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10 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
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SALL3
spalt like transcription factor 3
Chromosome 18 · 18q23
NCBI Gene: 27164Ensembl: ENSG00000256463.11HGNC: HGNC:10527UniProt: A0A384MEH2
26PubMed Papers
0Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
DNA-binding transcription factor activity, RNA polymerase II-specificregulation of transcription by RNA polymerase IInucleuslimb morphogenesis
✦AI Summary

SALL3 (spalt like transcription factor 3) is a zinc finger transcription factor located on chromosome 18 that functions as a developmental regulator and tumor suppressor 1. The protein acts as a DNA-binding transcription factor with RNA polymerase II-specific activity, operating through direct interaction with epigenetic regulators. Mechanistically, SALL3 inhibits DNA methyltransferase 3A (DNMT3A) by binding to its PWWP domain through its double zinc finger motif, thereby suppressing aberrant CpG island methylation 2. Additionally, SALL3 modulates DNA methyltransferase activity and influences gene body methylation patterns, serving as a critical regulator of cell lineage differentiation in pluripotent stem cells 3. SALL3 expression correlates positively with ectodermal differentiation while inversely regulating mesoderm/endoderm differentiation capacity 3. In neural development, SALL3 promotes dopaminergic neuron differentiation by regulating tyrosine hydroxylase expression 4. Clinically, SALL3 functions as a tumor suppressor; its aberrant promoter hypermethylation and subsequent downregulation occur in hepatocellular carcinoma 5 and cervical cancer, particularly in HPV-positive cases 6. Loss of SALL3 impairs neuroectodermal differentiation and alters pluripotency states 7, while SALL3 haploinsufficiency may contribute to 18q deletion syndrome phenotypes 1.

Sources cited
1
SALL3 is a zinc finger protein family member mapped to 18q23, expressed in fetal brain and adult tissues; haploinsufficiency may contribute to 18q deletion syndrome
PMID: 10610715
2
SALL3 directly interacts with DNMT3A via its double zinc finger motif and inhibits CpG island methylation; SALL3 depletion increases methyltransferase activity
PMID: 19139273
3
SALL3 mRNA is downregulated in hepatocellular carcinoma tissues due to promoter CpG island hypermethylation; demethylating agents restore SALL3 expression
PMID: 22690083
4
SALL3 expression predicts hiPSC differentiation propensity, promoting ectoderm differentiation while inhibiting mesoderm/endoderm differentiation through modulation of DNMT3B and DNA methylation
PMID: 31092818
5
SALL3 promoter hypermethylation and downregulation occur in cervical cancer, particularly in HPV-positive samples
PMID: 31699190
6
SALL3 hypermethylation in cervical cancer associates with HPV infection; demethylation restores SALL3 expression and reduces cell proliferation
PMID: 26697877
7
SALL3 regulates tyrosine hydroxylase expression and promotes dopaminergic neuron development in the olfactory bulb
PMID: 21701790
8
SALL3 downregulation mediates loss of neuroectodermal differentiation in hESCs with chromosome 18q loss; SALL3 restoration rescues differentiation capacity
PMID: 38552632
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
COQ2Protein interaction90%PPDPFLShared pathway25%ETV3LShared pathway25%ERFLShared pathway25%NKX1-2Shared pathway25%NHSL2Shared pathway25%
Tissue Expression

No tissue expression data available for this gene.

Gene Interaction Network
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SALL3COQ2PPDPFLETV3LERFLNKX1-2NHSL2
PROTEIN STRUCTURE
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PDB7Y3L · 2.50 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.75LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.54 [0.39–0.75]
RankingsWhere SALL3 stands among ~20K protein-coding genes
  • #12,872of 20,598
    Most Researched26
  • #6,007of 17,882
    Most Constrained (LOEUF)0.75
Genes detectedSALL3
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Aberrant methylation and downregulation of sall3 in human hepatocellular carcinoma.
PMID: 22690083
World J Gastroenterol · 2012
1.00
2
SALL3, a new member of the human spalt-like gene family, maps to 18q23.
PMID: 10610715
Genomics · 1999
0.90
3
SALL3 expression balance underlies lineage biases in human induced pluripotent stem cell differentiation.
PMID: 31092818
Nat Commun · 2019
0.80
4
SALL3 mediates the loss of neuroectodermal differentiation potential in human embryonic stem cells with chromosome 18q loss.
PMID: 38552632
Stem Cell Reports · 2024
0.70
5
SALL3 interacts with DNMT3A and shows the ability to inhibit CpG island methylation in hepatocellular carcinoma.
PMID: 19139273
Mol Cell Biol · 2009
0.60