RBM23

RNA binding motif protein 23, the group of RNA binding motif containing

Basic information

Region (hg38): 14:22893203-22919182

Previous symbols: [ "RNPC4" ]

Links

ENSG00000100461 ∙ NCBI:55147 ∙ ∙ HGNC:20155 ∙ Uniprot:Q86U06 ∙ 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 RBM23 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBM23 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			27	2		29
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			7			7
Total	0	0	35	2	0

Variants in RBM23

This is a list of pathogenic ClinVar variants found in the RBM23 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-22901833-G-A		not specified	Uncertain significance (Jun 07, 2023)
14-22901871-G-A		not specified	Uncertain significance (Feb 17, 2024)
14-22902006-C-T		not specified	Uncertain significance (May 16, 2022)
14-22902276-C-A		not specified	Uncertain significance (Aug 31, 2022)
14-22902291-T-G		not specified	Uncertain significance (May 15, 2024)
14-22902309-C-G		not specified	Uncertain significance (Sep 01, 2021)
14-22902338-A-C		not specified	Uncertain significance (Apr 11, 2023)
14-22902358-G-A		not specified	Uncertain significance (Apr 26, 2023)
14-22904286-C-T		not specified	Uncertain significance (Dec 21, 2022)
14-22904287-G-A		not specified	Uncertain significance (Oct 12, 2021)
14-22904292-G-A		not specified	Uncertain significance (Apr 19, 2023)
14-22904876-T-C		not specified	Uncertain significance (Feb 17, 2022)
14-22904963-T-C		not specified	Likely benign (Aug 16, 2022)
14-22904984-G-C		not specified	Uncertain significance (Dec 15, 2023)
14-22904987-A-T		not specified	Uncertain significance (Feb 16, 2023)
14-22905111-T-C		not specified	Uncertain significance (May 29, 2024)
14-22905159-G-C		not specified	Uncertain significance (Sep 16, 2021)
14-22905231-T-C		not specified	Uncertain significance (Sep 20, 2023)
14-22905240-C-T		not specified	Uncertain significance (Sep 27, 2022)
14-22905370-C-T		not specified	Uncertain significance (Mar 07, 2023)
14-22905376-C-T		not specified	Uncertain significance (Jan 31, 2024)
14-22905416-C-A		not specified	Uncertain significance (Dec 14, 2023)
14-22905421-C-T		not specified	Uncertain significance (Feb 27, 2023)
14-22906237-C-T		not specified	Likely benign (May 02, 2024)
14-22906238-G-A		not specified	Uncertain significance (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBM23	protein_coding	protein_coding	ENST00000359890	13	18540

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.82e-11	0.574	124618	0	198	124816	0.000793

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.471	310	288	1.08	0.0000190	2862
Missense in Polyphen		57	49.785	1.1449		530
Synonymous	0.00965	91	91.1	0.999	0.00000455	885
Loss of Function	1.36	20	27.7	0.722	0.00000187	262

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00161	0.00161
Ashkenazi Jewish	0.000795	0.000795
East Asian	0.000389	0.000389
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000584	0.000574
Middle Eastern	0.000389	0.000389
South Asian	0.00431	0.00245
Other	0.000826	0.000824

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable RNA-binding protein. May be involved in pre- mRNA splicing process.

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.960
• rvis_EVS: -0.13
• rvis_percentile_EVS: 43.91

Haploinsufficiency Scores

• pHI: 0.127
• hipred: N
• hipred_score: 0.352
• ghis: 0.517

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000281

Gene Damage Prediction

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

Gene ontology

• Biological process: mRNA processing;3'-UTR-mediated mRNA destabilization
• Cellular component: nucleus;cytoplasmic stress granule;membrane;ribonucleoprotein complex
• Molecular function: RNA binding;mRNA binding;protein binding;U1 snRNP binding