YBX1
Y-box binding protein 1, the group of U11 small nuclear ribonucleoprotein|Y-box binding proteins|U11/U12 di-snRNP
Basic information
Region (hg38): 1:42682418-42703805
Previous symbols: [ "NSEP1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the YBX1 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 | 17 | 17 | ||||
| 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 | 17 | 0 | 0 |
Variants in YBX1
This is a list of pathogenic ClinVar variants found in the YBX1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-42682609-C-G | not specified | Uncertain significance (Jan 30, 2024) | ||
| 1-42682620-G-C | not specified | Uncertain significance (Oct 20, 2024) | ||
| 1-42682623-C-T | not specified | Uncertain significance (Nov 17, 2022) | ||
| 1-42682630-C-T | not specified | Uncertain significance (Feb 28, 2025) | ||
| 1-42682636-A-C | not specified | Uncertain significance (Nov 11, 2024) | ||
| 1-42682653-A-T | not specified | Uncertain significance (Oct 16, 2024) | ||
| 1-42682674-G-A | not specified | Uncertain significance (Jan 23, 2023) | ||
| 1-42682712-C-T | YBX1-related disorder | Likely benign (Nov 22, 2023) | ||
| 1-42682720-A-G | not specified | Uncertain significance (Jan 17, 2025) | ||
| 1-42682721-G-C | not specified | Uncertain significance (Feb 11, 2025) | ||
| 1-42682725-G-A | not specified | Uncertain significance (Dec 19, 2023) | ||
| 1-42696223-A-T | not specified | Uncertain significance (Nov 25, 2024) | ||
| 1-42696666-G-C | not specified | Uncertain significance (Apr 22, 2022) | ||
| 1-42696741-A-G | not specified | Uncertain significance (Jun 21, 2023) | ||
| 1-42696753-C-T | not specified | Uncertain significance (Dec 01, 2022) | ||
| 1-42696794-A-G | YBX1-related disorder | Likely benign (Jul 31, 2019) | ||
| 1-42696824-A-C | not specified | Uncertain significance (Oct 10, 2023) | ||
| 1-42696881-G-T | not specified | Uncertain significance (Dec 07, 2024) | ||
| 1-42697195-G-A | not specified | Uncertain significance (Apr 16, 2024) | ||
| 1-42697202-G-T | YBX1-related disorder | Benign (Jun 23, 2020) | ||
| 1-42700781-G-A | not specified | Likely benign (May 23, 2024) | ||
| 1-42700815-G-A | not specified | Uncertain significance (Jan 31, 2025) | ||
| 1-42700869-C-T | not specified | Uncertain significance (Sep 30, 2024) | ||
| 1-42701007-G-A | not specified | Uncertain significance (May 06, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| YBX1 | protein_coding | protein_coding | ENST00000321358 | 7 | 19923 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.946 | 0.0535 | 125744 | 0 | 4 | 125748 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.72 | 118 | 183 | 0.644 | 0.0000119 | 2086 |
| Missense in Polyphen | 26 | 44.485 | 0.58447 | 595 | ||
| Synonymous | 0.294 | 57 | 59.9 | 0.952 | 0.00000352 | 642 |
| Loss of Function | 3.50 | 2 | 18.1 | 0.111 | 0.00000108 | 196 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000881 | 0.00000879 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Mediates pre-mRNA alternative splicing regulation. Binds to splice sites in pre-mRNA and regulates splice site selection. Binds and stabilizes cytoplasmic mRNA. Contributes to the regulation of translation by modulating the interaction between the mRNA and eukaryotic initiation factors (By similarity). Regulates the transcription of numerous genes. Its transcriptional activity on the multidrug resistance gene MDR1 is enhanced in presence of the APEX1 acetylated form at 'Lys-6' and 'Lys-7'. Binds to promoters that contain a Y-box (5'-CTGATTGGCCAA-3'), such as MDR1 and HLA class II genes. Promotes separation of DNA strands that contain mismatches or are modified by cisplatin. Has endonucleolytic activity and can introduce nicks or breaks into double-stranded DNA (in vitro). May play a role in DNA repair. Component of the CRD-mediated complex that promotes MYC mRNA stability. Binds preferentially to the 5'-[CU]CUGCG-3' motif in vitro. {ECO:0000250, ECO:0000269|PubMed:10817758, ECO:0000269|PubMed:11698476, ECO:0000269|PubMed:12604611, ECO:0000269|PubMed:14718551, ECO:0000269|PubMed:18335541, ECO:0000269|PubMed:18809583, ECO:0000269|PubMed:19029303, ECO:0000269|PubMed:19483673}.;
- Pathway
- Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;MECP2 and Associated Rett Syndrome;mRNA Processing;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;Signal Transduction;Metabolism of RNA;mRNA Splicing - Major Pathway;Noncanonical activation of NOTCH3;NOTCH3 Activation and Transmission of Signal to the Nucleus;Signaling by NOTCH3;Signaling by NOTCH;transcriptional activation of dbpb from mrna;IL2;mRNA Splicing - Minor Pathway;mRNA Splicing;Signaling events mediated by PTP1B;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Intolerance Scores
- loftool
- 0.451
- rvis_EVS
- 0.28
- rvis_percentile_EVS
- 71.08
Haploinsufficiency Scores
- pHI
- 0.934
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.485
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.948
Mouse Genome Informatics
- Gene name
- Ybx1
- Phenotype
- homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); embryo phenotype; skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); liver/biliary system phenotype; respiratory system phenotype;
Zebrafish Information Network
- Gene name
- ybx1
- Affected structure
- whole organism
- Phenotype tag
- abnormal
- Phenotype quality
- decreased life span
Gene ontology
- Biological process
- mRNA splicing, via spliceosome;regulation of transcription, DNA-templated;transcription by RNA polymerase II;Notch signaling pathway;positive regulation of transcription by RNA polymerase II;positive regulation of cell division;CRD-mediated mRNA stabilization;protein localization to cytoplasmic stress granule
- Cellular component
- extracellular region;nucleus;nucleoplasm;U12-type spliceosomal complex;cytoplasm;cytosol;cytoplasmic stress granule;nuclear membrane;intracellular membrane-bounded organelle;extracellular exosome;CRD-mediated mRNA stability complex;histone pre-mRNA 3'end processing complex;ribonucleoprotein complex
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;double-stranded DNA binding;single-stranded DNA binding;DNA-binding transcription factor activity;RNA binding;protein binding;GTPase binding