SATB2 p.Ser440=
c.1320C>T · rs770384540 · VCV848678
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00127%, nfe)
Conditions
1
chromosome 2q32-q33 deletion syndrome
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 3.4 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 9.829 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00127%
European (non-Finnish) · 15/1,179,958 alleles
Filtering AF
0.000763%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000605%
Overall
0.000929%
15/1,613,848 alleles · very rare
exomes 13/1,461,712 · genomes 2/152,136 · joint denominator
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
- SATB2
- Protein
- p.Ser440=
- Coding
- c.1320C>T
- MANE Select
- NM_001172509
- dbSNP
- rs770384540
- Type
- single nucleotide variant
- Location
- chr2:199328764 (GRCh38)
- Gene constraint
- LOEUF 0.077 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 66.87 · 3 PDB
- Residue 440
- the 'disordered' region
Similar variants
- SATB2 c.1174-2A>G Pathogenic ★★ same condition
- SATB2 c.474-2A>G Pathogenic ★★ same condition
- SATB2 c.597+1G>A Pathogenic/Likely pathogenic ★★ same condition
- SATB2 c.700+1G>A Likely pathogenic ★★ same condition
- SATB2 p.Arg239Ter Pathogenic ★★ same condition
- SATB2 p.Arg283Ter Pathogenic ★★ same condition
- SATB2 p.Arg389Cys Pathogenic/Likely pathogenic ★★ same condition
- SATB2 p.Arg389Leu 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-ser440 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown