RBMX
RNA binding motif protein X-linked, the group of RNA binding motif containing|Small nucleolar RNA protein coding host genes|Heterogeneous nuclear ribonucleoproteins
Basic information
Region (hg38): X:136848004-136880764
Links
Phenotypes
GenCC
Source:
- syndromic X-linked intellectual disability Shashi type (Moderate), mode of inheritance: XL
- syndromic X-linked intellectual disability Shashi type (Limited), mode of inheritance: Unknown
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Intellectual developmental disorder, X-linked, syndromic 11 (Shashi type); Intellectual developmental disorder, X-linked syndromic, Gustavson type | XL | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Audiologic/Otolaryngologic; Craniofacial; Musculoskeletal; Neurologic | 10677307; 25256757; 37277488 |
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn_genetic_diseases (12 variants)
- Syndromic_X-linked_intellectual_disability_Shashi_type (10 variants)
- not_specified (7 variants)
- not_provided (4 variants)
- RBMX-related_disorder (2 variants)
- Severe_X-linked_intellectual_disability,_Gustavson_type (2 variants)
- CIC-rearranged_sarcoma (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBMX gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002139.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 5 | |||||
| missense | 19 | 20 | ||||
| nonsense | 0 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 2 | |||||
| Total | 1 | 1 | 23 | 4 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RBMX | protein_coding | protein_coding | ENST00000320676 | 8 | 32761 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.829 | 0.171 | 124927 | 0 | 3 | 124930 | 0.0000120 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.90 | 62 | 168 | 0.369 | 0.0000139 | 2424 |
| Missense in Polyphen | 18 | 43.401 | 0.41474 | 733 | ||
| Synonymous | -0.498 | 54 | 49.5 | 1.09 | 0.00000353 | 809 |
| Loss of Function | 3.05 | 2 | 14.6 | 0.137 | 0.00000127 | 258 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000367 | 0.0000367 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000263 | 0.0000177 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: RNA-binding protein that plays several role in the regulation of pre- and post-transcriptional processes. Implicated in tissue-specific regulation of gene transcription and alternative splicing of several pre-mRNAs. Binds to and stimulates transcription from the tumor suppressor TXNIP gene promoter; may thus be involved in tumor suppression. When associated with SAFB, binds to and stimulates transcription from the SREBF1 promoter. Associates with nascent mRNAs transcribed by RNA polymerase II. Component of the supraspliceosome complex that regulates pre-mRNA alternative splice site selection. Can either activate or suppress exon inclusion; acts additively with TRA2B to promote exon 7 inclusion of the survival motor neuron SMN2. Represses the splicing of MAPT/Tau exon 10. Binds preferentially to single- stranded 5'-CC[A/C]-rich RNA sequence motifs localized in a single-stranded conformation; probably binds RNA as a homodimer. Binds non-specifically to pre-mRNAs. Plays also a role in the cytoplasmic TNFR1 trafficking pathways; promotes both the IL-1- beta-mediated inducible proteolytic cleavage of TNFR1 ectodomains and the release of TNFR1 exosome-like vesicles to the extracellular compartment. {ECO:0000269|PubMed:12165565, ECO:0000269|PubMed:12761049, ECO:0000269|PubMed:16707624, ECO:0000269|PubMed:18445477, ECO:0000269|PubMed:18541147, ECO:0000269|PubMed:19282290, ECO:0000269|PubMed:21327109}.;
- Disease
- DISEASE: Mental retardation, X-linked, syndromic, 11 (MRXS11) [MIM:300238]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRXS11 patients manifest moderate intellectual disability and craniofacial dysmorphism. {ECO:0000269|PubMed:25256757}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Spliceosome - Homo sapiens (human);mRNA Processing;Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Intolerance Scores
- loftool
- 0.132
- rvis_EVS
- 0.33
- rvis_percentile_EVS
- 73.11
Haploinsufficiency Scores
- pHI
- 0.261
- hipred
- Y
- hipred_score
- 0.698
- ghis
- 0.540
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.970
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rbmx
- Phenotype
- homeostasis/metabolism phenotype; growth/size/body region phenotype; immune system phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Gene ontology
- Biological process
- regulation of alternative mRNA splicing, via spliceosome;mRNA splicing, via spliceosome;osteoblast differentiation;transcription by RNA polymerase II;mRNA splice site selection;membrane protein ectodomain proteolysis;RNA metabolic process;positive regulation of transcription by RNA polymerase II;negative regulation of mRNA splicing, via spliceosome;positive regulation of mRNA splicing, via spliceosome;protein complex oligomerization;protein homooligomerization;cellular response to interleukin-1
- Cellular component
- extracellular space;nucleus;nucleoplasm;spliceosomal complex;nuclear euchromatin;membrane;supraspliceosomal complex;extracellular exosome;catalytic step 2 spliceosome;ribonucleoprotein complex
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;chromatin binding;RNA binding;single-stranded RNA binding;mRNA binding;protein binding;protein domain specific binding;identical protein binding