TENT4A

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

Basic information

Region (hg38): 5:6713432-6757044

Previous symbols: [ "POLS", "PAPD7" ]

Links

ENSG00000112941

∙ NCBI:11044 ∙ OMIM:605198 ∙ HGNC:16705 ∙ Uniprot:Q5XG87 ∙ 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 TENT4A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TENT4A 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 clinvar	1 clinvar		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	1	0

Variants in TENT4A

This is a list of pathogenic ClinVar variants found in the TENT4A region.

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

Position	Phenotype	Significance	ClinVar
5-6738710-G-T	not specified	Uncertain significance (May 05, 2023)	2544317
5-6739764-A-C	not specified	Uncertain significance (May 09, 2023)	2546127
5-6739766-C-T	not specified	Uncertain significance (May 26, 2022)	3176011
5-6739811-G-A	not specified	Uncertain significance (Jun 28, 2022)	3176012
5-6739851-C-T	not specified	Uncertain significance (Mar 21, 2024)	3325378
5-6742532-G-A	not specified	Uncertain significance (Aug 17, 2021)	3176013
5-6742562-G-A	not specified	Uncertain significance (Nov 14, 2023)	3176014
5-6742580-A-G	not specified	Uncertain significance (Mar 18, 2024)	3325380
5-6746227-T-C	not specified	Uncertain significance (Apr 28, 2022)	3176015
5-6748496-A-G	not specified	Uncertain significance (Nov 30, 2022)	3176016
5-6748547-G-A	not specified	Uncertain significance (Mar 16, 2024)	3325379
5-6748554-C-T	not specified	Uncertain significance (Jan 10, 2022)	3176017
5-6748583-G-A	not specified	Uncertain significance (Aug 05, 2023)	2593139
5-6749641-C-G	not specified	Uncertain significance (Mar 18, 2024)	3325381
5-6750370-A-G	not specified	Uncertain significance (Dec 31, 2023)	3176018
5-6750379-A-G	not specified	Uncertain significance (Jun 16, 2024)	3325382
5-6750406-C-T	not specified	Uncertain significance (Jun 03, 2024)	3325376
5-6750409-A-G	not specified	Uncertain significance (May 05, 2022)	3175998
5-6751094-C-T	not specified	Uncertain significance (Jun 10, 2022)	3175999
5-6751124-C-G	not specified	Uncertain significance (Apr 15, 2024)	3325377
5-6752960-G-A	not specified	Uncertain significance (Dec 09, 2023)	3176000
5-6752982-C-T	not specified	Uncertain significance (Sep 16, 2021)	3176001
5-6752990-C-G	not specified	Uncertain significance (Dec 13, 2022)	3176002
5-6752997-C-T	not specified	Uncertain significance (Apr 07, 2022)	3176003
5-6753009-C-T	not specified	Uncertain significance (Oct 26, 2022)	3176004

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TENT4A	protein_coding	protein_coding	ENST00000230859	12	42444

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000656	125734	0	13	125747	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.31	216	335	0.645	0.0000200	3525
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000881	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.0000329	0.0000327
Other	0.000164	0.000163

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. 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

loftool
rvis_EVS: -1
rvis_percentile_EVS: 8.37

Haploinsufficiency Scores

pHI: 0.587
hipred: Y
hipred_score: 0.688
ghis: 0.629

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap: N
gene_indispensability_pred
gene_indispensability_score

Mouse Genome Informatics

Gene name: Tent4a
Phenotype

Gene ontology

Biological process: double-strand break repair;mRNA processing;sister chromatid cohesion;mitotic chromosome condensation;response to drug;histone mRNA catabolic process;snoRNA polyadenylation
Cellular component: nucleus;nucleoplasm;nucleolus;Golgi apparatus;TRAMP complex;nuclear membrane
Molecular function: polynucleotide adenylyltransferase activity;ATP binding;SMC family protein binding;metal ion binding