DES p.Lys144=
c.432G>A · VCV3501192
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00026%, nfe)
Conditions
1
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 5.1 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 13.6 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00026%
European (non-Finnish) · 3/1,155,668 alleles
Filtering AF
6.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000192%
3/1,565,328 alleles · very rare
exomes 3/1,412,950 · genomes 0/152,378 · 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
- DES
- Protein
- p.Lys144=
- Coding
- c.432G>A
- MANE Select
- NM_001927
- Type
- single nucleotide variant
- Location
- chr2:219418894 (GRCh38)
- Gene constraint
- LOEUF 0.81 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.73
- Residue 144
- the if rod domain; the 'linker 1' region
Similar variants
- DES p.Arg212Ter Pathogenic/Likely pathogenic ★★ same condition
- DES p.Arg454Trp Pathogenic/Likely pathogenic ★★ same condition
- DES p.Glu401Asp Pathogenic/Likely pathogenic ★★ same condition
- DES c.1245-3T>G Uncertain significance ★★ same condition
- DES c.639+4A>G Uncertain significance ★★ same condition
- DES p.Ala135Gly Uncertain significance ★★ ⚠ same condition
- DES p.Ala137Val Uncertain significance ★★ ⚠ same condition
- DES p.Ala213= Uncertain significance ★★ 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/des-p-lys144 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown