TENT5C
protein-codingterminal nucleotidyltransferase 5C, the group of Terminal nucleotidyltransferases
Gene summary
Enables poly(A) RNA polymerase activity. Involved in mRNA stabilization and negative regulation of cell differentiation. Located in centrosome; cytoplasm; and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]
- FAM46C
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~22.3 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 TENT5C variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_017709.4. 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 | 56 | 2 | 58 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 57 | 2 | 0 | 59 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_060179.2 | 1 | MANE Select | |
| Ensembl | ENSP00000358458.3 | 1 | MANE Select | |
| Ensembl | ENSP00000550549.1 | 1 | Standard | |
| Ensembl | ENSP00000550549.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- mRNA stabilization
Molecular Function
- RNA binding
- protein binding
- RNA adenylyltransferase activity
Cellular Component
- nucleus
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000369448
- Coding exons
- 1
- Length
- 22439
- Individuals with no LoFs
- 125723
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 2
- Defined
- 125725
- p
- 0.00000795
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.99 | 146 | 231 | 0.632 | 0.0000146 | 2601 |
| Missense (PolyPhen) | 50 | 108.26 | 0.46186 | 1217 | ||
| Synonymous | -1.13 | 109 | 95.0 | 1.15 | 0.00000648 | 774 |
| Loss of Function | 2.83 | 0 | 9.30 | 0.00 | 5.00e-7 | 113 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Nucleotidyltransferase that act as a non-canonical poly(A) RNA polymerase which enhances mRNA stability and gene expression. Mainly targets mRNAs encoding endoplasmic reticulum- targeted protein and may be involved in induction of cell death. {ECO:0000269|PubMed:27060136, ECO:0000269|PubMed:28931820}.;
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- RVIS EVS
- -0.11
- RVIS percentile EVS
- 45.26
Essentials
- Essential (gene trap)
- N