TENT5A

terminal nucleotidyltransferase 5A, the group of Terminal nucleotidyltransferases

Basic information

Region (hg38): 6:81491438-81752774

Previous symbols: [ "C6orf37", "FAM46A" ]

Links

ENSG00000112773 ∙ NCBI:55603 ∙ OMIM:611357 ∙ HGNC:18345 ∙ Uniprot:Q96IP4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• osteogenesis imperfecta (Supportive), mode of inheritance: AD
• osteogenesis imperfecta, type 18 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Osteogenesis imperfecta, type XVIII	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Musculoskeletal	29358272

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TENT5A gene.

• not provided (106 variants)
• Osteogenesis imperfecta, type 18 (4 variants)
• Inborn genetic diseases (4 variants)
• not specified (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TENT5A 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	37	8	46
missense			28	3	3	34
nonsense						0
start loss						0
frameshift			2			2
inframe indel			15	7	3	25
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	4	5
Total	0	0	46	48	18

Variants in TENT5A

This is a list of pathogenic ClinVar variants found in the TENT5A region.

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

Position	Type	Phenotype	Significance	ClinVar
6-81749628-CT-C			Benign (May 11, 2021)
6-81749699-T-C			Uncertain significance (Nov 08, 2021)
6-81749709-G-A			Likely benign (Jul 08, 2022)
6-81749713-A-C			Likely benign (Dec 30, 2023)
6-81749732-T-C		not specified	Uncertain significance (Feb 05, 2024)
6-81749737-C-T			Likely benign (Jan 21, 2022)
6-81749740-G-A		TENT5A-related disorder	Benign/Likely benign (Jan 22, 2024)
6-81749748-G-A			Uncertain significance (Nov 01, 2021)
6-81749788-T-C		TENT5A-related disorder	Benign/Likely benign (Jan 06, 2024)
6-81749794-A-G			Likely benign (Jan 08, 2024)
6-81749860-C-T			Likely benign (Dec 07, 2023)
6-81749864-C-T			Uncertain significance (Jul 20, 2022)
6-81749877-T-A			Uncertain significance (Sep 12, 2022)
6-81749887-G-A			Benign (Jan 17, 2024)
6-81749896-C-T			Likely benign (Dec 27, 2023)
6-81749946-C-T		not specified	Uncertain significance (Aug 14, 2023)
6-81749959-G-A			Likely benign (Aug 10, 2023)
6-81749975-C-T			Uncertain significance (Jan 21, 2022)
6-81749976-G-A			Uncertain significance (Aug 31, 2022)
6-81749980-T-C			Likely benign (Jun 07, 2022)
6-81749985-A-G			Likely benign (Aug 17, 2023)
6-81750021-T-G		not specified	Uncertain significance (Sep 12, 2023)
6-81750026-T-C			Uncertain significance (Dec 07, 2023)
6-81750038-A-G			Uncertain significance (Jun 14, 2022)
6-81750048-A-G			Uncertain significance (Aug 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TENT5A	protein_coding	protein_coding	ENST00000320172	2	261336

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.925	0.0751	123216	0	23	123239	0.0000933

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.05	161	253	0.637	0.0000122	2922
Missense in Polyphen		45	109.2	0.41208		1338
Synonymous	-0.568	114	107	1.07	0.00000519	867
Loss of Function	3.04	1	12.7	0.0789	6.37e-7	159

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000602	0.0000602
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000194	0.000182
Middle Eastern	0.00	0.00
South Asian	0.0000333	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable nucleotidyltransferase that may act as a non- canonical poly(A) RNA polymerase. {ECO:0000305|PubMed:27060136}.

Recessive Scores

• pRec: 0.106

Intolerance Scores

• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.21

Haploinsufficiency Scores

• pHI: 0.946
• hipred: Y
• hipred_score: 0.563
• ghis: 0.404

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Tent5a
• Phenotype: craniofacial phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; limbs/digits/tail phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive 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)

Gene ontology

• Biological process: response to bacterium
• Molecular function: RNA binding;protein binding;RNA adenylyltransferase activity