TENT5C

terminal nucleotidyltransferase 5C, the group of Terminal nucleotidyltransferases

Basic information

Region (hg38): 1:117606047-117628389

Previous symbols: [ "FAM46C" ]

Links

ENSG00000183508 ∙ NCBI:54855 ∙ OMIM:613952 ∙ HGNC:24712 ∙ Uniprot:Q5VWP2 ∙ 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 TENT5C gene.

• not specified (8 variants)
• Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TENT5C 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in TENT5C

This is a list of pathogenic ClinVar variants found in the TENT5C region.

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

Position	Type	Phenotype	Significance	ClinVar
1-117622914-G-A		not specified	not provided (Sep 19, 2013)
1-117622957-C-G		not specified	Uncertain significance (Oct 25, 2023)
1-117622977-G-A		not specified	Uncertain significance (Feb 06, 2024)
1-117622981-G-A		not specified	Uncertain significance (Jul 12, 2022)
1-117623008-C-T		not specified	Uncertain significance (Sep 16, 2021)
1-117623019-A-G		not specified	Uncertain significance (May 27, 2022)
1-117623034-C-T		not specified	Uncertain significance (Jul 19, 2022)
1-117623041-G-A		not specified	Likely benign (Dec 18, 2023)
1-117623069-C-G		not specified	not provided (Sep 19, 2013)
1-117623073-G-A		not specified	Uncertain significance (Feb 13, 2023)
1-117623308-C-T		not specified	Uncertain significance (Mar 24, 2023)
1-117623314-C-T		not specified	Uncertain significance (Oct 26, 2022)
1-117623320-G-A		not specified	Uncertain significance (Jan 19, 2024)
1-117623449-T-C		not specified	Uncertain significance (Jul 19, 2022)
1-117623452-A-G		not specified	Uncertain significance (Aug 22, 2023)
1-117623641-C-T		not specified	not provided (Sep 19, 2013)
1-117623643-G-T		not specified	not provided (Sep 19, 2013)
1-117623670-C-T		not specified	Uncertain significance (Jun 06, 2023)
1-117623709-A-G		not specified	not provided (Sep 19, 2013)
1-117623757-G-A		not specified	not provided (Sep 19, 2013)
1-117623763-G-A		not specified	not provided (Sep 19, 2013)
1-117623799-C-T		not specified	Uncertain significance (Jan 26, 2022)
1-117623814-G-A		not specified	Uncertain significance (Oct 06, 2021)
1-117623904-A-G		not specified	Uncertain significance (Dec 01, 2022)
1-117623923-A-G		not specified	Uncertain significance (Sep 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TENT5C	protein_coding	protein_coding	ENST00000369448	1	22439

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.948	0.0522	125723	0	2	125725	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.99	146	231	0.632	0.0000146	2601
Missense in Polyphen		50	108.26	0.46186		1217
Synonymous	-1.13	109	95.0	1.15	0.00000648	774
Loss of Function	2.83	0	9.30	0.00	5.00e-7	113

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000544	0.0000544
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 which enhances mRNA stability and gene expression. Mainly targets mRNAs encoding endoplasmic reticulum- targeted protein and may be involved in induction of cell death. {ECO:0000269|PubMed:27060136, ECO:0000269|PubMed:28931820}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.26

Haploinsufficiency Scores

• pHI: 0.566
• hipred: Y
• hipred_score: 0.568
• ghis: 0.397

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Tent5c
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; craniofacial phenotype; homeostasis/metabolism phenotype; renal/urinary system phenotype; skeleton phenotype; embryo phenotype; liver/biliary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype; immune system phenotype

Gene ontology

• Biological process: mRNA stabilization
• Cellular component: nucleus;cytoplasm
• Molecular function: RNA binding;protein binding;RNA adenylyltransferase activity