SON p.Thr788=
c.2364T>C · rs140574025 · VCV783877
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.848%, 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 -8.2 | GERP -2.7 |
| Overall | ||
| CADD | 0.229 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.848%
African / African-American · 612/72,192 alleles
Filtering AF
0.792%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.77%
Overall
0.0421%
677/1,606,748 alleles · rare
exomes 237/1,460,488 · genomes 440/146,260 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.848% | 118 |
| Remaining individualsnot grpmax-eligible | 0.0433% | 2,309 |
| Admixed American | 0.0387% | 2,585 |
| Finnishnot grpmax-eligible | 0.00158% | 63,400 |
| European (non-Finnish) | 0.00119% | 84,154 |
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.Thr788=
- Coding
- c.2364T>C
- MANE Select
- NM_138927
- dbSNP
- rs140574025
- Type
- single nucleotide variant
- Location
- chr21:33551595 (GRCh38)
- Gene constraint
- LOEUF 0.051 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 36.48 · 4 PDB
- Residue 788
- the '17 x 10 aa tandem repeats of l-a-[st]-[nsg]-[ts]-mdsqm' region
Similar variants
- SON p.Thr788Ala Likely benign ★ ⚠ same residue
- SON c.6321+1G>A Pathogenic ★★ same type
- SON p.Arg1081Ter Pathogenic ★★ same type
- SON p.Arg1112Ter Pathogenic ★★ same type
- SON p.Arg1825Ter Pathogenic ★★ same type
- SON p.Arg2008Ter Pathogenic ★★ same type
- SON p.Gln96Ter Pathogenic/Likely pathogenic ★★ same type
- SON c.6657+160A>C 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-thr788 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown