SOST p.Pro66=
c.198C>T · rs373309667 · VCV747371
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.024%, 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 0.62 | GERP -0.049, phastCons 1 |
| Overall | ||
| CADD | 9.316 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.024%
African / African-American · 18/74,902 alleles
Filtering AF
0.0155%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0128%
Overall
0.00273%
44/1,613,826 alleles · ultra-rare
exomes 33/1,461,654 · genomes 11/152,172 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.024% | 4,161 |
| Admixed American | 0.0117% | 8,571 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,619 |
| European (non-Finnish) | 0.00127% | 78,663 |
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
- SOST
- Protein
- p.Pro66=
- Coding
- c.198C>T
- MANE Select
- NM_025237
- dbSNP
- rs373309667
- Type
- single nucleotide variant
- Location
- chr17:43758544 (GRCh38)
- Gene constraint
- LOEUF 1.634 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 70.73 · 3 PDB
- Residue 66
- the 'disordered' region
Similar variants
- SOST p.Gln24Ter Pathogenic ★★ same type
- SOST p.Arg160Pro Uncertain significance ★★ ⚠ same type
- SOST p.Asn117Ser Uncertain significance ★★ ⚠ same type
- SOST p.Gly62Arg Uncertain significance ★★ ⚠ same type
- SOST c.-10G>A Likely benign ★★ same type
- SOST c.-21T>G Likely benign ★★ same type
- SOST c.*1004G>A Benign ★★ same type
- SOST c.*1391G>C 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/sost-p-pro66 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown