TRDN p.Leu51=
c.153T>C · rs899552776 · VCV2625265
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00017%, nfe)
Conditions
2
Cardiovascular phenotype
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 0.33 | GERP -4, phastCons 0.67 |
| Overall | ||
| CADD | 5.617 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00017%
European (non-Finnish) · 2/1,179,860 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,614,010 alleles · very rare
exomes 2/1,461,684 · genomes 0/152,326 · joint denominator
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- TRDN
- Protein
- p.Leu51=
- Coding
- c.153T>C
- MANE Select
- NM_006073
- dbSNP
- rs899552776
- Type
- single nucleotide variant
- Location
- chr6:123571002 (GRCh38)
- Gene constraint
- LOEUF 1.359 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 47.65
Similar variants
- TRDN c.22+1G>T Pathogenic ★★ same condition
- TRDN c.22+29A>G Pathogenic ★★ same condition
- TRDN c.391+1G>A Likely pathogenic ★★ same condition
- TRDN p.Gln205Ter Pathogenic/Likely pathogenic ★★ same condition
- TRDN p.Glu168Ter Pathogenic/Likely pathogenic ★★ same condition
- TRDN p.Glu181Ter Pathogenic/Likely pathogenic ★★ same condition
- TRDN p.Lys177Ter Pathogenic ★★ same condition
- TRDN p.Met1Thr 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/trdn-p-leu51 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown