SALL4 spalt like transcription factor 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SALL4provided by HGNC
Official Full Name: spalt like transcription factor 4provided by HGNC
Primary source: HGNC:HGNC:15924
See related: Ensembl:ENSG00000101115 MIM:607343; AllianceGenome:HGNC:15924
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: DRRS; IVIC; HSAL4; ZNF797
Summary: This gene encodes a zinc finger transcription factor thought to play a role in the development of abducens motor neurons. Defects in this gene are a cause of Duane-radial ray syndrome (DRRS). Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]
Expression: Biased expression in testis (RPKM 2.4), thyroid (RPKM 1.3) and 4 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 20q13.2

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (51782331..51802521, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	20	NC_060944.1 (53553791..53573978, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (50398870..50419060, complement)

Chromosome 20 - NC_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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?

SALL4 Phenotype in Four Generations of One Family: An Interplay of the Upper Limb, Kidneys, and the Pituitary.
Title: SALL4 Phenotype in Four Generations of One Family: An Interplay of the Upper Limb, Kidneys, and the Pituitary.
SALL4 in gastrointestinal tract cancers: upstream and downstream regulatory mechanisms.
Title: SALL4 in gastrointestinal tract cancers: upstream and downstream regulatory mechanisms.
SALL4 is a CRL3[REN/KCTD11] substrate that drives Sonic Hedgehog-dependent medulloblastoma.
Title: SALL4 is a CRL3(REN/KCTD11) substrate that drives Sonic Hedgehog-dependent medulloblastoma.
SALL4 advances the proliferation and tumor cell stemness of colon cancer cells through the transcription and regulation of ROBO2.
Title: SALL4 advances the proliferation and tumor cell stemness of colon cancer cells through the transcription and regulation of ROBO2.
Acute lymphoblastic leukemia in children and SALL4 and BMI-1 gene expression.
Title: Acute lymphoblastic leukemia in children and SALL4 and BMI-1 gene expression.
Evaluation of Lineage/Site-specific Nuclear Immunohistochemical Markers SATB2, Cyclin D1, SALL4, and BCOR in High-grade Endometrial Carcinomas.
Title: Evaluation of Lineage/Site-specific Nuclear Immunohistochemical Markers SATB2, Cyclin D1, SALL4, and BCOR in High-grade Endometrial Carcinomas.
SALL4-related gene signature defines a specific stromal subset of pancreatic ductal adenocarcinoma with poor prognostic features.
Title: SALL4-related gene signature defines a specific stromal subset of pancreatic ductal adenocarcinoma with poor prognostic features.
SALL4 correlates with proliferation, metastasis, and poor prognosis in prostate cancer by affecting MAPK pathway.
Title: SALL4 correlates with proliferation, metastasis, and poor prognosis in prostate cancer by affecting MAPK pathway.
Dual-Regulated Mechanism of EZH2 and KDM6A on SALL4 Modulates Tumor Progression via Wnt/beta-Catenin Pathway in Gastric Cancer.
Title: Dual-Regulated Mechanism of EZH2 and KDM6A on SALL4 Modulates Tumor Progression via Wnt/β-Catenin Pathway in Gastric Cancer.
Salt-like transcription factor 4 promotes laryngeal cancer progression through transcriptional activation of ubiquitin-specific protease 21 to stabilize Yin Yang 1.
Title: Salt-like transcription factor 4 promotes laryngeal cancer progression through transcriptional activation of ubiquitin-specific protease 21 to stabilize Yin Yang 1.

Submit: New GeneRIF Correction See all GeneRIFs (172)

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

Associated conditions

Description	Tests
Duane-radial ray syndrome MedGen: C1623209 OMIM: 607323 GeneReviews: SALL4-Related Disorders	not available
Oculootoradial syndrome MedGen: C1327918 OMIM: 147750 GeneReviews: Not available	not available

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2021-01-11) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2021-01-11) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Cross-Disorder Genome-Wide Analyses Suggest a Complex Genetic Relationship Between Tourette's Syndrome and OCD. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide study of single-nucleotide polymorphisms associated with azoospermia and severe oligozoospermia. 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

RH46384 (e-PCR)
- UniSTS:4916

AL022348 (e-PCR)
- UniSTS:161

NoName (e-PCR)
- UniSTS:481534

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
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in embryonic limb morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in inner cell mass cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in neural tube closure	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in somatic stem cell population maintenance	IEA Inferred from Electronic Annotation more info
involved_in ventricular septum development	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in heterochromatin	IEA Inferred from Electronic Annotation more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
part_of protein-containing complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: sal-like protein 4

Names: zinc finger protein 797; zinc finger protein SALL4

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_008000.1 RefSeqGene

Range

5001..23468

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_675

mRNA and Protein(s)

NM_001318031.2 → NP_001304960.1 sal-like protein 4 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.

Source sequence(s)

AA419623, AA854044, AI638036, AL034420, AY170621, AY172738, BE549760, CN271900, DA666635, DA747867

Consensus CDS

CCDS82629.1

UniProtKB/Swiss-Prot

Q9UJQ4

Related

ENSP00000379319.3, ENST00000395997.3

Conserved Domains (3) summary

sd00017
Location:435 → 455

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:435 → 455

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:447 → 472

zf-H2C2_2; Zinc-finger double domain
NM_020436.5 → NP_065169.1 sal-like protein 4 isoform 1

See identical proteins and their annotated locations for NP_065169.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AA419623, AA854044, AI638036, AL034420, AY172738, BE549760, CN271900, DA666635, DA747867

Consensus CDS

CCDS13438.1

UniProtKB/Swiss-Prot

A2A2D8, Q540H3, Q6Y8G6, Q9UJQ4

Related

ENSP00000217086.4, ENST00000217086.9

Conserved Domains (3) summary

sd00017
Location:568 → 588

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:626 → 648

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:580 → 605

zf-H2C2_2; Zinc-finger double domain