DSE p.Ile790=
c.2370T>C · rs145906435 · VCV680405
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00534%, afr)
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 -4.2 | GERP -4.1 |
| Overall | ||
| CADD | 2.891 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00534%
African / African-American · 4/74,906 alleles
Filtering AF
0.00175%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00104%
Overall
0.000248%
4/1,613,994 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.Ile790=
- Coding
- c.2370T>C
- MANE Select
- NM_013352
- dbSNP
- rs145906435
- Type
- single nucleotide variant
- Location
- chr6:116436838 (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-ile790 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown