This gene encodes a sal-like C2H2-type zinc-finger protein, and belongs to a family of evolutionarily conserved genes found in species as diverse as Drosophila, C. elegans, and vertebrates. Mutations in some of these genes are associated with congenital disorders in human, suggesting their importance in embryonic development. This protein binds to DNA methyltransferase 3 alpha ... See more...

Aliases for SALL3 Gene

Aliases for SALL3 Gene

  • Spalt Like Transcription Factor 3 2 3 5
  • ZNF796 2 3 4
  • Zinc Finger Protein 796 3 4
  • Sal-Like Protein 3 3 4
  • HSALL3 3 4
  • Epididymis Secretory Sperm Binding Protein 3
  • C2H2 Zinc Finger Protein SALL3 3
  • Spalt-Like Zinc Finger Protein 3
  • Zinc Finger Protein SALL3 4
  • Sal (Drosophila)-Like 3 2
  • Sal-Like 3 (Drosophila) 2
  • SALL3 5

External Ids for SALL3 Gene

Previous GeneCards Identifiers for SALL3 Gene

  • GC18U990052
  • GC18P076766
  • GC18P076475
  • GC18P074839
  • GC18P074841
  • GC18P073383

Summaries for SALL3 Gene

Entrez Gene Summary for SALL3 Gene

  • This gene encodes a sal-like C2H2-type zinc-finger protein, and belongs to a family of evolutionarily conserved genes found in species as diverse as Drosophila, C. elegans, and vertebrates. Mutations in some of these genes are associated with congenital disorders in human, suggesting their importance in embryonic development. This protein binds to DNA methyltransferase 3 alpha (DNMT3A), and reduces DNMT3A-mediated CpG island methylation. It is suggested that silencing of this gene, resulting in acceleration of DNA methylation, may have a role in oncogenesis. [provided by RefSeq, Oct 2011]

GeneCards Summary for SALL3 Gene

SALL3 (Spalt Like Transcription Factor 3) is a Protein Coding gene. Diseases associated with SALL3 include Chromosome 18Q Deletion Syndrome and Ivic Syndrome. An important paralog of this gene is SALL1.

UniProtKB/Swiss-Prot Summary for SALL3 Gene

Gene Wiki entry for SALL3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SALL3 Gene

Genomics for SALL3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SALL3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH18J078978 Promoter/Enhancer 1.6 UCNEbase EPDnew Ensembl ENCODE 600.7 +1.3 1326 6.4 TEAD4 POLR2A EZH2 ZBTB20 YY1 ZNF335 ZNF398 TAF1 NANOG HLF LINC01896 SALL3 HSALNG0122726 ATP9B
GH18J078814 Enhancer 0.5 FANTOM5 Ensembl 4.7 -165.6 -165594 0.6 BHLHE40 SALL3 RF00017-2709 HSALNG0122715
GH18J078977 Promoter/Enhancer 0.9 EPDnew Ensembl ENCODE 0.7 -2.2 -2234 0.3 EZH2 LINC01896 SALL3 RF00994-452
GH18J078984 Promoter/Enhancer 0.9 Ensembl ENCODE 0.7 +4.9 4934 0.8 CTCF FOXA1 RFX1 RAD21 POLR2A EZH2 FOXA2 SMC3 SIN3A ZBTB33 SALL3 HSALNG0122726 ATP9B
GH18J078975 Enhancer 0.9 UCNEbase FANTOM5 Ensembl 0.4 -5.9 -5939 1.9 POLR2A EZH2 ETS1 POU5F1 LINC01896 SALL3 RF00994-452
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SALL3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SALL3

Top Transcription factor binding sites by QIAGEN in the SALL3 gene promoter:
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • Evi-1
  • FOXL1
  • POU3F2
  • POU3F2 (N-Oct-5a)

Genomic Locations for SALL3 Gene

Genomic Locations for SALL3 Gene
chr18:78,980,275-79,002,677
(GRCh38/hg38)
Size:
22,403 bases
Orientation:
Plus strand
chr18:76,740,275-76,762,677
(GRCh37/hg19)
Size:
22,403 bases
Orientation:
Plus strand

Genomic View for SALL3 Gene

Genes around SALL3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SALL3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SALL3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SALL3 Gene

Proteins for SALL3 Gene

  • Protein details for SALL3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BXA9-SALL3_HUMAN
    Recommended name:
    Sal-like protein 3
    Protein Accession:
    Q9BXA9
    Secondary Accessions:
    • Q9UGH1

    Protein attributes for SALL3 Gene

    Size:
    1300 amino acids
    Molecular mass:
    135346 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • [Isoform 1]: Lacks two zinc finger domains. Major isoform with isoform 2.
    • [Isoform 2]: Lacks two zinc finger domains. Major isoform with isoform 1.

    Alternative splice isoforms for SALL3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SALL3 Gene

Post-translational modifications for SALL3 Gene

  • Ubiquitination at Lys1198
  • Modification sites at PhosphoSitePlus

Other Protein References for SALL3 Gene

No data available for DME Specific Peptides for SALL3 Gene

Domains & Families for SALL3 Gene

Gene Families for SALL3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for SALL3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SALL3 Gene

GenScript: Design optimal peptide antigens:
  • SALL3 protein (A9JR48_HUMAN)
  • Zinc finger protein SALL3 (SALL3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9BXA9

UniProtKB/Swiss-Prot:

SALL3_HUMAN :
  • Belongs to the sal C2H2-type zinc-finger protein family.
Family:
  • Belongs to the sal C2H2-type zinc-finger protein family.
genes like me logo Genes that share domains with SALL3: view

Function for SALL3 Gene

Molecular function for SALL3 Gene

UniProtKB/Swiss-Prot Function:
Probable transcription factor.
GENATLAS Biochemistry:
spalt (sal)-like,Drosophila SAL like gene 3,expressed in fetal brain and in several adult tissues,haploinsufficency in the 18q deletion syndrome and may be contributing to the phenotype

Phenotypes From GWAS Catalog for SALL3 Gene

Gene Ontology (GO) - Molecular Function for SALL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0003700 DNA-binding transcription factor activity IBA 21873635
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with SALL3: view
genes like me logo Genes that share phenotypes with SALL3: view

Animal Models for SALL3 Gene

MGI Knock Outs for SALL3:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SALL3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SALL3 Gene

Localization for SALL3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SALL3 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SALL3 gene
Compartment Confidence
nucleus 4
plasma membrane 1
extracellular 1
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for SALL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA 21873635
genes like me logo Genes that share ontologies with SALL3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SALL3 Gene

Pathways & Interactions for SALL3 Gene

PathCards logo

SuperPathways for SALL3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SALL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IBA 21873635
GO:0021891 olfactory bulb interneuron development IEA --
GO:0035136 forelimb morphogenesis IEA --
GO:0035137 hindlimb morphogenesis IEA --
GO:0045879 negative regulation of smoothened signaling pathway IEA --
genes like me logo Genes that share ontologies with SALL3: view

No data available for Pathways by source and SIGNOR curated interactions for SALL3 Gene

Drugs & Compounds for SALL3 Gene

No Compound Related Data Available

Transcripts for SALL3 Gene

mRNA/cDNA for SALL3 Gene

1 REFSEQ mRNAs :
4 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SALL3

Alternative Splicing Database (ASD) splice patterns (SP) for SALL3 Gene

No ASD Table

Relevant External Links for SALL3 Gene

GeneLoc Exon Structure for
SALL3

Expression for SALL3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SALL3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SALL3 Gene

This gene is overexpressed in Vagina (x6.1), Brain - Spinal cord (cervical c-1) (x5.5), Brain - Caudate (basal ganglia) (x4.4), Brain - Amygdala (x4.2), and Brain - Nucleus accumbens (basal ganglia) (x4.1).

Protein differential expression in normal tissues from HIPED for SALL3 Gene

This gene is overexpressed in Saliva (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SALL3 Gene



Protein tissue co-expression partners for SALL3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SALL3

SOURCE GeneReport for Unigene cluster for SALL3 Gene:

Hs.700557

mRNA Expression by UniProt/SwissProt for SALL3 Gene:

Q9BXA9-SALL3_HUMAN
Tissue specificity: Widely expressed in adult with highest levels in heart. Expressed in fetal brain (in neurons of hippocampus, cortex, mediodorsal and ventrolateral thalamic nuclei, putamen, cerebellum and brainstem).
genes like me logo Genes that share expression patterns with SALL3: view

No data available for Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for SALL3 Gene

Orthologs for SALL3 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SALL3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SALL3 30 31
  • 98.4 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SALL3 31
  • 85 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia SALL3 30
  • 83.16 (n)
Dog
(Canis familiaris)
Mammalia SALL3 31
  • 81 (a)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Sall3 30
  • 80.99 (n)
Mouse
(Mus musculus)
Mammalia Sall3 30 17 31
  • 79 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SALL3 31
  • 77 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SALL3 30 31
  • 71.51 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SALL3 31
  • 74 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia sall3 30
  • 65.82 (n)
African clawed frog
(Xenopus laevis)
Amphibia sal1-A 30
Zebrafish
(Danio rerio)
Actinopterygii LOC560775 30
  • 65.3 (n)
sall3a 31
  • 56 (a)
OneToMany
sall3b 31
  • 53 (a)
OneToMany
Fruit Fly
(Drosophila melanogaster)
Insecta salr 31
  • 27 (a)
ManyToMany
salm 31
  • 26 (a)
ManyToMany
Worm
(Caenorhabditis elegans)
Secernentea sem-4 31
  • 30 (a)
OneToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes FZF1 31
  • 27 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 29 (a)
ManyToMany
-- 31
  • 25 (a)
ManyToMany
Species where no ortholog for SALL3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for SALL3 Gene

ENSEMBL:
Gene Tree for SALL3 (if available)
TreeFam:
Gene Tree for SALL3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SALL3: view image

Paralogs for SALL3 Gene

(33) SIMAP similar genes for SALL3 Gene using alignment to 3 proteins:

  • SALL3_HUMAN
  • A9JR48_HUMAN
  • I3L3L8_HUMAN

Pseudogenes.org Pseudogenes for SALL3 Gene

genes like me logo Genes that share paralogs with SALL3: view

Variants for SALL3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SALL3 Gene

SNP ID Clinical significance and condition Chr 18 pos Variation AA Info Type
746821 Benign: not provided 78,993,059(+) C/T SYNONYMOUS_VARIANT
754090 Likely Benign: not provided 78,992,546(+) G/A SYNONYMOUS_VARIANT
777279 Benign: not provided 78,994,226(+) G/A SYNONYMOUS_VARIANT
rs760494400 Likely Benign: Anophthalmia - microphthalmia 78,994,245(+) G/A MISSENSE_VARIANT
VAR_035552 A colorectal cancer sample p.Arg143His

Additional dbSNP identifiers (rs#s) for SALL3 Gene

Structural Variations from Database of Genomic Variants (DGV) for SALL3 Gene

Variant ID Type Subtype PubMed ID
dgv564n67 CNV gain 20364138
dgv565n67 CNV gain 20364138
dgv6099n54 CNV gain 21841781
dgv6100n54 CNV loss 21841781
dgv6101n54 CNV gain 21841781
dgv6102n54 CNV gain+loss 21841781
dgv6103n54 CNV loss 21841781
dgv6104n54 CNV gain+loss 21841781
esv2666555 CNV deletion 23128226
esv2717497 CNV deletion 23290073
esv29012 CNV loss 19812545
esv3643277 CNV loss 21293372
esv3643278 CNV gain 21293372
nsv1065902 CNV gain 25217958
nsv1071874 CNV deletion 25765185
nsv1133432 CNV deletion 24896259
nsv1141945 CNV deletion 24896259
nsv1143887 CNV deletion 24896259
nsv2377 CNV insertion 18451855
nsv458313 CNV loss 19166990
nsv577793 CNV loss 21841781
nsv577794 CNV gain 21841781
nsv577795 CNV loss 21841781
nsv577796 CNV loss 21841781
nsv577799 CNV gain+loss 21841781
nsv577800 CNV loss 21841781
nsv577821 CNV loss 21841781
nsv828333 CNV loss 20364138
nsv828338 CNV gain 20364138
nsv828342 CNV gain 20364138

Variation tolerance for SALL3 Gene

Residual Variation Intolerance Score: 37.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.15; 69.47% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SALL3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SALL3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SALL3 Gene

Disorders for SALL3 Gene

MalaCards: The human disease database

(6) MalaCards diseases for SALL3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
chromosome 18q deletion syndrome
  • chromosome 18q- syndrome
ivic syndrome
  • radial ray defects, hearing impairment, external ophthalmoplegia, and thrombocytopenia
ureteral benign neoplasm
  • neoplasm of ureter
duane-radial ray syndrome
  • drrs
townes-brocks syndrome
  • renal-ear-anal-radial syndrome
- elite association - COSMIC cancer census association via MalaCards
Search SALL3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SALL3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with SALL3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SALL3 Gene

Publications for SALL3 Gene

  1. SALL3, a new member of the human spalt-like gene family, maps to 18q23. (PMID: 10610715) Kohlhase J … Engel W (Genomics 1999) 2 3 4
  2. Maternal genes and facial clefts in offspring: a comprehensive search for genetic associations in two population-based cleft studies from Scandinavia. (PMID: 20634891) Jugessur A … Murray JC (PloS one 2010) 3 41
  3. Genome-wide association study of rheumatoid arthritis in the Spanish population: KLF12 as a risk locus for rheumatoid arthritis susceptibility. (PMID: 18668548) Julià A … Marsal S (Arthritis and rheumatism 2008) 3 41
  4. SALL3 expression balance underlies lineage biases in human induced pluripotent stem cell differentiation. (PMID: 31092818) Kuroda T … Sato Y (Nature communications 2019) 3
  5. [Correlation between Methylation of SALL3 and Cervical Cancer]. (PMID: 31699190) Zhao J … Yang XF (Zhongguo yi xue ke xue yuan xue bao. Acta Academiae Medicinae Sinicae 2019) 3

Products for SALL3 Gene

Sources for SALL3 Gene