TRNT1

Chr 3

tRNA nucleotidyl transferase 1

Also known as: CCA1, CGI-47, MtCCA, RPEM, SIFD

NCBI Gene: 51095ENSG00000072756UniProt: Q96Q11

The protein encoded by this gene is a CCA-adding enzyme which belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family. This essential enzyme functions by catalyzing the addition of the conserved nucleotide triplet CCA to the 3' terminus of tRNA molecules. Mutations in this gene result in sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtSideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay
UniProtRetinitis pigmentosa and erythrocytic microcytosis

Clinical highlights

Gene-disease validity (ClinGen)
congenital sideroblastic anemia-B-cell immunodeficiency-periodic fever-developmental delay syndrome · ARDefinitivesufficient evidence for diagnostic panels
Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype), though the gene is not strongly LoF-constrained in the population — weigh truncating variants against that tolerance.Curated gene-level mechanism — a prior for triage, not a per-variant call.
1
Active trials
15
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.88
LOEUF
LOF
Mechanism· G2P
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GeneReview available — TRNT1
Authoritative clinical overview · Recommended first read
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Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?
0.88LOEUF
pLI 0.000
Z-score 1.95
OE 0.50 (0.30–0.88)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?
-1.15Z-score
OE missense 1.22 (1.10–1.34)
273 obs / 224.7 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?
LoF OE?0.50 (0.30–0.88)
0≤0.351.4
Missense OE?1.22 (1.10–1.34)
0≤0.61.4
Synonymous OE?0.97
0≤1.21.6
LoF obs/exp: 9 / 17.9Missense obs/exp: 273 / 224.7Syn Z: 0.24

ClinVar Variant Classifications

0 submitted variants in ClinVar

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.

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients