RNFT1
protein-codingring finger protein, transmembrane 1, the group of Ring finger proteins
Gene summary
Enables ubiquitin binding activity and ubiquitin protein ligase activity. Involved in positive regulation of ERAD pathway and protein autoubiquitination. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~12.5 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 RNFT1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_016125.4. 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 | 61 | 4 | 65 | |||
| nonsense | 0 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 65 | 5 | 0 | 70 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_057209.3 | 9 | MANE Select | |
| Ensembl | ENSP00000304670.8 | 9 | MANE Select | |
| Ensembl | ENSP00000436533.1 | 3 | Standard | |
| Ensembl | ENSP00000436144.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- protein ubiquitination
Molecular Function
- transferase activity
- metal ion binding
Cellular Component
- endoplasmic reticulum membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000305783
- Coding exons
- 9
- Length
- 12522
- 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 | 0.663 | 197 | 225 | 0.876 | 0.0000108 | 2830 |
| Missense (PolyPhen) | 51 | 55.033 | 0.92672 | 764 | ||
| Synonymous | 1.32 | 62 | 76.7 | 0.809 | 0.00000359 | 812 |
| Loss of Function | 1.83 | 13 | 22.3 | 0.582 | 0.00000112 | 288 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0021 | 0.0020 | notable |
| Latino/Admixed American | 0.00084 | 0.00084 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00034 | 0.00033 | rare |
| Finnish | 0.000098 | 0.000092 | rare |
| European (Non-Finnish) | 0.00047 | 0.00045 | rare |
| South Asian | 0.00014 | 0.00013 | rare |
| Other | 0.00065 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: E3 ubiquitin-protein ligase that acts in the endoplasmic reticulum (ER)-associated degradation (ERAD) pathway, which targets misfolded proteins that accumulate in the endoplasmic reticulum (ER) for ubiquitination and subsequent proteasome- mediated degradation. Protects cells from ER stress-induced apoptosis. {ECO:0000269|PubMed:27485036}.;
Recessive Scores
- pRec
- 0.0942
Intolerance Scores
- LoFtool
- 0.766
- RVIS EVS
- 0
- RVIS percentile EVS
- 53.73
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.489
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |