TENT4A
protein-codingterminal nucleotidyltransferase 4A, the group of Terminal nucleotidyltransferases|Non-canonical poly(A) polymerases
Gene summary
The protein encoded by this gene is a DNA polymerase that is likely involved in DNA repair. In addition, the encoded protein may be required for sister chromatid adhesion. Alternatively spliced transcript variants that encode different isoforms have been described. [provided by RefSeq, Jan 2010]
- POLS
- PAPD7
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~43.6 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 TENT4A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006999.6. 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 | 2 | 2 | 4 | |||
| missense | 76 | 2 | 78 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 78 | 4 | 0 | 82 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_008930.2 | 13 | MANE Select | |
| Ensembl | ENSP00000230859.7 | 13 | MANE Select | |
| RefSeq | NP_001165276.2 | 13 | Standard | |
| Ensembl | ENSP00000427232.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- double-strand break repair
- mRNA processing
- sister chromatid cohesion
- mitotic chromosome condensation
- response to drug
Molecular Function
- polynucleotide adenylyltransferase activity
- ATP binding
- SMC family protein binding
- metal ion binding
Cellular Component
- nucleus
- nucleoplasm
- nucleolus
- Golgi apparatus
- TRAMP complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000230859
- Coding exons
- 12
- Length
- 42444
- Individuals with no LoFs
- 125734
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 13
- Defined
- 125747
- p
- 0.0000517
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.31 | 216 | 335 | 0.645 | 0.0000200 | 3525 |
| Missense (PolyPhen) | 35 | 121.76 | 0.28745 | 1306 | ||
| Synonymous | -0.0157 | 141 | 141 | 1.00 | 0.00000989 | 1095 |
| Loss of Function | 4.50 | 1 | 25.6 | 0.0391 | 0.00000124 | 308 |
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 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000088 | 0.000088 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalytic subunit of a TRAMP-like complex which has a poly(A) RNA polymerase activity and is involved in a post- transcriptional quality control mechanism. Polyadenylation with short oligo(A) tails is required for the degradative activity of the exosome on several of its nuclear RNA substrates. Has no terminal uridylyltransferase activity, and does not play a role in replication-dependent histone mRNA degradation via uridylation. {ECO:0000269|PubMed:23376078}.;
Recessive Scores
- pRec
- 0.167
Intolerance Scores
- RVIS EVS
- -1
- RVIS percentile EVS
- 8.37
Essentials
- Essential (gene trap)
- N