SOS1 p.Pro1069=
c.3207T>C · rs2528915093 · VCV2016437
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
RASopathy
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.2 | GERP -5.2, phastCons 0.001 |
| Overall | ||
| CADD | 6.491 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- SOS1
- Protein
- p.Pro1069=
- Coding
- c.3207T>C
- MANE Select
- NM_005633
- dbSNP
- rs2528915093
- Type
- single nucleotide variant
- Location
- chr2:38995262 (GRCh38)
- Gene constraint
- LOEUF 0.288 · pLI 1.00 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 77.12 · 92 PDB
- Residue 1069
- the 'disordered' region
Similar variants
- SOS1 p.Arg552Gly Pathogenic ★★★ ⚠ same condition
- SOS1 p.Arg552Lys Pathogenic ★★★ ⚠ same condition
- SOS1 p.Arg552Met Likely pathogenic ★★★ ⚠ same condition
- SOS1 p.Arg552Ser Pathogenic ★★★ ⚠ same condition
- SOS1 p.Arg552Thr Pathogenic ★★★ ⚠ same condition
- SOS1 p.Arg552Trp Likely pathogenic ★★★ same condition
- SOS1 p.Glu846Lys Pathogenic ★★★ same condition
- SOS1 p.Met269Thr Pathogenic ★★★ ⚠ same condition
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/sos1-p-pro1069 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown