RBMXL1

RBMX like 1, the group of RNA binding motif containing

Basic information

Region (hg38): 1:88979456-88992960

Links

ENSG00000213516 ∙ NCBI:494115 ∙ ∙ HGNC:25073 ∙ Uniprot:Q96E39 ∙ 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 RBMXL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBMXL1 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			30			30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	0	0

Variants in RBMXL1

This is a list of pathogenic ClinVar variants found in the RBMXL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-88982677-C-T		not specified	Uncertain significance (Aug 23, 2021)
1-88982682-T-C		not specified	Uncertain significance (May 04, 2023)
1-88982724-C-T		not specified	Uncertain significance (Oct 22, 2021)
1-88982746-C-T		not specified	Uncertain significance (Apr 01, 2024)
1-88982778-G-C		not specified	Uncertain significance (Sep 27, 2021)
1-88982838-C-T		not specified	Uncertain significance (Aug 30, 2022)
1-88982868-T-C		not specified	Uncertain significance (Oct 27, 2023)
1-88982871-C-G		not specified	Uncertain significance (Nov 08, 2021)
1-88982883-C-A		not specified	Uncertain significance (Aug 02, 2022)
1-88982905-T-G		not specified	Uncertain significance (Jan 04, 2024)
1-88982967-C-T		not specified	Uncertain significance (Nov 21, 2022)
1-88983111-C-A		not specified	Uncertain significance (Aug 02, 2023)
1-88983111-C-T		not specified	Uncertain significance (Apr 10, 2023)
1-88983135-G-A		not specified	Uncertain significance (Dec 03, 2021)
1-88983147-C-T		not specified	Uncertain significance (Nov 17, 2022)
1-88983158-T-G		not specified	Uncertain significance (Nov 09, 2023)
1-88983172-T-C		not specified	Uncertain significance (Jan 10, 2023)
1-88983195-T-C		not specified	Uncertain significance (Jan 29, 2024)
1-88983234-G-A		not specified	Uncertain significance (Nov 27, 2023)
1-88983263-A-C		not specified	Uncertain significance (Dec 26, 2023)
1-88983274-G-A		not specified	Uncertain significance (Oct 25, 2022)
1-88983274-G-C		not specified	Uncertain significance (Mar 28, 2023)
1-88983289-T-C		not specified	Uncertain significance (Mar 04, 2024)
1-88983343-G-A		not specified	Uncertain significance (Dec 13, 2023)
1-88983343-G-C		not specified	Uncertain significance (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBMXL1	protein_coding	protein_coding	ENST00000399794	1	13505

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0293	0.928	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.335	201	215	0.936	0.0000134	2422
Missense in Polyphen		30	37.804	0.79356		497
Synonymous	-0.685	78	70.7	1.10	0.00000375	825
Loss of Function	1.75	4	9.95	0.402	9.36e-7	143

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.000163	0.000163
South Asian	0.000163	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-binding protein which may be involved in pre-mRNA splicing. {ECO:0000250}.
• Pathway: Spliceosome - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.423
• rvis_EVS: 0.73
• rvis_percentile_EVS: 86.08

Haploinsufficiency Scores

• pHI: 0.201
• hipred: Y
• hipred_score: 0.546
• ghis: 0.521

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.165

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;RNA splicing;positive regulation of mRNA splicing, via spliceosome
• Cellular component: nucleus;spliceosomal complex;ribonucleoprotein complex
• Molecular function: RNA binding