TENT2

terminal nucleotidyltransferase 2, the group of Terminal nucleotidyltransferases|Non-canonical poly(A) polymerases

Basic information

Region (hg38): 5:79612120-79688246

Previous symbols: [ "PAPD4" ]

Links

ENSG00000164329 ∙ NCBI:167153 ∙ OMIM:614121 ∙ HGNC:26776 ∙ Uniprot:Q6PIY7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TENT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TENT2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	0	0

Variants in TENT2

This is a list of pathogenic ClinVar variants found in the TENT2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-79619727-C-T		not specified	Uncertain significance (Jul 09, 2021)
5-79619734-T-G		not specified	Uncertain significance (Feb 27, 2023)
5-79619755-T-A		not specified	Uncertain significance (Jan 08, 2024)
5-79619755-T-C		not specified	Uncertain significance (Dec 13, 2023)
5-79620003-A-C		not specified	Uncertain significance (Jul 14, 2021)
5-79623262-G-A		not specified	Uncertain significance (Mar 29, 2022)
5-79623311-C-T		not specified	Uncertain significance (May 27, 2022)
5-79623388-C-G		not specified	Uncertain significance (Sep 20, 2022)
5-79623434-G-A		not specified	Uncertain significance (Dec 26, 2023)
5-79623437-A-C		not specified	Uncertain significance (Nov 03, 2023)
5-79623449-T-C		not specified	Uncertain significance (Jun 02, 2024)
5-79641149-A-G		not specified	Uncertain significance (May 24, 2024)
5-79641152-C-T		not specified	Uncertain significance (Jun 22, 2021)
5-79641172-A-T		not specified	Uncertain significance (Jan 29, 2024)
5-79642866-G-A		not specified	Uncertain significance (Aug 02, 2021)
5-79642871-A-C		not specified	Uncertain significance (Jun 09, 2022)
5-79648619-G-T		not specified	Uncertain significance (Feb 07, 2023)
5-79649137-G-A		not specified	Uncertain significance (Feb 16, 2023)
5-79649152-G-C		not specified	Uncertain significance (Sep 29, 2023)
5-79649169-A-T		not specified	Uncertain significance (Jan 17, 2023)
5-79649173-T-C		not specified	Uncertain significance (Mar 31, 2024)
5-79656958-C-A		not specified	Uncertain significance (Feb 27, 2024)
5-79656999-C-A		not specified	Uncertain significance (Nov 06, 2023)
5-79668899-T-G		not specified	Uncertain significance (Dec 13, 2021)
5-79668946-G-A		not specified	Uncertain significance (Apr 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TENT2	protein_coding	protein_coding	ENST00000453514	14	74529

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.69e-8	0.996	125656	0	80	125736	0.000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.999	205	249	0.822	0.0000127	3152
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00101	0.00100
Ashkenazi Jewish	0.000405	0.000397
East Asian	0.000164	0.000163
Finnish	0.000870	0.000832
European (Non-Finnish)	0.000268	0.000264
Middle Eastern	0.000164	0.000163
South Asian	0.0000988	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• 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

Haploinsufficiency Scores

• pHI: 0.199
• hipred: N
• hipred_score: 0.492
• ghis: 0.641

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Tent2
• Phenotype: cellular phenotype

Gene ontology

• Biological process: hematopoietic progenitor cell differentiation;mRNA processing;hippocampus development;neuron differentiation;RNA stabilization;RNA polyadenylation;retina development in camera-type eye;histone mRNA catabolic process;dark adaptation;negative regulation of miRNA catabolic process
• Cellular component: cytosol;nuclear RNA-directed RNA polymerase complex
• Molecular function: polynucleotide adenylyltransferase activity;protein binding;ATP binding;5'-3' RNA polymerase activity;metal ion binding;adenylyltransferase activity