RBMX2

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

Basic information

Region (hg38): X:130401987-130413656

Links

ENSG00000134597 ∙ NCBI:51634 ∙ ∙ HGNC:24282 ∙ Uniprot:Q9Y388 ∙ 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 RBMX2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBMX2 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			19	3		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	19	3	0

Variants in RBMX2

This is a list of pathogenic ClinVar variants found in the RBMX2 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-130402255-C-T		not specified	Likely benign (Jul 11, 2023)
X-130402285-G-C		not specified	Uncertain significance (Apr 09, 2024)
X-130402319-G-T		not specified	Uncertain significance (Nov 21, 2024)
X-130402342-G-C		not specified	Uncertain significance (Nov 29, 2021)
X-130409342-C-A		not specified	Uncertain significance (Feb 11, 2025)
X-130409354-A-G		not specified	Uncertain significance (Dec 06, 2024)
X-130409363-G-A		not specified	Uncertain significance (Oct 29, 2021)
X-130411460-G-A		not specified	Likely benign (May 26, 2024)
X-130411514-A-G		not specified	Uncertain significance (Dec 22, 2023)
X-130411524-A-C		not specified	Uncertain significance (Nov 14, 2024)
X-130412408-C-T		not specified	Uncertain significance (Mar 15, 2024)
X-130412451-G-A		not specified	Uncertain significance (Jun 19, 2024)
X-130412468-A-G		not specified	Uncertain significance (Dec 26, 2023)
X-130412483-C-T		not specified	Likely benign (Jan 03, 2024)
X-130412484-C-T		not specified	Uncertain significance (Aug 20, 2024)
X-130412691-G-A		not specified	Uncertain significance (Oct 29, 2021)
X-130412716-G-C		not specified	Uncertain significance (Aug 20, 2024)
X-130412718-A-T		not specified	Uncertain significance (Aug 20, 2024)
X-130412726-C-T		not specified	Uncertain significance (Apr 06, 2024)
X-130412739-G-A		Abnormality of neuronal migration	Likely benign (-)
X-130412757-G-A		not specified	Uncertain significance (Jul 08, 2022)
X-130412790-G-A		not specified	Likely benign (Feb 17, 2025)
X-130412804-C-T		not specified	Uncertain significance (Mar 10, 2025)
X-130412811-G-A		not specified	Uncertain significance (Dec 15, 2023)
X-130412820-C-G		not specified	Uncertain significance (Jan 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBMX2	protein_coding	protein_coding	ENST00000305536	6	11375

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.939	0.0608	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.917	100	129	0.773	0.0000107	2110
Missense in 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

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.396

Intolerance Scores

• loftool: 0.198
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.56

Haploinsufficiency Scores

• pHI: 0.0606
• hipred: Y
• hipred_score: 0.594
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.129

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rbmx2

Gene ontology

• Biological process: mRNA splicing, via spliceosome
• Cellular component: U2 snRNP
• Molecular function: first spliceosomal transesterification activity;RNA binding;protein binding