SATB2

Chr 2

SATB homeobox 2

Also known as: C2DELq32q33, DEL2Q32Q33, GLSS

NCBI Gene: 23314ENSG00000119042UniProt: Q9UPW6

This gene encodes a DNA binding protein that specifically binds nuclear matrix attachment regions. The encoded protein is involved in transcription regulation and chromatin remodeling. Defects in this gene are associated with isolated cleft palate and cognitive disability. Alternate splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, Feb 2010]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtCleft palate isolated

Clinical highlights

Gene-disease validity (ClinGen)
SATB2 associated disorder · ADDefinitivesufficient evidence for diagnostic panels
Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype) and the gene is intolerant of it in the population — truncating, frameshift and canonical splice variants carry more prior weight here than missense.Curated gene-level mechanism — a prior for triage, not a per-variant call.
0
Active trials
208
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.09
LOEUF· LoF intol.
LOF
Mechanism· G2P
📖
GeneReview available — SATB2
Authoritative clinical overview · Recommended first read
Open GeneReview ↗
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?
0.09LOEUF
pLI 1.000
Z-score 5.32
OE 0.00 (0.00–0.09)
Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint?
4.05Z-score
OE missense 0.44 (0.39–0.50)
183 obs / 415.3 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios?
LoF OE?0.00 (0.00–0.09)
0≤0.351.4
Missense OE?0.44 (0.39–0.50)
0≤0.61.4
Synonymous OE?1.10
0≤1.21.6
LoF obs/exp: 0 / 32.9Missense obs/exp: 183 / 415.3Syn Z: -1.02

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

SATB2 · protein map & ClinVar variants

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

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

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients