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SALL1 spalt-like transcription factor 1 [ Homo sapiens (human) ]

Gene ID: 6299, updated on 19-Dec-2014
Official Symbol
SALL1provided by HGNC
Official Full Name
spalt-like transcription factor 1provided by HGNC
Primary source
HGNC:HGNC:10524
See related
Ensembl:ENSG00000103449; HPRD:03742; MIM:602218; Vega:OTTHUMG00000133176
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
TBS; HSAL1; Sal-1; ZNF794; HEL-S-89
Summary
The protein encoded by this gene is a zinc finger transcriptional repressor and may be part of the NuRD histone deacetylase complex (HDAC). Defects in this gene are a cause of Townes-Brocks syndrome (TBS) as well as bronchio-oto-renal syndrome (BOR). Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
See SALL1 in Epigenomics, MapViewer
Location:
16q12.1
Exon count:
5
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 16 NC_000016.10 (51135975..51152314, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (51169886..51185183, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101927334 Neighboring gene collagen alpha-3(IV) chain-like Neighboring gene superoxide dismutase 1, soluble pseudogene 2 Neighboring gene uracil-DNA glycosylase-like Neighboring gene uracil-DNA glycosylase pseudogene 1 Neighboring gene uncharacterized LOC102723323

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Townes syndrome
MedGen: C0265246 OMIM: 107480 GeneReviews: Townes-Brocks Syndrome
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-04-26)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-04-26)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
A genome-wide association study of optic disc parameters.
NHGRI GWA Catalog
Genome-wide association study identifies 8 novel loci associated with blood pressure responses to interventions in Han Chinese.
NHGRI GWA Catalog
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies in >80 000 subjects identifies multiple loci for C-reactive protein levels.
NHGRI GWA Catalog
Weight loss after gastric bypass is associated with a variant at 15q26.1.
NHGRI GWA Catalog
  • Wnt Signaling Pathway NetPath, organism-specific biosystem (from WikiPathways)
    Wnt Signaling Pathway NetPath, organism-specific biosystemWnt family of proteins are a large family of cysteine-rich secreted glycoproteins that regulate cell-cell interactions. They bind to members of the Frizzled family of 7 transmembrane receptors. Bindi...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding NAS
Non-traceable Author Statement
more info
PubMed 
beta-catenin binding IDA
Inferred from Direct Assay
more info
PubMed 
chromatin binding IEA
Inferred from Electronic Annotation
more info
 
contributes_to histone deacetylase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
sequence-specific DNA binding transcription factor activity NAS
Non-traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
adrenal gland development IEP
Inferred from Expression Pattern
more info
PubMed 
branching involved in ureteric bud morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
embryonic digestive tract development IMP
Inferred from Mutant Phenotype
more info
PubMed 
embryonic digit morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
forelimb morphogenesis IEA
Inferred from Electronic Annotation
more info
 
gonad development IEP
Inferred from Expression Pattern
more info
PubMed 
heart development IMP
Inferred from Mutant Phenotype
more info
PubMed 
hindlimb morphogenesis IEA
Inferred from Electronic Annotation
more info
 
histone deacetylation ISS
Inferred from Sequence or Structural Similarity
more info
 
inductive cell-cell signaling ISS
Inferred from Sequence or Structural Similarity
more info
 
kidney development IMP
Inferred from Mutant Phenotype
more info
PubMed 
kidney epithelium development ISS
Inferred from Sequence or Structural Similarity
more info
 
limb development IMP
Inferred from Mutant Phenotype
more info
PubMed 
mesenchymal to epithelial transition involved in metanephros morphogenesis IEP
Inferred from Expression Pattern
more info
PubMed 
negative regulation of smoothened signaling pathway IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription from RNA polymerase II promoter IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
neural tube closure IEA
Inferred from Electronic Annotation
more info
 
olfactory bulb interneuron differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
olfactory bulb mitral cell layer development IMP
Inferred from Mutant Phenotype
more info
PubMed 
olfactory nerve development ISS
Inferred from Sequence or Structural Similarity
more info
 
outer ear morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
pituitary gland development IEP
Inferred from Expression Pattern
more info
PubMed 
positive regulation of Wnt signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription from RNA polymerase II promoter IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
regulation of neural precursor cell proliferation IEA
Inferred from Electronic Annotation
more info
 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
ureteric bud development ISS
Inferred from Sequence or Structural Similarity
more info
 
ureteric bud invasion ISS
Inferred from Sequence or Structural Similarity
more info
 
ventricular septum development ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
colocalizes_with NuRD complex ISS
Inferred from Sequence or Structural Similarity
more info
 
chromocenter IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
heterochromatin IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
sal-like protein 1
Names
sal-like protein 1
zinc finger protein 794
zinc finger protein SALL1
zinc finger protein Spalt-1
epididymis secretory protein Li 89

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_007990.1 

    Range
    5001..20298
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_674

mRNA and Protein(s)

  1. NM_001127892.1NP_001121364.1  sal-like protein 1 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a.
    Source sequence(s)
    AC009166, AK307835, Y18265
    Consensus CDS
    CCDS45483.1
    UniProtKB/Swiss-Prot
    Q9NSC2
    Related
    ENSP00000407914, ENST00000440970
    Conserved Domains (4) summary
    smart00355
    Location:669691
    ZnF_C2H2; zinc finger
    cd11674
    Location:9671058
    lambda-1; inner capsid protein lambda-1 or VP3
    pfam00096
    Location:10371059
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:623648
    zf-H2C2_2; Zinc-finger double domain
  2. NM_002968.2NP_002959.2  sal-like protein 1 isoform a

    See proteins identical to NP_002959.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (a).
    Source sequence(s)
    AC009166, BP229682, DA318592
    Consensus CDS
    CCDS10747.1
    UniProtKB/Swiss-Prot
    Q9NSC2
    Related
    ENSP00000251020, OTTHUMP00000164231, ENST00000251020, OTTHUMT00000256883
    Conserved Domains (4) summary
    smart00355
    Location:766788
    ZnF_C2H2; zinc finger
    cd11674
    Location:10641155
    lambda-1; inner capsid protein lambda-1 or VP3
    pfam00096
    Location:11341156
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:720745
    zf-H2C2_2; Zinc-finger double domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000016.10 

    Range
    51135975..51152314
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006721241.1XP_006721304.1  

    See proteins identical to XP_006721304.1

    UniProtKB/Swiss-Prot
    Q9NSC2
    Conserved Domains (4) summary
    smart00355
    Location:766788
    ZnF_C2H2; zinc finger
    cd11674
    Location:10641155
    lambda-1; inner capsid protein lambda-1 or VP3
    pfam00096
    Location:11341156
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:720745
    zf-H2C2_2; Zinc-finger double domain

Alternate CHM1_1.1

Genomic

  1. NC_018927.2 

    Range
    52577216..52592517
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

  1. AC_000148.1 

    Range
    37057983..37073288
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)