RBMX2

protein-coding

RNA binding motif protein X-linked 2, the group of RNA binding motif containing

Gene summary

Enables RNA binding activity. Involved in mRNA splicing, via spliceosome. Located in nuclear membrane and nucleolus. Part of U2-type precatalytic spliceosome. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_016024.4

Inheritance

—

ClinVar variants

U:62B:6

Top phenotype

Abnormality of neuronal migration

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chrX:130,401,987-130,413,656

External References & Databases

Ensembl (ENSG00000134597)

Transcript & Mutation Effects

hg38 • Region Span ~11.7 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 RBMX2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 37

not providedTotal: 2

Abnormality of neuronal migrationTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016024.4. 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			3 clinvar	1 clinvar		4
missense			42 clinvar	5 clinvar		47
nonsense			2 clinvar			2
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			14 clinvar			14
Total	0	0	62	6	0	68

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016024.4	RefSeq	NP_057108.2	6	MANE Select
ENST00000305536.11	Ensembl	ENSP00000339090.4	6	MANE Select
ENST00000370947.1	Ensembl	ENSP00000359985.1	3	Standard
ENST00000370947.2	Ensembl	ENSP00000359985.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

mRNA splicing, via spliceosome

Molecular Function

first spliceosomal transesterification activity
RNA binding
protein binding

Cellular Component

U2 snRNP

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000305536
Coding exons: 6
Length: 11375
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.917	100	129	0.773	0.0000107	2110
Missense (PolyPhen)		7	20.079	0.34862		423
Synonymous	0.797	40	47.0	0.852	0.00000356	596
Loss of Function	2.76	0	8.87	0.00	6.26e-7	187

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

Recessive Scores

pRec: 0.396

Intolerance Scores

LoFtool: 0.198
RVIS EVS: 0.17
RVIS percentile EVS: 65.56

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.129

Gene Damage Prediction

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