TRDN p.Val561=
c.1683T>C · rs777229118 · VCV1550621
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.067%, eas)
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 2 | GERP -3.3 |
| Overall | ||
| CADD | 7.432 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.067%
East Asian · 28/41,802 alleles
Filtering AF
0.0475%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.041%
Overall
0.00188%
29/1,540,550 alleles · ultra-rare
exomes 22/1,388,588 · genomes 7/151,962 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.067% | 1,493 |
| South Asian | 0.00121% | 82,382 |
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.Val561=
- Coding
- c.1683T>C
- MANE Select
- NM_006073
- dbSNP
- rs777229118
- Type
- single nucleotide variant
- Location
- chr6:123271176 (GRCh38)
- Gene constraint
- LOEUF 1.359 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 47.65
- Residue 561
- the 'disordered' region
Similar variants
- TRDN p.Val561Asp Uncertain significance ★★ ⚠ same residue
- TRDN p.Val561Ala 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-val561 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown