RBMXL3

protein-coding

RBMX like 3, the group of RNA binding motif containing

Gene summary

Enables RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be located in organelle. Predicted to be part of ribonucleoprotein complex. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

CXorf55

MANE transcript

NM_001145346.2

Inheritance

—

ClinVar variants

U:266B:32

Top phenotype

Kleine-Levin syndrome

gnomAD constraint

pLI —, LoF o/e —

Max pathogenic AF

—

Genomic locus

chrX:115,189,410-115,192,868

External References & Databases

Ensembl (ENSG00000175718)

Transcript & Mutation Effects

hg38 • Region Span ~3.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RBMXL3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 282

not providedTotal: 23

Kleine-Levin syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001145346.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				16 clinvar		16
missense			266 clinvar	16 clinvar		282
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	266	32	0	298

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001145346.2	RefSeq	NP_001138818.1	1	MANE Select
ENST00000424776.5	Ensembl	ENSP00000417451.3	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Spliceosome - Homo sapiens (human)

Biological Process

mRNA splicing, via spliceosome

Molecular Function

mRNA binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000424776
Coding exons: 1
Length: 3469

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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 4.93
RVIS percentile EVS: 99.81

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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