TRNT1
Chr 3ARtRNA nucleotidyl transferase 1
Also known as: CCA1, CGI-47, MtCCA, RPEM, SIFD
The TRNT1 protein is a CCA-adding enzyme that catalyzes the addition of the essential CCA nucleotide sequence to the 3' terminus of tRNA molecules, which is necessary for amino acid attachment and tRNA processing. Mutations cause autosomal recessive disorders including sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay, as well as retinitis pigmentosa with erythrocytic microcytosis. The gene shows low constraint against loss-of-function variants (pLI 0.0002, LOEUF 0.88), consistent with recessive inheritance where heterozygous carriers are typically unaffected.
Definitive — sufficient evidence for diagnostic panels
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Typical tolerance to LoF variation
Tolerant to missense variation
Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.
The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
100 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 9 | 0 | 4 | 0 | 13 |
Likely Pathogenic | 2 | 1 | 0 | 0 | 3 |
VUS | 1 | 32 | 3 | 1 | 37 |
Likely Benign | 0 | 1 | 10 | 23 | 34 |
Benign | 0 | 0 | 1 | 0 | 1 |
Conflicting | — | 1 | |||
| Total | 12 | 34 | 18 | 24 | 89 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
TRNT1 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
3D Protein StructureAlphaFold
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
External Resources
Links to major genomics databases and tools