Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
congenital sideroblastic anemia-B-cell immunodeficiency-periodic fever-developmental delay syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2 | GERP -0.53, phastCons 0.99 |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- TRNT1
- Protein
- p.Pro23=
- Coding
- c.68=
- MANE Select
- NM_182916
- dbSNP
- rs334773
- Type
- single nucleotide variant
- Location
- chr3:3129108 (GRCh38)
- Gene constraint
- LOEUF 1.232 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.00 · 3 PDB
- Residue 23
- a UniProt-annotated variant site (in)
Disease context
congenital sideroblastic anemia-B-cell immunodeficiency-periodic fever-developmental delay syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Congenital sideroblastic anemia-B-cell immunodeficiency-periodic fever-developmental delay syndrome (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
Similar variants
- TRNT1 p.Pro23Ala Benign/Likely benign ★★ same residue
- TRNT1 p.Pro23Leu Likely benign ★ same residue
- TRNT1 p.Pro23Val Benign ★ same residue
- TRNT1 p.Arg190Ile Pathogenic ★★ same condition
- TRNT1 p.Arg412Ter Pathogenic/Likely pathogenic ★★ same condition
- TRNT1 p.Glu277Ter Pathogenic/Likely pathogenic ★★ same condition
- TRNT1 p.Ile223Thr Pathogenic ★★ same condition
- TRNT1 p.Lys416Glu Pathogenic/Likely pathogenic ★★ ⚠ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/trnt1-p-pro23 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown