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

Summary

Official Symbol: SALL1provided by HGNC
Official Full Name: spalt like transcription factor 1provided by HGNC
Primary source: HGNC:HGNC:10524
See related: Ensembl:ENSG00000103449 MIM:602218; AllianceGenome:HGNC:10524
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]
Expression: Biased expression in kidney (RPKM 14.2), thyroid (RPKM 12.6) and 8 other tissues See more
Orthologs: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 16q12.1

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (51135982..51152334, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (56933839..56950190, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (51169893..51185181, complement)

Chromosome 16 - NC_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A novel SALL1 C757T mutation in a Chinese family causes a rare disease --Townes-Brocks syndrome.
Title: A novel SALL1 C757T mutation in a Chinese family causes a rare disease --Townes-Brocks syndrome.
miR-4286 promotes prostate cancer progression by targeting the expression of SALL1.
Title: miR-4286 promotes prostate cancer progression by targeting the expression of SALL1.
Chromosomal Microarray Analysis Identifies a Novel SALL1 Deletion, Supporting the Association of Haploinsufficiency with a Mild Phenotype of Townes-Brocks Syndrome.
Title: Chromosomal Microarray Analysis Identifies a Novel SALL1 Deletion, Supporting the Association of Haploinsufficiency with a Mild Phenotype of Townes-Brocks Syndrome.
Townes-Brocks syndrome with craniosynostosis in two siblings.
Title: Townes-Brocks syndrome with craniosynostosis in two siblings.
Hsa_circ_0043265 Restrains Cell Proliferation, Migration and Invasion of Tongue Squamous Cell Carcinoma via Targeting the miR-1243/SALL1 Axis.
Title: Hsa_circ_0043265 Restrains Cell Proliferation, Migration and Invasion of Tongue Squamous Cell Carcinoma via Targeting the miR-1243/SALL1 Axis.
SOX2/SALL4 stemness axis modulates Notch signaling genes to maintain self-renewal capacity of esophageal squamous cell carcinoma.
Title: SOX2/SALL4 stemness axis modulates Notch signaling genes to maintain self-renewal capacity of esophageal squamous cell carcinoma.
In human glioblastoma cells and cerebral glioma tissues, SALL1 acted as a tumor suppressor gene by inhibiting Wnt/ss-catenin signaling.
Title: Spalt-Like Transcription Factor 1 (SALL1) Gene Expression Inhibits Cell Proliferation and Cell Migration of Human Glioma Cells Through the Wnt/β-Catenin Signaling Pathway.
Data identified SALL1 as a novel tumor suppressor in breast cancer. SALL1 can induce tumor cell senescence as a novel mechanism of tumor suppressor function. This molecular process acts through NuRD recruitment and is controlled by the MAPK and mTOR signaling pathways.
Title: SALL1 functions as a tumor suppressor in breast cancer by regulating cancer cell senescence and metastasis through the NuRD complex.
SALL1 mutations might cause Townes-Brocks Syndrome.
Title: Truncated SALL1 Impedes Primary Cilia Function in Townes-Brocks Syndrome.
Inhibition of SALL1 correlates with reduced levels of CDH1, an important contributor to epithelial-to-mesenchymal transition.
Title: An in vivo RNAi screen identifies SALL1 as a tumor suppressor in human breast cancer with a role in CDH1 regulation.

Submit: New GeneRIF Correction See all GeneRIFs (32)

Phenotypes

Go to the top of the page Help

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

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Townes-Brocks syndrome 1 MedGen: C4551481 OMIM: 107480 GeneReviews: SALL1-Related Townes-Brocks Syndrome	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2021-01-27) ClinGen Genome Curation Page Haploinsufficency Little evidence for dosage pathogenicity (Last evaluated 2021-01-27) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
A genome-wide association study of optic disc parameters. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies 8 novel loci associated with blood pressure responses to interventions in Han Chinese. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis of genome-wide association studies identifies novel loci that influence cupping and the glaucomatous process. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis of genome-wide association studies in &gt;80 000 subjects identifies multiple loci for C-reactive protein levels. EBI GWAS Catalog EBI GWAS CatalogPubMed
Weight loss after gastric bypass is associated with a variant at 15q26.1. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

AF021116 (e-PCR)
- UniSTS:53632

SHGC-9504 (e-PCR)
- UniSTS:69525

SALL1__5538 (e-PCR)
- UniSTS:464094

RH47686 (e-PCR)
- UniSTS:92136

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 DNA-binding transcription repressor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables beta-catenin binding	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in adrenal gland development	IEP Inferred from Expression Pattern more info	PubMed
involved_in branching involved in ureteric bud morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in embryonic digestive tract development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in embryonic digit morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in gonad development	IEP Inferred from Expression Pattern more info	PubMed
involved_in heart development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in inductive cell-cell signaling	ISS Inferred from Sequence or Structural Similarity more info
involved_in kidney development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in kidney epithelium development	ISS Inferred from Sequence or Structural Similarity more info
involved_in limb development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mesenchymal to epithelial transition involved in metanephros morphogenesis	IEP Inferred from Expression Pattern more info	PubMed
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in olfactory bulb interneuron differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in olfactory bulb mitral cell layer development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in olfactory nerve development	ISS Inferred from Sequence or Structural Similarity more info
involved_in pituitary gland development	IEP Inferred from Expression Pattern more info	PubMed
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of Wnt signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in ureteric bud development	ISS Inferred from Sequence or Structural Similarity more info
involved_in ureteric bud invasion	ISS Inferred from Sequence or Structural Similarity more info
involved_in ventricular septum development	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in chromocenter	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in heterochromatin	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

Go to the top of the page Help

Preferred Names: sal-like protein 1

Names: epididymis secretory protein Li 89; zinc finger protein 794; zinc finger protein SALL1; zinc finger protein Spalt-1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_007990.1 RefSeqGene

Range

5001..20298

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_674

mRNA and Protein(s)

NM_001127892.2 → NP_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/TrEMBL

H3BSM9

Related

ENSP00000456777.2, ENST00000570206.2

Conserved Domains (5) summary

cd11674
Location:967 → 1058

lambda-1; inner capsid protein lambda-1 or VP3

sd00017
Location:611 → 631

ZF_C2H2; C2H2 Zn finger [structural motif]

sd00019
Location:906 → 926

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:1037 → 1059

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:623 → 648

zf-H2C2_2; Zinc-finger double domain
NM_002968.3 → NP_002959.2 sal-like protein 1 isoform a

See identical proteins and their annotated locations for 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

Q99881, Q9NSC2, Q9NSC3, Q9P1R0

UniProtKB/TrEMBL

V9HVY5

Related

ENSP00000251020.4, ENST00000251020.9

Conserved Domains (5) summary

cd11674
Location:1064 → 1155

lambda-1; inner capsid protein lambda-1 or VP3

sd00017
Location:708 → 728

ZF_C2H2; C2H2 Zn finger [structural motif]

sd00019
Location:1003 → 1023

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:1134 → 1156

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:720 → 745

zf-H2C2_2; Zinc-finger double domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

51135982..51152334 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047434443.1 → XP_047290399.1 sal-like protein 1 isoform X1

UniProtKB/Swiss-Prot

Q99881, Q9NSC2, Q9NSC3, Q9P1R0

UniProtKB/TrEMBL

V9HVY5

Related

ENSP00000407914.2, ENST00000440970.6
XM_047434442.1 → XP_047290398.1 sal-like protein 1 isoform X1

UniProtKB/Swiss-Prot

Q99881, Q9NSC2, Q9NSC3, Q9P1R0

UniProtKB/TrEMBL

V9HVY5

Related

ENSP00000509873.1, ENST00000685868.1
XM_047434444.1 → XP_047290400.1 sal-like protein 1 isoform X1

UniProtKB/Swiss-Prot

Q99881, Q9NSC2, Q9NSC3, Q9P1R0

UniProtKB/TrEMBL

V9HVY5

Alternate T2T-CHM13v2.0

Genomic

NC_060940.1 Alternate T2T-CHM13v2.0

Range

56933839..56950190 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054313590.1 → XP_054169565.1 sal-like protein 1 isoform X1

UniProtKB/TrEMBL

V9HVY5
XM_054313589.1 → XP_054169564.1 sal-like protein 1 isoform X1

UniProtKB/TrEMBL

V9HVY5