SATB1 p.Pro614=
c.1842A>C · VCV4961468
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0022%, sas)
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 -20 | GERP -3 |
| Overall | ||
| CADD | 0.032 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0022%
South Asian · 2/91,050 alleles
Filtering AF
0.000365%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000137%
Overall
0.000434%
7/1,613,342 alleles · very rare
exomes 6/1,461,184 · genomes 1/152,158 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0022% | 45,525 |
| African / African-American | 0.00133% | 74,910 |
| European (non-Finnish) | 0.000339% | 294,988 |
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.Pro614=
- Coding
- c.1842A>C
- MANE Select
- NM_002971
- Type
- single nucleotide variant
- Location
- chr3:18349620 (GRCh38)
- Gene constraint
- LOEUF 0.209 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 65.88 · 8 PDB
- Residue 614
- a UniProt-annotated variant site (in defda; reduced transcriptional repression); the 'disordered' region
Similar variants
- 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
- SATB1 p.Pro181Ala 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-pro614 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown