SON p.Arg2000del
c.5995AGA[1] · VCV3363677
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
Variant & gene context
- Gene
- SON
- Protein
- p.Arg2000del
- Coding
- c.5995AGA[1]
- MANE Select
- NM_138927
- Type
- Microsatellite
- Location
- chr21:33555226 (GRCh38)
- Gene constraint
- LOEUF 0.051 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 36.48 · 4 PDB
- Residue 2000
- the 'disordered' region; the '2 x 19 aa repeats of p-s-r-r-r-r-s-r-s-v-v-r-r-r-s-f-s-i-s' region
Similar variants
- SON p.Arg2000Thr Uncertain significance ★ ⚠ same residue
- SON p.Gln874fs Pathogenic ★★ same type
- SON p.Leu1593fs Pathogenic ★★ same type
- SON p.1957SRTPSRR[3] Uncertain significance ★★ same type
- SON c.6322-16_6322-13del Benign/Likely benign ★★ same type
- SON p.1036AYERSMMS[1] Likely benign ★★ same type
- SON p.1957SRTPSRR[4] Likely benign ★★ same type
- SON p.224EQS[1] Likely benign ★★ 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/son-p-arg2000del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown