TENT5D

terminal nucleotidyltransferase 5D, the group of Terminal nucleotidyltransferases

Basic information

Region (hg38): X:80335504-80445311

Previous symbols: [ "FAM46D" ]

Links

ENSG00000174016 ∙ NCBI:169966 ∙ OMIM:300976 ∙ HGNC:28399 ∙ Uniprot:Q8NEK8 ∙ 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 TENT5D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TENT5D 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				1		1
missense			16	2		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	3	0

Variants in TENT5D

This is a list of pathogenic ClinVar variants found in the TENT5D region.

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

Position	Type	Phenotype	Significance	ClinVar
X-80442562-A-G		not specified	Uncertain significance (Jan 02, 2024)
X-80442672-C-T		not specified	Uncertain significance (Aug 11, 2023)
X-80442778-A-G		not specified	Uncertain significance (Jan 16, 2024)
X-80442817-G-A		not specified	Uncertain significance (Feb 22, 2023)
X-80442870-T-C		not specified	Uncertain significance (Feb 16, 2023)
X-80442890-G-T		not specified	Uncertain significance (Feb 03, 2022)
X-80442906-C-G		not specified	Uncertain significance (Nov 15, 2021)
X-80442907-C-T		not specified	Likely benign (Oct 25, 2022)
X-80442930-G-A		not specified	Uncertain significance (Sep 01, 2021)
X-80442996-A-G		not specified	Uncertain significance (Sep 27, 2024)
X-80443093-A-T		not specified	Uncertain significance (Jan 25, 2023)
X-80443205-C-T			Likely benign (Feb 01, 2023)
X-80443209-T-C		not specified	Uncertain significance (Mar 31, 2023)
X-80443420-C-T		not specified	Uncertain significance (Sep 04, 2024)
X-80443569-A-G		not specified	Uncertain significance (Jan 31, 2023)
X-80443597-C-T		not specified	Uncertain significance (Jan 23, 2023)
X-80443653-G-A		not specified	Likely benign (Sep 13, 2023)
X-80443671-C-T		not specified	Uncertain significance (Jul 20, 2021)
X-80443692-T-A		not specified	Uncertain significance (May 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TENT5D	protein_coding	protein_coding	ENST00000538312	1	109808

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.830	0.167	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.957	109	141	0.773	0.00000986	2606
Missense in Polyphen		18	60.893	0.2956		1179
Synonymous	-0.455	54	49.9	1.08	0.00000364	718
Loss of Function	2.24	0	5.85	0.00	3.64e-7	140

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Nucleotidyltransferase that act as a non-canonical poly(A) RNA polymerase. {ECO:0000269|PubMed:27060136, ECO:0000269|PubMed:28931820}.

Recessive Scores

• pRec: 0.0747

Intolerance Scores

• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.66

Haploinsufficiency Scores

• pHI: 0.292
• hipred: N
• hipred_score: 0.335
• ghis: 0.385

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Tent5d

Gene ontology

• Molecular function: protein binding;RNA adenylyltransferase activity