DES p.Thr77=
c.231C>A · rs2545246734 · VCV2672861
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.63e-05%, nfe)
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 0.73 | GERP -0.86, phastCons 0.32 |
| Overall | ||
| CADD | 9.717 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.63e-05%
European (non-Finnish) · 1/1,158,244 alleles
Overall
7.05e-05%
1/1,418,848 alleles · very rare
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
- DES
- Protein
- p.Thr77=
- Coding
- c.231C>A
- MANE Select
- NM_001927
- dbSNP
- rs2545246734
- Type
- single nucleotide variant
- Location
- chr2:219418693 (GRCh38)
- Gene constraint
- LOEUF 0.81 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.73
- Residue 77
- a modified residue (phosphothreonine; by rock1); the 'head' region
Similar variants
- DES p.Thr77Ala Conflicting classifications of pathogenicity ★ ⚠ same residue
- DES p.Thr77Ile Uncertain significance ★ ⚠ same residue
- DES p.Thr77Pro Uncertain significance ★ ⚠ same residue
- DES p.Thr77del Uncertain significance ★ same residue
- DES c.1289-2A>G Pathogenic/Likely pathogenic ★★ same type
- DES c.579-2A>C Likely pathogenic ★★ same type
- DES c.735+1G>A Pathogenic/Likely pathogenic ★★ same type
- DES c.735+1G>C Pathogenic/Likely 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/des-p-thr77 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown