Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	57167
Gene name	Spalt like transcription factor 4
Gene symbol	SALL4
Synonyms (NCBI Gene)	DRRSHSAL4IVICZNF797
Chromosome	20
Chromosome location	20q13.2
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 en

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SNP ID	Visualize variation	Clinical significance	Consequence
rs74315424	G>A	Pathogenic	Stop gained, coding sequence variant, intron variant
rs74315425	G>A	Pathogenic	Stop gained, coding sequence variant
rs74315426	T>A	Pathogenic	Stop gained, coding sequence variant
rs74315427	G>A	Pathogenic	Stop gained, coding sequence variant, intron variant
rs74315428	G>A	Pathogenic	Stop gained, coding sequence variant
rs74315429	T>C	Pathogenic	Coding sequence variant, missense variant
rs113920122	C>G,T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant, intron variant
rs142551587	C>G,T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs143601538	A>G	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, intron variant, synonymous variant
rs143818932	A>C,G	Conflicting-interpretations-of-pathogenicity, likely-benign	Missense variant, coding sequence variant, intron variant, synonymous variant
rs146143890	C>T	Conflicting-interpretations-of-pathogenicity, likely-benign	Coding sequence variant, synonymous variant
rs146604877	G>A,C	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant, intron variant
rs149430070	T>C	Conflicting-interpretations-of-pathogenicity, likely-benign	Genic upstream transcript variant, coding sequence variant, synonymous variant, upstream transcript variant
rs797044509	->G	Pathogenic	Coding sequence variant, frameshift variant
rs879255537	->C	Pathogenic	Coding sequence variant, frameshift variant
rs1057521145	G>A	Pathogenic	Stop gained, coding sequence variant
rs1131691536	G>-	Pathogenic	Coding sequence variant, intron variant, frameshift variant
rs1555850609	TGGGGGTTTGC>-	Pathogenic	Intron variant, coding sequence variant, frameshift variant
rs1555850961	C>-	Pathogenic	Coding sequence variant, frameshift variant
rs1568864697	A>-	Pathogenic	Intron variant, coding sequence variant, frameshift variant
rs1568865283	->C	Pathogenic	Coding sequence variant, frameshift variant
rs1568866374	T>-	Likely-pathogenic	Splice acceptor variant
rs1601166963	T>-	Pathogenic	Frameshift variant, coding sequence variant
rs1601168015	C>-	Pathogenic	Frameshift variant, coding sequence variant, intron variant
rs1601168967	A>-	Pathogenic	Frameshift variant, coding sequence variant, intron variant
rs1601170510	C>-	Pathogenic	Frameshift variant, coding sequence variant
rs1601170799	->G	Pathogenic	Frameshift variant, coding sequence variant
rs1601171949	G>-	Pathogenic	Frameshift variant, coding sequence variant

Show/Hide all (47)

miRTarBase ID	miRNA	Experiments	Reference
MIRT016935	hsa-miR-335-5p	Microarray	18185580
MIRT438578	hsa-miR-107	ImmunofluorescenceLuciferase reporter assayqRT-PCRWestern blot	23811124
MIRT438578	hsa-miR-107	ImmunofluorescenceLuciferase reporter assayqRT-PCRWestern blot	23811124
MIRT438578	hsa-miR-107	ImmunofluorescenceLuciferase reporter assayqRT-PCRWestern blot	23811124
MIRT438578	hsa-miR-107	ImmunofluorescenceLuciferase reporter assayqRT-PCRWestern blot	23811124
MIRT731777	hsa-miR-219a-5p	Luciferase reporter assayqRT-PCRWestern blot	26238082
MIRT731777	hsa-miR-219a-5p	Luciferase reporter assayqRT-PCRWestern blot	26238082
MIRT1324926	hsa-miR-103a	CLIP-seq
MIRT1324927	hsa-miR-129-5p	CLIP-seq
MIRT1324928	hsa-miR-1305	CLIP-seq
MIRT1324929	hsa-miR-153	CLIP-seq
MIRT1324930	hsa-miR-15a	CLIP-seq
MIRT1324931	hsa-miR-15b	CLIP-seq
MIRT1324932	hsa-miR-16	CLIP-seq
MIRT1324933	hsa-miR-195	CLIP-seq
MIRT1324934	hsa-miR-219-5p	CLIP-seq
MIRT1324935	hsa-miR-3074-3p	CLIP-seq
MIRT1324936	hsa-miR-30a	CLIP-seq
MIRT1324937	hsa-miR-30b	CLIP-seq
MIRT1324938	hsa-miR-30c	CLIP-seq
MIRT1324939	hsa-miR-30d	CLIP-seq
MIRT1324940	hsa-miR-30e	CLIP-seq
MIRT1324941	hsa-miR-330-3p	CLIP-seq
MIRT1324942	hsa-miR-424	CLIP-seq
MIRT1324943	hsa-miR-4445	CLIP-seq
MIRT1324944	hsa-miR-448	CLIP-seq
MIRT1324945	hsa-miR-450b-5p	CLIP-seq
MIRT1324946	hsa-miR-4782-3p	CLIP-seq
MIRT1324947	hsa-miR-497	CLIP-seq
MIRT1324948	hsa-miR-507	CLIP-seq
MIRT1324949	hsa-miR-508-3p	CLIP-seq
MIRT1324950	hsa-miR-518a-5p	CLIP-seq
MIRT1324951	hsa-miR-527	CLIP-seq
MIRT1324952	hsa-miR-544b	CLIP-seq
MIRT1324953	hsa-miR-557	CLIP-seq
MIRT1324954	hsa-miR-579	CLIP-seq
MIRT1324934	hsa-miR-219-5p	CLIP-seq
MIRT1324936	hsa-miR-30a	CLIP-seq
MIRT1324937	hsa-miR-30b	CLIP-seq
MIRT1324938	hsa-miR-30c	CLIP-seq
MIRT1324939	hsa-miR-30d	CLIP-seq
MIRT1324940	hsa-miR-30e	CLIP-seq
MIRT1324941	hsa-miR-330-3p	CLIP-seq
MIRT1324943	hsa-miR-4445	CLIP-seq
MIRT1324946	hsa-miR-4782-3p	CLIP-seq
MIRT1324949	hsa-miR-508-3p	CLIP-seq
MIRT1324952	hsa-miR-544b	CLIP-seq

Show/Hide all (2)

Transcription factor	Regulation	Reference
SALL4	Unknown	20505821
STAT3	Activation	19151334

Show/Hide all (24)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IEA
GO:0000792	Component	Heterochromatin	IEA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA
GO:0001701	Process	In utero embryonic development	IEA
GO:0001833	Process	Inner cell mass cell proliferation	IEA
GO:0001843	Process	Neural tube closure	IEA
GO:0003281	Process	Ventricular septum development	IEA
GO:0003677	Function	DNA binding	IEA
GO:0005515	Function	Protein binding	IPI	21914818
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005737	Component	Cytoplasm	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0007507	Process	Heart development	IEA
GO:0008270	Function	Zinc ion binding	IEA
GO:0009888	Process	Tissue development	IEA
GO:0021915	Process	Neural tube development	IEA
GO:0030326	Process	Embryonic limb morphogenesis	IEA
GO:0032991	Component	Protein-containing complex	IEA
GO:0035019	Process	Somatic stem cell population maintenance	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0046872	Function	Metal ion binding	IEA

MIM	HGNC	e!Ensembl
607343	15924	ENSG00000101115

Q9UJQ4

Protein name

Sal-like protein 4 (Zinc finger protein 797) (Zinc finger protein SALL4)

Protein function

Transcription factor with a key role in the maintenance and self-renewal of embryonic and hematopoietic stem cells.

PDB

5XWR , 6UML , 7BQU , 7BQV , 7Y3I , 7Y3K , 7Y3M , 8CUC , 8U15 , 8U16 , 8U17

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00096	zf-C2H2	382 → 404	Zinc finger, C2H2 type	Domain
PF00096	zf-C2H2	410 → 432	Zinc finger, C2H2 type	Domain
PF00096	zf-C2H2	594 → 616	Zinc finger, C2H2 type	Domain
PF00096	zf-C2H2	626 → 648	Zinc finger, C2H2 type	Domain
PF00096	zf-C2H2	872 → 892	Zinc finger, C2H2 type	Domain
PF00096	zf-C2H2	898 → 920	Zinc finger, C2H2 type	Domain

Tissue specificity

TISSUE SPECIFICITY: Expressed in testis. Constitutively expressed in acute myeloid leukemia (AML). {ECO:0000269|PubMed:16763212}.

Sequence

MSRRKQAKPQHINSEEDQGEQQPQQQTPEFADAAPAAPAAGELGAPVNHPGNDEVASEDE
ATVKRLRREETHVCEKCCAEFFSISEFLEHKKNCTKNPPVLIMNDSEGPVPSEDFSGAVL
SHQPTSPGSKDCHRENGGSSEDMKEKPDAESVVYLKTETALPPTPQDISYLAKGKVANTN
VTLQALRGTKVAVNQRSADALPAPVPGANSIPWVLEQILCLQQQQLQQIQLTEQIRIQVN
MWASHALHSSGAGADTLKTLGSHMSQQVSAAVALLSQKAGSQGLSLDALKQAKLPHANIP
SATSSLSPGLAPFTLKPDGTRVLPNVMSRLPSALLPQAPGSVLFQSPFSTVALDTSKKGK
GKPPNISAVDVKPKDEAALYKHKCKYCSKVFGTDSSLQIHLRSHTGERPFVCSVCGHRFT
TKGNLKVHFHRHPQVKANPQLFAEFQDKVAAGNGIPYALSVPDPIDEPSLSLDSKPVLVT
TSVGLPQNLSSGTNPKDLTGGSLPGDLQPGPSPESEGGPTLPGVGPNYNSPRAGGFQGSG
TPEPGSETLKLQQLVENIDKATTDPNECLICHRVLSCQSSLKMHYRTHTGERPFQCKICG
RAFSTKGNLKTHLGVHRTNTSIKTQHSCPICQKKFTNAVMLQQHIRMHMGGQIPNTPLPE
NPCDFTGSEPMTVGENGSTGAICHDDVIESIDVEEVSSQEAPSSSSKVPTPLPSIHSASP
TLGFAMMASLDAPGKVGPAPFNLQRQGSRENGSVESDGLTNDSSSLMGDQEYQSRSPDIL
ETTSFQALSPANSQAESIKSKSPDAGSKAESSENSRTEMEGRSSLPSTFIRAPPTYVKVE
VPGTFVGPSTLSPGMTPLLAAQPRRQAKQHGCTRCGKNFSSASALQIHERTHTGEKPFVC
NICGRAFTTKGNLKVHYMTHGANNNSARRGRKLAIENTMALLGTDGKRVSEIFPKEILAP
SVNVDPVVWNQYTSMLNGGLAVKTNEISVIQSGGVPTLPVSLGATSVVNNATVSKMDGSQ
SGISADVEKPSATDGVPKHQFPHFLEENKIAVS

Sequence length

1053

Interactions

View interactions

	Reactome
			POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation Transcriptional regulation of pluripotent stem cells Regulation of PTEN gene transcription

384

Show/Hide Causal Diseases (3)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Duane-radial ray syndrome	Likely pathogenic; Pathogenic	rs2122966358, rs2122963183, rs2122967143, rs2078032400, rs2122962507, rs2122964551, rs2122965458, rs74315424, rs1601170510, rs1601170799, rs1601168967, rs74315425, rs1601168015, rs1601171949, rs74315426 View all (20 more)	RCV001843831 RCV001920960 RCV002020060 RCV001942194 RCV001922917 RCV002245303 RCV002269253 RCV000003482 RCV000003483 RCV000003484 RCV000003485 RCV000003486 RCV000003487 RCV000003488 RCV000003489 RCV000003490 RCV000003492 RCV000003493 RCV002470640 RCV002839463 RCV002877524 RCV003000119 RCV000239600 RCV002790040 RCV003228721 RCV003330141 RCV003778267 RCV003501578 RCV003500139 RCV000529255 RCV000704462 RCV000693201 RCV004760767 RCV001059757 RCV001172279
Oculootoradial syndrome	Pathogenic; Likely pathogenic	rs1601166963, rs1568866374	RCV000003494 RCV001262787
SALL4-related disorder	Pathogenic; Likely pathogenic	rs2515716795, rs2515714748, rs2515716591	RCV004529310 RCV004529282 RCV004528735

Show/Hide Unknown Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Familial cancer of breast	Conflicting classifications of pathogenicity	rs145275500	RCV005906602
SALL4-Related Spectrum Disorders	Uncertain significance	rs138721208	RCV000284529

Show/Hide Text Mining Associations (96)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Abortion Missed	Associate	37611564
Acrorenal mandibular syndrome	Associate	12843316, 27661448, 37611564
Ameloblastoma	Associate	37559082
Atrial Fibrillation	Associate	28849223
Brain Stem Neoplasms	Associate	28126467
Breast Neoplasms	Associate	23954296, 25919570, 29356399, 29511085, 33308020, 36362083
Capillary Malformation Arteriovenous Malformation	Associate	12395297, 31388035
Carcinogenesis	Associate	26617716
Carcinoma Hepatocellular	Associate	24012616, 24860834, 26973422, 29976840, 30588199, 33406418, 36575044
Carcinoma Neuroendocrine	Associate	34106411
Carcinoma Pancreatic Ductal	Associate	29958885, 36587397
Carcinoma Renal Cell	Associate	32468053
Carcinoma Squamous Cell	Associate	24525512
Central Nervous System Vascular Malformations	Associate	17197532
Cholangiocarcinoma	Associate	30588199
Cognition Disorders	Associate	17197532
Coloboma	Associate	27661448
Colonic Neoplasms	Stimulate	35692499
Colorectal Neoplasms	Associate	23363002, 26617716, 28869451, 32719361, 35692499, 36434637
Coronary Disease	Associate	35619068
Deafness	Associate	17197532
Delayed Cranial Ossification due to CBFB Haploinsufficiency	Associate	27661448
Diabetes Mellitus	Associate	31615341
Duane Retraction Syndrome	Associate	12395297, 12843316, 17197532, 18055799, 23687435, 26791099, 27661448, 30067223, 35179219, 36635047, 36829172, 37611564
Dwarfism Pituitary	Associate	36714562, 37611564
Ear Diseases	Associate	30067223
Ectromelia	Associate	30067223
Endodermal Sinus Tumor	Associate	26076062, 31375771
Endometrial Neoplasms	Associate	26407074, 28272224, 39258697
Endometriosis	Associate	19690622
Epilepsy Absence	Associate	30067223
Esophageal Squamous Cell Carcinoma	Associate	31864704, 32819319
Eye Abnormalities	Associate	27661448
Fetal Diseases	Associate	12843316
Fibrosis of Extraocular Muscles Congenital 3B	Associate	29110737
Foot Deformities	Associate	26791099
Glioma	Associate	27938503, 29436585, 30423818
Glioma	Stimulate	28887597
Glycosuria Renal	Associate	21258884
Granulosa Cell Tumor	Associate	26076062
Growth Disorders	Associate	37611564
Heart Defects Congenital	Associate	30067223
Heart Diseases	Associate	24486774, 31388035
Hepatitis B	Stimulate	24012616
Holt Oram syndrome	Associate	12789647, 12843316, 36829172, 37611564
Inflammation	Associate	35059465
Kidney Diseases	Associate	27661448, 37611564
Kyphoscoliosis 1	Associate	36829172
Leukemia	Associate	21526180, 31653163, 35613022
Leukemia B Cell	Associate	16998462, 31653163
Leukemia Biphenotypic Acute	Associate	24463278
Leukemia Myelogenous Chronic BCR ABL Positive	Associate	28103766
Leukemia Myeloid Acute	Associate	16998462, 21526180, 31210317, 31653163
Lymphatic Metastasis	Associate	23363002, 28869451
Lymphatic Metastasis	Stimulate	33308020
Lymphoma	Associate	16998462
Lymphoma Non Hodgkin	Associate	24525512
Malignant Teratocarcinosarcoma	Associate	34106411
Mandibular Injuries	Associate	37611564
Melanoma	Associate	24525512
Microphthalmos	Associate	27661448
Midline granulomatosis	Associate	37611564
Multiple Myeloma	Associate	16998462
Myelodysplastic Syndromes	Associate	35613022
Narcolepsy	Associate	26333835
Neoplasm Metastasis	Stimulate	26407074, 35090523, 35692499
Neoplasm Metastasis	Associate	29958885, 37119046
Neoplasms	Associate	23363002, 24012616, 24525512, 24860834, 25464862, 26407074, 26617716, 28759035, 28887597, 29356399, 29511085, 29958885, 29976840, 32819319, 33406418 View all (9 more)
Neoplasms	Stimulate	33308020
Neoplasms Germ Cell and Embryonal	Associate	24525512
Neuroblastoma	Associate	32599975
Oculootoradial syndrome	Associate	36829172
Optic Nerve Aplasia Bilateral	Associate	37611564
Optic Nerve Hypoplasia	Associate	27661448
Ovarian Neoplasms	Associate	22962582, 24525512, 35090523
Papillorenal syndrome	Associate	26571382
Personality Disorders	Associate	36362083
Precursor B Cell Lymphoblastic Leukemia Lymphoma	Associate	24463278
Precursor Cell Lymphoblastic Leukemia Lymphoma	Associate	16998462
Prostatic Neoplasms	Associate	37119046, 37143720
Quadricuspid Aortic Valve	Associate	36756699
Radial Neuropathy	Associate	37611564
Radial Ray Deficiency X Linked	Associate	27661448, 37611564
Rhabdoid Tumor	Associate	24525512, 39412932
Rhabdomyosarcoma	Associate	24525512
Rufous oculocutaneous albinism	Associate	23363002
Salter Harris Fractures	Associate	36714562
Seminoma	Associate	23411938
Squamous Cell Carcinoma of Head and Neck	Associate	31799662
Stomach Neoplasms	Associate	24525512, 34332604, 34706681, 37974386
Syndrome	Associate	30067223
Teratogenesis	Associate	31388035
Testicular Germ Cell Tumor	Associate	33224314, 37508506
Thrombosis	Stimulate	26973422
Upper Extremity Deformities Congenital	Associate	37611564
Wilms Tumor	Associate	21258884, 24525512, 26317783

SALL4 (spalt like transcription factor 4)