SATB2 p.Asp15=
c.45C>T · rs771997100 · VCV1349373
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0174%, amr)
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 8 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 14.55 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0174%
Admixed American · 9/51,618 alleles
Filtering AF
0.00907%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00671%
Overall
0.000584%
9/1,540,994 alleles · ultra-rare
exomes 5/1,388,894 · genomes 4/152,100 · 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.Asp15=
- Coding
- c.45C>T
- MANE Select
- NM_001172509
- dbSNP
- rs771997100
- Type
- single nucleotide variant
- Location
- chr2:199455993 (GRCh38)
- Gene constraint
- LOEUF 0.077 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 66.87 · 3 PDB
- Residue 15
- 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-asp15 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown