The protein functions as a transcriptional repressor that binds to AT-rich DNA sequences at matrix attachment regions and recruits chromatin-remodeling factors to regulate gene expression, playing essential roles in T-cell maturation, globin gene switching, and neuronal differentiation. Mutations cause den Hoed-de Boer-Voisin syndrome and developmental delay with dysmorphic facies and dental anomalies through an autosomal dominant inheritance pattern. The gene is highly intolerant to loss-of-function variants, and mutations can cause disease predominantly through haploinsufficiency mechanisms.

OMIMResearchSummary from RefSeq, OMIM, UniProt, Mechanism
LOFmechanismADLOEUF 0.292 OMIM phenotypes
Clinical SummarySATB1
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Gene-Disease Validity (ClinGen)
complex neurodevelopmental disorder · ADDefinitive

Definitive — sufficient evidence for diagnostic panels

Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.99). One damaged copy is likely sufficient to cause disease.
Some data sources returned errors (1)

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Dual constrained — LoF & missense intolerant
LoF Constraint
0.29LOEUF
pLI 0.991
Z-score 5.02
OE 0.15 (0.080.29)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint
3.98Z-score
OE missense 0.46 (0.410.52)
202 obs / 436.1 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios
LoF OE0.15 (0.080.29)
00.351.4
Missense OE0.46 (0.410.52)
00.61.4
Synonymous OE1.10
01.21.6
LoF obs/exp: 6 / 40.4Missense obs/exp: 202 / 436.1Syn Z: -1.07
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
moderateSATB1-related developmental disorderLOFAD
DN
0.3097th %ile
GOF
0.3789th %ile
LOF
0.79top 5%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · 1 literature citation · LOEUF 0.29

Literature Evidence

LOFThese findings suggested haploinsufficiency as a mechanism; however, some of the mutations were demonstrated to escape nonsense-mediated mRNA decay.PMID:33513338

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

SATB1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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