TENT5A

protein-coding

terminal nucleotidyltransferase 5A, the group of Terminal nucleotidyltransferases

Gene summary

Enables poly(A) RNA polymerase activity. Predicted to be involved in mRNA stabilization; positive regulation of bone mineralization; and positive regulation of osteoblast differentiation. Predicted to act upstream of or within response to bacterium. Predicted to be located in cytoplasm. Implicated in lung non-small cell carcinoma; osteoarthritis; and osteogenesis imperfecta type 18. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C6orf37
FAM46A

MANE transcript

NM_017633.3

Inheritance

ClinVar variants

P:4U:71B:82

Top phenotype

Osteogenesis imperfecta, type XVIII

gnomAD constraint

pLI —, LoF o/e 0.08

Max pathogenic AF

—

Genomic locus

chr6:81,491,439-81,752,774

External References & Databases

Ensembl (ENSG00000112773)

Transcript & Mutation Effects

hg38 • Region Span ~261.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

osteogenesis imperfecta, type 18STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0044329

Submitter: PanelApp Australia

osteogenesis imperfecta, type 18STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0044329

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Osteogenesis imperfecta, type XVIIIAR

Manifestation: Musculoskeletal

Intervention: General

Rationale: 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

Refs: 29358272

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TENT5A variants in ClinVar

6 Conditions Cataloged

not providedTotal: 142

not specifiedTotal: 54

Osteogenesis imperfecta, type 18Total: 8

TENT5A-related disorderTotal: 6

Pyloric stenosisTotal: 3

Esophageal atresiaTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017633.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	75 clinvar	1 clinvar	78
missense	2 clinvar	1 clinvar	66 clinvar	5 clinvar	1 clinvar	75
nonsense						0
start loss						0
frameshift	1 clinvar		3 clinvar			4
splice donor/acceptor (+/-2bp)						0
Total	3	1	71	80	2	157

Highest pathogenic variant AF is 6.8494467e-7

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017633.3	RefSeq	NP_060103.2	2	MANE Select
ENST00000320172.11	Ensembl	ENSP00000318298.6	2	MANE Select
ENST00000369754.7	Ensembl	ENSP00000358769.3	3	Standard
ENST00000369756.3	Ensembl	ENSP00000358771.3	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

response to bacterium

Molecular Function

RNA binding
protein binding
RNA adenylyltransferase activity

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000320172
Coding exons: 2
Length: 261336
Individuals with no LoFs: 123216
Homozygous LoFs: 0
Heterozygous LoFs: 23
Defined: 123239
p: 0.0000933

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.05	161	253	0.637	0.0000122	2922
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000060	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00019	0.00018	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (gene trap): N