SMAD2 p.Ser2=
c.6G>T · rs1244575923 · VCV1619712
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.26 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.4 | GERP -0.81, phastCons 1 |
| Overall | ||
| CADD | 16.98 | 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
- SMAD2
- Protein
- p.Ser2=
- Coding
- c.6G>T
- MANE Select
- NM_005901
- dbSNP
- rs1244575923
- Type
- single nucleotide variant
- Location
- chr18:47896751 (GRCh38)
- Gene constraint
- LOEUF 0.249 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.50 · 10 PDB
- Residue 2
- a modified residue (n-acetylserine)
Similar variants
- SMAD2 p.Ser2Leu Uncertain significance ★ ⚠ same residue
- SMAD2 c.237-2A>G Likely pathogenic ★★ same type
- SMAD2 p.Arg120Ter Pathogenic/Likely pathogenic ★★ same type
- SMAD2 p.Arg182Ter Pathogenic ★★ same type
- SMAD2 p.Arg321Ter Pathogenic/Likely pathogenic ★★ same type
- SMAD2 p.Gln264Ter Pathogenic/Likely pathogenic ★★ same type
- SMAD2 p.Tyr406Cys Pathogenic/Likely pathogenic ★★ same type
- SMAD2 c.520+4G>A 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/smad2-p-ser2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown