SON p.Val308del
c.921_923del · VCV4707731
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.016%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.17 | GERP -2.2, phastCons 0.011 |
| Overall | ||
| CADD | 7.967 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.016%
African / African-American · 12/74,936 alleles
Filtering AF
0.00921%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00722%
Overall
0.000867%
14/1,614,062 alleles · ultra-rare
exomes 6/1,461,868 · genomes 8/152,194 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.016% | 6,245 |
| European (non-Finnish) | 0.000169% | 590,019 |
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
- SON
- Protein
- p.Val308del
- Coding
- c.921_923del
- MANE Select
- NM_138927
- Type
- Deletion
- Location
- chr21:33550150 (GRCh38)
- Gene constraint
- LOEUF 0.051 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 36.48 · 4 PDB
- Residue 308
- the 'disordered' region
Similar variants
- SON p.Val308= Likely benign ★★ same residue
- SON p.Arg1906fs Pathogenic ★★ same type
- SON p.Lys128fs Pathogenic ★★ same type
- SON p.Lys1888fs Pathogenic/Likely pathogenic ★★ same type
- SON p.Met1284fs Pathogenic/Likely pathogenic ★★ same type
- SON p.Thr1633fs Pathogenic/Likely pathogenic ★★ same type
- SON p.Val1918fs Pathogenic/Likely pathogenic ★★ same type
- SON p.729NTMDSQMLAS[2] 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/son-p-val308del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown