TRIM16
protein-codingtripartite motif containing 16, the group of Tripartite motif family
Gene summary
The protein encoded by this gene is a tripartite motif (TRIM) family member that contains two B box domains and a coiled-coiled region that are characteristic of the B box zinc finger protein family. While it lacks a RING domain found in other TRIM proteins, the encoded protein can homodimerize or heterodimerize with other TRIM proteins and has E3 ubiquitin ligase activity. This gene is also a tumor suppressor and is involved in secretory autophagy. [provided by RefSeq, Jan 2017]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~56.4 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 TRIM16 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001348119.1. 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 | 2 | 3 | |||
| missense | 86 | 7 | 93 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 89 | 9 | 0 | 98 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001335048.1 | 6 | MANE Select | |
| Ensembl | ENSP00000497185.2 | 6 | MANE Select | |
| RefSeq | NP_001335049.1 | 6 | Standard | |
| RefSeq | NP_001335050.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- response to retinoic acid
- histone H3 acetylation
- histone H4 acetylation
- positive regulation of keratinocyte differentiation
- positive regulation of transcription, DNA-templated
Molecular Function
- DNA binding
- protein binding
- zinc ion binding
- transferase activity
- interleukin-1 binding
Cellular Component
- cytoplasm
- cytosol
- plasma membrane
- PML body
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000578237
- Coding exons
- 6
- Length
- 56352
- Individuals with no LoFs
- 125445
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 302
- Defined
- 125748
- p
- 0.00121
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.336 | 300 | 317 | 0.947 | 0.0000180 | 3716 |
| Missense (PolyPhen) | 112 | 95.544 | 1.1722 | 1131 | ||
| Synonymous | 1.10 | 116 | 132 | 0.878 | 0.00000807 | 1068 |
| Loss of Function | 1.10 | 16 | 21.5 | 0.743 | 0.00000100 | 276 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00057 | 0.00055 | rare |
| Latino/Admixed American | 0.00020 | 0.00020 | rare |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.0082 | 0.0082 | notable |
| Finnish | 0.000093 | 0.000092 | rare |
| European (Non-Finnish) | 0.00040 | 0.00036 | rare |
| South Asian | 0.0030 | 0.0029 | notable |
| Other | 0.00066 | 0.00065 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May play a role in the regulation of keratinocyte differentiation.;
Intolerance Scores
- RVIS EVS
- 0.02
- RVIS percentile EVS
- 55.69
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.440
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |