SATB1

Chr 3

SATB homeobox 1

Also known as: DEFDA, DHDBV, KTZSL

NCBI Gene: 6304ENSG00000182568UniProt: Q01826

This gene encodes a matrix protein which binds nuclear matrix and scaffold-associating DNAs through a unique nuclear architecture. The protein recruits chromatin-remodeling factors in order to regulate chromatin structure and gene expression. [provided by RefSeq, Apr 2016]

Primary Disease Associations & Inheritance

UniProtDen Hoed-de Boer-Voisin syndrome
UniProtDevelopmental delay with dysmorphic facies and dental anomalies
240
ClinVar variants
59
Pathogenic / LP
0.99
pLI score· haploinsufficient
0
Active trials
Clinical Summary— SATB1
🧬
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.
📋
ClinVar Variants
59 Pathogenic / Likely Pathogenic· 148 VUS of 240 total submissions
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Dual constrained — LoF & missense intolerant
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.29LOEUF
pLI 0.991
Z-score 5.02
OE 0.15 (0.08–0.29)
Highly constrained

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

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
3.98Z-score
OE missense 0.46 (0.41–0.52)
202 obs / 436.1 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.15 (0.08–0.29)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.46 (0.41–0.52)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.10
0≤1.21.6
LoF obs/exp: 6 / 40.4Missense obs/exp: 202 / 436.1Syn Z: -1.07

ClinVar Variant Classifications

240 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic40
Likely Pathogenic19
VUS148
Likely Benign21
Benign7
Conflicting5
40
Pathogenic
19
Likely Pathogenic
148
VUS
21
Likely Benign
7
Benign
5
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
10
3
27
0
40
Likely Pathogenic
6
10
3
0
19
VUS
13
117
16
2
148
Likely Benign
0
7
4
10
21
Benign
0
2
3
2
7
Conflicting
—5
Total291395314240

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View 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.

Gene2Phenotype Curations

SATB1-related developmental disorder

moderate
ADLoss Of FunctionAbsent Gene Product
Dev. Disorders
G2P ↗

Gene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org

OMIM — Genotype-Phenotype

OMIM

No OMIM entries found.

Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Mutation-specific pathophysiological mechanisms define different neurodevelopmental disorders associated with SATB1 dysfunction.
den Hoed J et al.·Am J Hum Genet
2021Functional
SATB1 and 2 in colorectal cancer.
Brocato J et al.·Carcinogenesis
2015Review
SATB1-mediated chromatin landscape in T cells.
Zelenka T et al.·Nucleus
2020Review
The Role of SATB1 in Tumour Progression and Metastasis.
Glatzel-Plucińska N et al.·Int J Mol Sci
2019Review
SATB1 in Malignant T Cells.
Fredholm S et al.·J Invest Dermatol
2018
ECM-Induced IL-23 Drives Immune Suppression in Breast Cancer via Regulating PD-1 on Tregs.
Talarico G et al.·J Exp Clin Cancer Res
2025
The SATB1-MIR22-GBA axis mediates glucocerebroside accumulation inducing a cellular senescence-like phenotype in dopaminergic neurons.
Russo T et al.·Aging Cell
2024
Expression of SATB1 and HER2 in gastric cancer and its clinical significance.
Yuan CL et al.·Eur Rev Med Pharmacol Sci
2016
Prognostic significance of SATB1 in gastrointestinal cancer: a meta-analysis and literature review.
Zhang S et al.·Oncotarget
2017Meta-analysis
Differential SATB1 Expression Reveals Heterogeneity of Cutaneous T-Cell Lymphoma.
Gao Y et al.·J Invest Dermatol
2021
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
HDAC1 and SATB1 positively regulate immune responses in chicken macrophages.
Niu B et al.·Poult Sci
2026🔓 Open Access
Long Noncoding RNA SATB1-AS1 Suppresses Inflammatory Response and Injury in Dental Pulp Stem Cells Through the miR-15a-5p/E2F3 Axis.
Ding S et al.·Int Dent J
2026🔓 Open Access
SATB1 Exhibits a Protective Role in HAmylin-Oligomer-Induced Neuronal Damage and Cognition Decline.
Xing Y et al.·CNS Neurosci Ther
2026🔓 Open Access
NLRP3 facilitates α-synuclein-induced dopaminergic neuronal senescence in a mouse model of Parkinson's disease through SATB1/DNA damage/p21 signaling pathway.
Chen LL et al.·Acta Pharmacol Sin
2026Functional
Establishment of Autoreactive CD4+CD8+ T Cell Hybridomas from Sjögren's Disease Model, SATB1 Conditional Knockout Mice.
Mashimo S et al.·Int J Mol Sci
2025🔓 Open AccessFunctional
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools