RBM25

RNA binding motif protein 25, the group of Spliceosomal A complex|RNA binding motif containing

Basic information

Region (hg38): 14:73058532-73123899

Previous symbols: [ "RNPC7" ]

Links

ENSG00000119707

∙ NCBI:58517 ∙ OMIM:612427 ∙ HGNC:23244 ∙ Uniprot:P49756 ∙ 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 RBM25 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBM25 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			12 clinvar	1 clinvar		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	0

Variants in RBM25

This is a list of pathogenic ClinVar variants found in the RBM25 region.

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

Position	Phenotype	Significance	ClinVar
14-73064954-C-CT	CIC-rearranged sarcoma	not provided (-)	805975
14-73076357-C-T	not specified	Uncertain significance (Dec 15, 2023)	3152272
14-73099382-T-G	not specified	Uncertain significance (Apr 08, 2024)	3313253
14-73103406-G-A	not specified	Uncertain significance (Feb 06, 2023)	2480924
14-73103468-A-G	not specified	Uncertain significance (Mar 15, 2024)	3313252
14-73105920-G-C	not specified	Uncertain significance (Dec 20, 2022)	2387496
14-73106025-T-G	not specified	Uncertain significance (Feb 12, 2024)	3152271
14-73106278-G-C	not specified	Uncertain significance (Sep 12, 2023)	2622815
14-73109367-C-T	not specified	Uncertain significance (Apr 23, 2024)	3313254
14-73109368-G-A	not specified	Uncertain significance (Dec 21, 2023)	3152273
14-73110867-A-C	not specified	Uncertain significance (Nov 10, 2022)	2412549
14-73110939-A-G	not specified	Likely benign (Feb 01, 2023)	2480459
14-73111002-T-C	not specified	Uncertain significance (Jan 26, 2022)	2272637
14-73111017-T-G	not specified	Uncertain significance (Jan 22, 2024)	3152274
14-73111093-A-G	not specified	Uncertain significance (Aug 05, 2023)	2588123
14-73111123-A-G	not specified	Uncertain significance (May 18, 2022)	2290187
14-73111692-A-C	not specified	Uncertain significance (Nov 10, 2022)	2325837
14-73119798-T-G	not specified	Uncertain significance (Jun 11, 2024)	3313255

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBM25	protein_coding	protein_coding	ENST00000261973	18	62979

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	8.70e-10	125733	0	2	125735	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.31	215	481	0.447	0.0000283	5548
Missense in Polyphen		18	79.718	0.2258		949
Synonymous	-0.807	159	147	1.08	0.00000719	1523
Loss of Function	7.16	1	61.7	0.0162	0.00000498	612

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000553	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000553	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: RNA-binding protein that acts as a regulator of alternative pre-mRNA splicing. Involved in apoptotic cell death through the regulation of the apoptotic factor BCL2L1 isoform expression. Modulates the ratio of proapoptotic BCL2L1 isoform S to antiapoptotic BCL2L1 isoform L mRNA expression. When overexpressed, stimulates proapoptotic BCL2L1 isoform S 5'-splice site (5'-ss) selection, whereas its depletion caused the accumulation of antiapoptotic BCL2L1 isoform L. Promotes BCL2L1 isoform S 5'-ss usage through the 5'-CGGGCA-3' RNA sequence. Its association with LUC7L3 promotes U1 snRNP binding to a weak 5' ss in a 5'-CGGGCA-3'-dependent manner. Binds to the exonic splicing enhancer 5'-CGGGCA-3' RNA sequence located within exon 2 of the BCL2L1 pre-mRNA. Also involved in the generation of an abnormal and truncated splice form of SCN5A in heart failure. {ECO:0000269|PubMed:18663000, ECO:0000269|PubMed:21859973}.;
Pathway: Spliceosome - Homo sapiens (human) (Consensus)

Recessive Scores

pRec: 0.141

Intolerance Scores

loftool: 0.194
rvis_EVS: -0.8
rvis_percentile_EVS: 12.24

Haploinsufficiency Scores

pHI: 0.772
hipred: Y
hipred_score: 0.775
ghis: 0.703

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.938

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Rbm25
Phenotype

Gene ontology

Biological process: regulation of alternative mRNA splicing, via spliceosome;mRNA processing;RNA splicing;regulation of apoptotic process
Cellular component: cytoplasm;nuclear speck
Molecular function: RNA binding;mRNA binding;protein binding