TENT5A

terminal nucleotidyltransferase 5A, the group of Terminal nucleotidyltransferases

Basic information

Region (hg38): 6:81491439-81752774

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 (134 variants)
not_specified (39 variants)
Osteogenesis_imperfecta,_type_18 (8 variants)
TENT5A-related_disorder (6 variants)
Pyloric_stenosis (3 variants)
Esophageal_atresia (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. These statistics are base on transcript: NM_000017633.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	66 clinvar	6 clinvar	73
missense	2 clinvar	1 clinvar	62 clinvar	5 clinvar	1 clinvar	71
nonsense						0
start loss						0
frameshift	1 clinvar		3 clinvar			4
splice donor/acceptor (+/-2bp)						0
Total	3	1	66	71	7

Highest pathogenic variant AF is 6.84945e-7

Loading clinvar variants...

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

loftool
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_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap: N
gene_indispensability_pred
gene_indispensability_score

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
Cellular component
Molecular function: RNA binding;protein binding;RNA adenylyltransferase activity