TENT4B

terminal nucleotidyltransferase 4B, the group of Terminal nucleotidyltransferases|Non-canonical poly(A) polymerases

Basic information

Region (hg38): 16:50152911-50235310

Previous symbols: [ "PAPD5" ]

Links

ENSG00000121274 ∙ NCBI:64282 ∙ OMIM:605540 ∙ HGNC:30758 ∙ Uniprot:Q8NDF8 ∙ 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 TENT4B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TENT4B 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			25	6		31
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	7	0

Variants in TENT4B

This is a list of pathogenic ClinVar variants found in the TENT4B region.

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

Position	Type	Phenotype	Significance	ClinVar
16-50152956-C-T		not specified	Uncertain significance (Jun 10, 2022)
16-50153807-C-G		not specified	Uncertain significance (Oct 27, 2023)
16-50153841-T-C		not specified	Likely benign (Dec 18, 2023)
16-50153853-C-T		not specified	Uncertain significance (Apr 07, 2023)
16-50153898-A-G		not specified	Likely benign (Apr 07, 2023)
16-50153908-T-A		not specified	Uncertain significance (Apr 07, 2023)
16-50153935-C-T		not specified	Uncertain significance (Nov 07, 2023)
16-50153956-A-G		not specified	Uncertain significance (Dec 20, 2023)
16-50153961-A-C		not specified	Uncertain significance (Jul 27, 2021)
16-50153977-G-C		not specified	Likely benign (Apr 07, 2023)
16-50154024-G-C		not specified	Uncertain significance (Mar 26, 2024)
16-50154037-C-T		not specified	Uncertain significance (Jun 03, 2024)
16-50154042-C-T		not specified	Likely benign (May 01, 2024)
16-50154070-C-T		not specified	Uncertain significance (Aug 03, 2022)
16-50154093-A-G		not specified	Uncertain significance (Dec 21, 2021)
16-50154141-T-C		not specified	Uncertain significance (Dec 06, 2021)
16-50154159-A-G		not specified	Uncertain significance (Jul 13, 2022)
16-50154187-G-A		not specified	Uncertain significance (Mar 17, 2023)
16-50154194-C-G		not specified	Uncertain significance (Apr 07, 2023)
16-50154198-G-A		not specified	Likely benign (Apr 07, 2023)
16-50154205-T-G		not specified	Likely benign (Apr 07, 2023)
16-50211417-G-A		not specified	Uncertain significance (Oct 03, 2022)
16-50211423-A-G		not specified	Uncertain significance (Aug 28, 2023)
16-50223205-A-G		not specified	Uncertain significance (Feb 28, 2023)
16-50224722-G-A		not specified	Uncertain significance (Mar 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TENT4B	protein_coding	protein_coding	ENST00000436909	13	82393

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000574	124629	0	6	124635	0.0000241

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.55	154	338	0.456	0.0000170	4511
Missense in Polyphen		12	78.284	0.15329		1045
Synonymous	0.684	127	137	0.926	0.00000750	1378
Loss of Function	4.77	2	30.3	0.0660	0.00000156	396

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000224	0.000223
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.00000895	0.00000885
Middle Eastern	0.0000556	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• 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. Doesn't need a cofactor for polyadenylation activity (in vitro) (PubMed:21788334, PubMed:21855801). Required for cytoplasmic polyadenylation of mRNAs involved in carbohydrate metabolism, including the glucose transporter SLC2A1/GLUT1 (PubMed:28383716). Plays a role in replication-dependent histone mRNA degradation, probably through terminal uridylation of mature histone mRNAs. May play a role in sister chromatid cohesion (PubMed:18172165). Mediates 3' adenylation of the microRNA MIR21 followed by its 3'- to-5' trimming by the exoribonuclease PARN leading to degradation (PubMed:25049417). Mediates 3' adenylation of H/ACA box snoRNAs (small nucleolar RNAs) followed by its 3'-to-5' trimming by the exoribonuclease PARN which enhances snoRNA stability and maturation (PubMed:22442037). {ECO:0000269|PubMed:18172165, ECO:0000269|PubMed:21788334, ECO:0000269|PubMed:21855801, ECO:0000269|PubMed:22442037, ECO:0000269|PubMed:25049417, ECO:0000269|PubMed:28383716}.

Recessive Scores

• pRec: 0.105

Intolerance Scores

• rvis_EVS: -0.18
• rvis_percentile_EVS: 39.95

Haploinsufficiency Scores

• pHI: 0.149
• hipred: Y
• hipred_score: 0.727
• ghis: 0.550

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Tent4b

Gene ontology

• Biological process: rRNA processing;mRNA polyadenylation;cell cycle;miRNA catabolic process;negative regulation of telomere maintenance via telomerase;carbohydrate homeostasis;ncRNA polyadenylation;ncRNA polyadenylation involved in polyadenylation-dependent ncRNA catabolic process;cell division;histone mRNA catabolic process;snoRNA polyadenylation;DNA biosynthetic process
• Cellular component: nucleolus;cytoplasm;TRAMP complex
• Molecular function: DNA binding;RNA binding;DNA-directed DNA polymerase activity;polynucleotide adenylyltransferase activity;protein binding;metal ion binding;telomerase RNA binding