RBPJL
protein-codingrecombination signal binding protein for immunoglobulin kappa J region like, the group of PTF1 complex
Gene summary
This gene encodes a member of the suppressor of hairless protein family. A similar protein in mouse is a transcription factor that binds to DNA sequences almost identical to that bound by the Notch receptor signaling pathway transcription factor recombining binding protein J. The mouse protein has been shown to activate transcription in concert with Epstein-Barr virus nuclear antigen-2. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
- RBPSUHL
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~11.0 kbGenCC 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 RBPJL variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014276.4. 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 | 1 | 1 | ||||
| missense | 78 | 4 | 82 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 78 | 1 | 4 | 83 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055091.2 | 12 | MANE Select | |
| Ensembl | ENSP00000341243.3 | 12 | MANE Select | |
| RefSeq | NP_001268377.1 | 12 | Standard | |
| RefSeq | NP_001268378.1 | 12 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Th1 and Th2 cell differentiation - Homo sapiens (human)
- Viral carcinogenesis - Homo sapiens (human)
- Notch signaling pathway - Homo sapiens (human)
- Epstein-Barr virus infection - Homo sapiens (human)
- Human papillomavirus infection - Homo sapiens (human)
Biological Process
- signal transduction
- positive regulation of transcription by RNA polymerase II
Molecular Function
- RNA polymerase II proximal promoter sequence-specific DNA binding
- DNA-binding transcription factor activity, RNA polymerase II-specific
- chromatin binding
- DNA-binding transcription factor activity
- sequence-specific DNA binding
Cellular Component
- nucleus
- transcription factor complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000343694
- Coding exons
- 12
- Length
- 10313
- Individuals with no LoFs
- 125621
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 126
- Defined
- 125748
- p
- 0.000505
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.03 | 277 | 330 | 0.840 | 0.0000205 | 3311 |
| Missense (PolyPhen) | 108 | 125.05 | 0.86366 | 1295 | ||
| Synonymous | -0.0784 | 149 | 148 | 1.01 | 0.00000990 | 1080 |
| Loss of Function | 1.23 | 20 | 26.9 | 0.743 | 0.00000140 | 283 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0.00026 | 0.00026 | rare |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0.00027 | 0.00027 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00051 | 0.00048 | rare |
| South Asian | 0.0017 | 0.0017 | notable |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Putative transcription factor, which cooperates with EBNA2 to activate transcription. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.143
Intolerance Scores
- LoFtool
- 0.538
- RVIS EVS
- 1
- RVIS percentile EVS
- 90.69
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.393
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |