TENT2
protein-codingterminal nucleotidyltransferase 2, the group of Terminal nucleotidyltransferases|Non-canonical poly(A) polymerases
Gene summary
Enables poly(A) RNA polymerase activity. Involved in histone mRNA catabolic process; mRNA 3'-end processing; and negative regulation of miRNA catabolic process. Predicted to be located in cytoplasm and nucleus. Predicted to be part of nuclear RNA-directed RNA polymerase complex. Predicted to be active in glutamatergic synapse; perforant pathway to dendrate granule cell synapse; and postsynapse. [provided by Alliance of Genome Resources, Jul 2025]
- PAPD4
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~76.1 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 TENT2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001114394.3. 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 | 67 | 67 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 71 | 0 | 0 | 71 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001107866.1 | 14 | MANE Select | |
| Ensembl | ENSP00000397563.1 | 14 | MANE Select | |
| RefSeq | NP_001107865.1 | 14 | Standard | |
| RefSeq | NP_001284673.1 | 14 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- hematopoietic progenitor cell differentiation
- mRNA processing
- hippocampus development
- neuron differentiation
- RNA stabilization
Molecular Function
- polynucleotide adenylyltransferase activity
- protein binding
- ATP binding
- 5'-3' RNA polymerase activity
- metal ion binding
Cellular Component
- cytosol
- nuclear RNA-directed RNA polymerase complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000453514
- Coding exons
- 14
- Length
- 74529
- Individuals with no LoFs
- 125656
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 80
- Defined
- 125736
- p
- 0.000318
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.999 | 205 | 249 | 0.822 | 0.0000127 | 3152 |
| Missense (PolyPhen) | 41 | 78.479 | 0.52244 | 957 | ||
| Synonymous | 0.312 | 81 | 84.7 | 0.957 | 0.00000403 | 889 |
| Loss of Function | 2.59 | 17 | 33.0 | 0.514 | 0.00000210 | 371 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00068 | 0.00068 | rare |
| Latino/Admixed American | 0.00033 | 0.00032 | rare |
| Ashkenazi Jewish | 0.00040 | 0.00040 | rare |
| East Asian | 0.00016 | 0.00016 | rare |
| Finnish | 0.00087 | 0.00083 | rare |
| European (Non-Finnish) | 0.00027 | 0.00026 | rare |
| South Asian | 0.000099 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Cytoplasmic poly(A) RNA polymerase that adds successive AMP monomers to the 3'-end of specific RNAs, forming a poly(A) tail. In contrast to the canonical nuclear poly(A) RNA polymerase, it only adds poly(A) to selected cytoplasmic mRNAs (PubMed:15070731). Does not play a role in replication-dependent histone mRNA degradation (PubMed:18172165). Adds a single nucleotide to the 3' end of specific miRNAs, monoadenylation stabilizes and prolongs the activity of some but not all miRNAs (PubMed:23200856). {ECO:0000269|PubMed:15070731, ECO:0000269|PubMed:18172165, ECO:0000269|PubMed:23200856}.;
Intolerance Scores
- RVIS EVS
- -0.23
- RVIS percentile EVS
- 37.32
Essentials
- Essential (gene trap)
- N