SATB1 p.Pro39=
c.117G>T · rs150879927 · VCV2653621
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0386%, nfe)
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 -7.5 | GERP -3.6 |
| Overall | ||
| CADD | 0.474 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0386%
European (non-Finnish) · 456/1,180,040 alleles
Filtering AF
0.0357%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0345%
Overall
0.0303%
489/1,614,078 alleles · ultra-rare
exomes 446/1,461,878 · genomes 43/152,200 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0386% | 2,588 |
| Finnishnot grpmax-eligible | 0.0187% | 5,336 |
| Remaining individualsnot grpmax-eligible | 0.0176% | 5,681 |
| Middle Eastern | 0.0164% | 6,084 |
| Admixed American | 0.00833% | 12,003 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,803 |
| African / African-American | 0.00267% | 37,456 |
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
- SATB1
- Protein
- p.Pro39=
- Coding
- c.117G>T
- MANE Select
- NM_002971
- dbSNP
- rs150879927
- Type
- single nucleotide variant
- Location
- chr3:18420851 (GRCh38)
- Gene constraint
- LOEUF 0.209 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 65.88 · 8 PDB
- Residue 39
- the 'disordered' region
Similar variants
- SATB1 p.Pro39Ser Uncertain significance ★ same residue
- SATB1 p.Arg427Gln Likely pathogenic ★★ ⚠ same type
- SATB1 p.Arg553Ter Pathogenic ★★ same type
- SATB1 p.Arg642Ter Pathogenic ★★ same type
- SATB1 p.Glu407Gln Pathogenic ★★ same type
- SATB1 p.Glu530Lys Pathogenic/Likely pathogenic ★★ same type
- SATB1 p.Arg380His Uncertain significance ★★ ⚠ same type
- SATB1 p.Arg627Gln 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/satb1-p-pro39 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown