RBM41

RNA binding motif protein 41, the group of RNA binding motif containing

Basic information

Region (hg38): X:107052095-107118823

Links

ENSG00000089682 ∙ NCBI:55285 ∙ ∙ HGNC:25617 ∙ Uniprot:Q96IZ5 ∙ 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 RBM41 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBM41 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			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	0

Variants in RBM41

This is a list of pathogenic ClinVar variants found in the RBM41 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-107067595-A-G		not specified	Uncertain significance (Dec 15, 2023)
X-107067597-C-T		not specified	Likely benign (Jun 01, 2023)
X-107067604-T-C		not specified	Uncertain significance (Sep 26, 2023)
X-107067633-A-G		not specified	Uncertain significance (Apr 27, 2022)
X-107067661-C-T		not specified	Uncertain significance (Jun 11, 2021)
X-107069280-C-G		not specified	Uncertain significance (Feb 19, 2025)
X-107069357-G-A		not specified	Uncertain significance (Jan 04, 2024)
X-107069375-G-A			Likely benign (-)
X-107069381-T-C		not specified	Uncertain significance (Dec 06, 2022)
X-107088449-C-G		not specified	Uncertain significance (Dec 31, 2024)
X-107088458-T-C		not specified	Uncertain significance (Oct 20, 2023)
X-107088471-T-C		not specified	Uncertain significance (Nov 22, 2023)
X-107088484-G-C		not specified	Uncertain significance (Jul 20, 2022)
X-107088659-A-G		not specified	Uncertain significance (Jan 04, 2024)
X-107088719-G-A		not specified	Uncertain significance (Nov 10, 2021)
X-107088794-T-C		not specified	Uncertain significance (Oct 06, 2022)
X-107088805-C-G		not specified	Uncertain significance (Apr 15, 2024)
X-107115487-C-G		not specified	Uncertain significance (Oct 30, 2023)
X-107115963-G-T		not specified	Uncertain significance (Feb 13, 2024)
X-107116047-A-C		not specified	Uncertain significance (Dec 21, 2023)
X-107116680-T-C		not specified	Uncertain significance (Jun 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBM41	protein_coding	protein_coding	ENST00000372479	7	54408

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.966	0.0345	125263	1	3	125267	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.683	131	155	0.846	0.0000117	2728
Missense in Polyphen		35	54.102	0.64693		928
Synonymous	-0.581	57	51.7	1.10	0.00000355	776
Loss of Function	3.33	1	14.9	0.0672	0.00000124	241

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000811	0.0000616
Ashkenazi Jewish	0.000135	0.0000996
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000252	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May bind RNA. {ECO:0000305}.

Recessive Scores

• pRec: 0.0959

Intolerance Scores

• loftool: 0.653
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.75

Haploinsufficiency Scores

• pHI: 0.130
• hipred: Y
• hipred_score: 0.533
• ghis: 0.610

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.747

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rbm41
• Phenotype: normal phenotype

Gene ontology

• Biological process: mRNA splicing, via spliceosome
• Cellular component: U12-type spliceosomal complex
• Molecular function: protein binding;U12 snRNA binding;pre-mRNA intronic binding