RNF19B
protein-codingring finger protein 19B, the group of Ring finger proteins|RBR E3 ubiquitin ligases
Gene summary
This gene encodes a multi-pass membrane protein containing two RING-type and one IBR-type zinc finger motifs. The encoded protin is an E3 ubiquitin-protein ligase that plays a role in the cytotoxic effects of natural killer (NK) cells. Alternative splicing results in multiple transcript variants. There are pseudogenes for this gene on chromosomes X and Y in a possible pseudoautosomal region. [provided by RefSeq, Jul 2014]
- IBRDC3
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~28.4 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 RNF19B variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001300826.2. 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 | 6 | 6 | ||||
| missense | 94 | 1 | 95 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 103 | 1 | 0 | 104 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001287755.1 | 9 | MANE Select | |
| Ensembl | ENSP00000235150.4 | 9 | MANE Select | |
| RefSeq | NP_001120833.1 | 9 | Standard | |
| RefSeq | NP_699172.2 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Immune System
- Adaptive Immune System
- Antigen processing: Ubiquitination & Proteasome degradation
- Class I MHC mediated antigen processing & presentation
Biological Process
- protein polyubiquitination
- adaptive immune response
- ubiquitin-dependent protein catabolic process
- positive regulation of proteasomal ubiquitin-dependent protein catabolic process
Molecular Function
- ubiquitin-protein transferase activity
- protein binding
- ubiquitin conjugating enzyme binding
- metal ion binding
- ubiquitin protein ligase activity
Cellular Component
- ubiquitin ligase complex
- cytoplasm
- endoplasmic reticulum membrane
- cytosol
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000373456
- Coding exons
- 9
- Length
- 28241
- Individuals with no LoFs
- 125715
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 33
- Defined
- 125748
- p
- 0.000131
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.27 | 233 | 353 | 0.660 | 0.0000183 | 4751 |
| Missense (PolyPhen) | 76 | 157.14 | 0.48364 | 1866 | ||
| Synonymous | -0.234 | 135 | 132 | 1.03 | 0.00000740 | 1476 |
| Loss of Function | 3.98 | 4 | 25.9 | 0.155 | 0.00000127 | 331 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00026 | 0.00025 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates, such as UCKL1 (PubMed:16709802, PubMed:27485036). Involved in the cytolytic activity of natural killer cells and cytotoxic T-cells (PubMed:10438909). Protects against staurosporin-induced cell death (PubMed:27485036). {ECO:0000269|PubMed:10438909, ECO:0000269|PubMed:16709802, ECO:0000269|PubMed:27485036}.;
Recessive Scores
- pRec
- 0.0930
Intolerance Scores
- LoFtool
- 0.382
- RVIS EVS
- -0.78
- RVIS percentile EVS
- 12.77
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.732
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |