SATB2 p.Pro287fs
c.857dup · VCV4884381
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
chromosome 2q32-q33 deletion syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 7 of 11 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 6 | GERP 2.2, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- SATB2
- Protein
- p.Pro287fs
- Coding
- c.857dup
- MANE Select
- NM_001172509
- Type
- Duplication
- Location
- chr2:199349016 (GRCh38)
- Gene constraint
- LOEUF 0.077 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 66.87 · 3 PDB
Similar variants
- SATB2 p.Pro287Ser Uncertain significance ★ ⚠ same residue
- SATB2 p.Pro287= Likely benign ★ same residue
- SATB2 c.598-13dup Benign ★★ same condition
- SATB2 c.344_346+1dup Pathogenic ★ same condition
- SATB2 p.Arg542fs Likely pathogenic ★ same condition
- SATB2 p.Asn531fs Pathogenic ★ same condition
- SATB2 p.Gln409fs Pathogenic ★ same condition
- SATB2 p.Gln569fs 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/satb2-p-pro287fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown