RBMXL3

RBMX like 3, the group of RNA binding motif containing

Basic information

Region (hg38): X:115189410-115192868

Previous symbols: [ "CXorf55" ]

Links

ENSG00000175718 ∙ NCBI:139804 ∙ ∙ HGNC:26859 ∙ Uniprot:Q8N7X1 ∙ 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 RBMXL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBMXL3 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				11		11
missense			122	9		131
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	122	21	0

Variants in RBMXL3

This is a list of pathogenic ClinVar variants found in the RBMXL3 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-115189446-T-C		not specified	Uncertain significance (Feb 22, 2023)
X-115189478-G-A		not specified	Uncertain significance (Feb 12, 2024)
X-115189625-G-A		not specified	Uncertain significance (Jan 31, 2024)
X-115189683-T-G		not specified	Uncertain significance (Apr 12, 2024)
X-115189710-A-G		not specified	Uncertain significance (Oct 13, 2023)
X-115189716-G-A		not specified	Uncertain significance (Jun 23, 2023)
X-115189736-C-T		not specified	Uncertain significance (Mar 29, 2023)
X-115189739-G-A		not specified	Uncertain significance (Nov 12, 2021)
X-115189754-T-C		not specified	Uncertain significance (Feb 02, 2024)
X-115189803-C-T			Likely benign (Feb 01, 2023)
X-115189833-G-A		not specified	Likely benign (Oct 06, 2021)
X-115189835-G-A		not specified	Uncertain significance (Apr 08, 2022)
X-115189841-G-T		not specified	Uncertain significance (Oct 29, 2021)
X-115189842-C-T		not specified	Uncertain significance (Jul 15, 2021)
X-115189904-C-T		not specified	Uncertain significance (Mar 20, 2024)
X-115189929-A-C		not specified	Uncertain significance (Oct 12, 2022)
X-115189944-C-T		not specified	Uncertain significance (Jan 09, 2024)
X-115189976-C-T		not specified	Uncertain significance (Mar 06, 2023)
X-115189977-G-C		not specified	Uncertain significance (Apr 04, 2024)
X-115190030-C-T		not specified	Uncertain significance (May 20, 2024)
X-115190042-G-A		not specified	Uncertain significance (Sep 26, 2023)
X-115190045-C-A		not specified	Uncertain significance (Jan 26, 2022)
X-115190075-A-G		not specified	Uncertain significance (May 29, 2024)
X-115190088-T-C		not specified	Uncertain significance (Jun 16, 2024)
X-115190093-G-A		not specified	Uncertain significance (Oct 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBMXL3	protein_coding	protein_coding	ENST00000424776	1	3469

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.839	601	546	1.10	0.0000546	6844
Missense in Polyphen		82	83.278	0.98465		1224
Synonymous	-1.23	256	232	1.10	0.0000247	2141
Loss of Function

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Pathway: Spliceosome - Homo sapiens (human) (Consensus)

Intolerance Scores

• rvis_EVS: 4.93
• rvis_percentile_EVS: 99.81

Haploinsufficiency Scores

• pHI: 0.0947
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Biological process: mRNA splicing, via spliceosome
• Molecular function: mRNA binding