SALL3 spalt like transcription factor 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SALL3provided by HGNC
Official Full Name: spalt like transcription factor 3provided by HGNC
Primary source: HGNC:HGNC:10527
See related: Ensembl:ENSG00000256463 MIM:605079; AllianceGenome:HGNC:10527
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: ZNF796
Summary: 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]
Expression: Biased expression in brain (RPKM 1.5), prostate (RPKM 0.7) and 2 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 18q23

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	18	NC_000018.10 (78979818..78998969)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	18	NC_060942.1 (79214396..79233545)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	18	NC_000018.9 (76739818..76758969)

Chromosome 18 - NC_000018.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Hypermethylation of SALL3 in promoter regions inhibits the expression of SALL3 in cervical cancer. Infection with high-risk HPV serotypes might increase the methylation of SALL3 promoter region, silence its expression,and thus promote the development of cervical cancer.
Title: [Correlation between Methylation of SALL3 and Cervical Cancer].
SALL3 expression in human induced pluripotent stem cells (hiPSCs) correlates positively with ectoderm differentiation capacity and negatively with mesoderm/endoderm differentiation capacity. Without affecting self-renewal of hiPSCs, SALL3 knockdown inhibits ectoderm differentiation and conversely enhances mesodermal/endodermal differentiation.
Title: SALL3 expression balance underlies lineage biases in human induced pluripotent stem cell differentiation.
Results found that SALL3 promoter methylation was associated with its transcriptional inhibition. Also, hypermethylation of CpG islands in the SALL3 promoter was independently associated with aggressive behavior of head and neck cancer (HNSCC) tumors, suggesting that SALL3 acts as a tumor suppressor gene and can serve as a prognostic biomarker in HNSCC.
Title: Epigenetic silencing of SALL3 is an independent predictor of poor survival in head and neck cancer.
sall3 shows aberrant methylation and downregulation in human hepatocellular carcinoma
Title: Aberrant methylation and downregulation of sall3 in human hepatocellular carcinoma.
Observational study of gene-disease association. (HuGE Navigator)
Title: Maternal genes and facial clefts in offspring: a comprehensive search for genetic associations in two population-based cleft studies from Scandinavia.
Studies indicate that vertebrate sal orthologues (spalt-like/sall) have important developmental roles during neural development and organogenesis and gentic diseases.
Title: Regulation and function of Spalt proteins during animal development.
This functional characterization of SALL3 sheds light on regulatory mechanisms for DNMT3A and provides new strategies to inhibit aberrant methylation in cancer.
Title: SALL3 interacts with DNMT3A and shows the ability to inhibit CpG island methylation in hepatocellular carcinoma.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of rheumatoid arthritis in the Spanish population: KLF12 as a risk locus for rheumatoid arthritis susceptibility. EBI GWAS Catalog EBI GWAS CatalogPubMed
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-15059 (e-PCR)
- UniSTS:37409

RH12091 (e-PCR)
- UniSTS:35132

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: sal-like protein 3

Names: C2H2 zinc finger protein SALL3; epididymis secretory sperm binding protein; hSALL3; spalt-like zinc finger protein; zinc finger protein 796

NCBI Reference Sequences (RefSeq)

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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

NG_030353.1 RefSeqGene

Range

4544..23695

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_171999.4 → NP_741996.2 sal-like protein 3

See identical proteins and their annotated locations for NP_741996.2

Status: VALIDATED

Source sequence(s)

AC099689

Consensus CDS

CCDS12013.1

UniProtKB/Swiss-Prot

Q9BXA9, Q9UGH1

UniProtKB/TrEMBL

A0A140TA70, A0A384MEH2

Related

ENSP00000441823.2, ENST00000537592.7

Conserved Domains (4) summary

COG5048
Location:412 → 734

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:681 → 701

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:1143 → 1163

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:693 → 718

zf-H2C2_2; Zinc-finger double domain