TRDN p.Thr43=
c.129G>A · rs373840513 · VCV391303
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0395%, sas)
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 -14 | GERP -4 |
| Overall | ||
| CADD | 0.934 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0395%
South Asian · 36/91,086 alleles
Filtering AF
0.0293%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0258%
Overall
0.00489%
79/1,613,974 alleles · ultra-rare
exomes 61/1,461,682 · genomes 18/152,292 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0395% | 2,530 |
| African / African-American | 0.028% | 3,573 |
| Middle Eastern | 0.0165% | 6,062 |
| Admixed American | 0.00666% | 15,005 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,830 |
| European (non-Finnish) | 0.00119% | 84,277 |
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.Thr43=
- Coding
- c.129G>A
- MANE Select
- NM_006073
- dbSNP
- rs373840513
- Type
- single nucleotide variant
- Location
- chr6:123571026 (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 p.Thr43Ala Uncertain significance ★★ ⚠ same residue
- TRDN p.Thr43Met Uncertain significance ★★ ⚠ same residue
- 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
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-thr43 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown