	0.00	7.58e-7	162

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000555	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000354	0.0000352
Middle Eastern	0.0000555	0.0000544
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: RNA-binding factor involved in multiple aspects of cellular processes like alternative splicing of pre-mRNA and translation regulation. Modulates alternative 5'-splice site and exon selection. Acts as a muscle cell differentiation-promoting factor. Activates exon skipping of the PTB pre-mRNA during muscle cell differentiation. Antagonizes the activity of the splicing factor PTBP1 to modulate muscle cell-specific exon selection of alpha tropomyosin. Binds to intronic pyrimidine-rich sequence of the TPM1 and MAPT pre-mRNAs. Required for the translational activation of PER1 mRNA in response to circadian clock. Binds directly to the 3'-UTR of the PER1 mRNA. Exerts a suppressive activity on Cap-dependent translation via binding to CU-rich responsive elements within the 3'UTR of mRNAs, a process increased under stress conditions or during myocytes differentiation. Recruits EIF4A1 to stimulate IRES-dependent translation initiation in respons to cellular stress. Associates to internal ribosome entry segment (IRES) in target mRNA species under stress conditions. Plays a role for miRNA-guided RNA cleavage and translation suppression by promoting association of AGO2- containing miRNPs with their cognate target mRNAs. Associates with miRNAs during muscle cell differentiation. Binds preferentially to 5'-CGCGCG[GCA]-3' motif in vitro. {ECO:0000269|PubMed:12628928, ECO:0000269|PubMed:16260624, ECO:0000269|PubMed:16777844, ECO:0000269|PubMed:16934801, ECO:0000269|PubMed:17284590, ECO:0000269|PubMed:17932509, ECO:0000269|PubMed:19801630, ECO:0000269|PubMed:21343338, ECO:0000269|PubMed:21518792}.;

Recessive Scores

pRec: 0.147

Intolerance Scores

loftool
rvis_EVS: -0.52
rvis_percentile_EVS: 21.2

Haploinsufficiency Scores

pHI: 0.617
hipred: Y
hipred_score: 0.743
ghis: 0.501

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.955

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

Gene name: Rbm4
Phenotype: homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; hematopoietic system phenotype; growth/size/body region phenotype; immune system phenotype;

Gene ontology

Biological process: regulation of alternative mRNA splicing, via spliceosome;cap-independent translational initiation;IRES-dependent translational initiation of linear mRNA;RNA processing;negative regulation of translation;cell differentiation;negative regulation of translation in response to stress;miRNA mediated inhibition of translation;entrainment of circadian clock by photoperiod;mRNA cis splicing, via spliceosome;negative regulation of translational initiation;response to arsenic-containing substance;regulation of nucleocytoplasmic transport;positive regulation of muscle cell differentiation;circadian regulation of translation
Cellular component: nucleus;nucleoplasm;nucleolus;cytoplasm;cytosol;cytoplasmic stress granule;nuclear speck
Molecular function: RNA binding;mRNA binding;mRNA 3'-UTR binding;protein binding;zinc ion binding;cyclin binding;miRNA binding;pre-mRNA intronic binding;pre-mRNA intronic pyrimidine-rich binding