RBMXL2

RBMX like 2, the group of RNA binding motif containing

Basic information

Region (hg38): 11:7088998-7091148

Links

ENSG00000170748 ∙ NCBI:27288 ∙ OMIM:605444 ∙ HGNC:17886 ∙ Uniprot:O75526 ∙ 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 RBMXL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBMXL2 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					1	1
missense			40	1	2	43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	40	1	5

Variants in RBMXL2

This is a list of pathogenic ClinVar variants found in the RBMXL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-7089006-C-G			Benign (Jun 21, 2021)
11-7089012-G-C			Benign (Jun 20, 2021)
11-7089131-C-G		not specified	Uncertain significance (May 25, 2022)
11-7089132-G-A			Benign (Nov 12, 2018)
11-7089316-G-A		not specified	Uncertain significance (Mar 25, 2024)
11-7089317-C-T			Benign (Jun 10, 2021)
11-7089323-A-C		not specified	Uncertain significance (Jun 17, 2024)
11-7089346-G-A		not specified	Uncertain significance (Jan 19, 2024)
11-7089392-G-A		not specified	Uncertain significance (Nov 10, 2024)
11-7089397-C-T		not specified	Uncertain significance (Nov 22, 2023)
11-7089403-G-T		not specified	Uncertain significance (Dec 03, 2021)
11-7089404-G-A		not specified	Uncertain significance (Dec 22, 2023)
11-7089419-G-C		not specified	Uncertain significance (Sep 16, 2021)
11-7089490-C-G		not specified	Uncertain significance (Sep 16, 2021)
11-7089494-G-C		not specified	Uncertain significance (Jul 27, 2024)
11-7089503-A-T		not specified	Uncertain significance (Apr 25, 2022)
11-7089520-A-G			Benign (Jun 09, 2021)
11-7089539-G-A		not specified	Uncertain significance (Nov 09, 2021)
11-7089613-G-A		not specified	Uncertain significance (Jun 29, 2023)
11-7089614-C-T		not specified	Uncertain significance (Feb 03, 2022)
11-7089639-C-G		not specified	Uncertain significance (Dec 11, 2023)
11-7089643-G-C		not specified	Uncertain significance (May 09, 2023)
11-7089653-G-A		not specified	Uncertain significance (Nov 15, 2021)
11-7089668-C-G		not specified	Uncertain significance (Dec 22, 2023)
11-7089700-C-A		not specified	Uncertain significance (Jan 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBMXL2	protein_coding	protein_coding	ENST00000306904	1	2215

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0748	0.915	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.242	253	264	0.958	0.0000209	2386
Missense in Polyphen		16	30.477	0.52499		285
Synonymous	-0.344	123	118	1.04	0.00000987	873
Loss of Function	2.23	4	12.5	0.320	9.96e-7	107

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

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

Haploinsufficiency Scores

• pHI: 0.139
• hipred: Y
• hipred_score: 0.507
• ghis: 0.422

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.460

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rbmxl2

Gene ontology

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