TRMT10A p.Arg91=
c.273T>G · rs1378017651 · VCV1539011
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.007 | GERP -0.9 |
| Overall | ||
| CADD | 11.09 | PHRED · no single calibrated threshold — expert panels disagree |
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
- TRMT10A
- Protein
- p.Arg91=
- Coding
- c.273T>G
- MANE Select
- NM_001134665
- dbSNP
- rs1378017651
- Type
- single nucleotide variant
- Location
- chr4:99558124 (GRCh38)
- Gene constraint
- LOEUF 1.181 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 76.77 · 1 PDB
- Residue 91
- the sam-dependent mtase trm10-type domain; a UniProt-annotated variant site (in mssgm1)
Similar variants
- TRMT10A p.Arg91Cys Uncertain significance ★★ ⚠ same residue
- TRMT10A p.Arg127Ter Pathogenic/Likely pathogenic ★★ same type
- TRMT10A p.Arg43Ter Pathogenic/Likely pathogenic ★★ same type
- TRMT10A p.Arg65Ter Pathogenic ★★ same type
- TRMT10A p.Arg76Ter Pathogenic/Likely pathogenic ★★ same type
- TRMT10A p.Arg93Ter Pathogenic/Likely pathogenic ★★ same type
- TRMT10A p.Glu27Ter Pathogenic ★★ same type
- TRMT10A p.Gly206Arg Pathogenic ★★ same type
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/trmt10a-p-arg91 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown