DSEL p.Arg589Ser
c.1767G>C · rs201924019 · VCV2361943
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0802%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.029 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.8 | GERP -2, phastCons 1 |
| Regional constraint | o/e 0.92 | unconstrained · MANE · 2,707 bp · p 0.014 · regional, not allelic |
| Overall | ||
| CADD | 18.26 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0802%
East Asian · 36/44,884 alleles
Filtering AF
0.0595%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0524%
Overall
0.00378%
61/1,613,968 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0802% | 1,247 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,209 |
| South Asian | 0.0132% | 7,589 |
| Admixed American | 0.00167% | 60,014 |
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
- DSEL
- Protein
- p.Arg589Ser
- Coding
- c.1767G>C
- MANE Select
- NM_032160
- dbSNP
- rs201924019
- Type
- single nucleotide variant
- Location
- chr18:67512842 (GRCh38)
- Gene constraint
- LOEUF 0.743 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.75
Similar variants
- DSEL p.Pro942Ser Benign ★★ same type
- DSEL p.Tyr730Cys Likely benign ★★ same type
- DSEL c.-1C>G Uncertain significance ★ same type
- DSEL p.Ala1110Val Uncertain significance ★ same type
- DSEL p.Ala178Thr Uncertain significance ★ same type
- DSEL p.Ala236Thr Uncertain significance ★ same type
- DSEL p.Ala278Thr Uncertain significance ★ same type
- DSEL p.Ala2Thr 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/dsel-p-arg589ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown