DSE p.Lys476=
c.1428G>A · rs1554228114 · VCV507176
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00659%, sas)
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 3.9 | GERP 0.29, phastCons 1 |
| Overall | ||
| CADD | 8.527 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00659%
South Asian · 6/91,078 alleles
Filtering AF
0.00286%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00195%
Overall
0.00041%
6/1,461,862 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
- DSE
- Protein
- p.Lys476=
- Coding
- c.1428G>A
- MANE Select
- NM_013352
- dbSNP
- rs1554228114
- Type
- single nucleotide variant
- Location
- chr6:116435896 (GRCh38)
- Gene constraint
- LOEUF 0.563 · pLI 0.06 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 86.59 · 1 PDB
Similar variants
- DSE c.416+1G>A Likely pathogenic ★★ same type
- DSE p.Ala122Thr Uncertain significance ★★ ⚠ same type
- DSE p.Ala135Val Uncertain significance ★★ ⚠ same type
- DSE p.Ala408Thr Uncertain significance ★★ ⚠ same type
- DSE p.Ala54Val Uncertain significance ★★ ⚠ same type
- DSE p.Ala584Val Uncertain significance ★★ ⚠ same type
- DSE p.Ala688Val Uncertain significance ★★ ⚠ same type
- DSE p.Ala695Thr Uncertain significance ★★ ⚠ 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/dse-p-lys476 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown