SALL4 (spalt like transcription factor 4)

Gene

• Entrez ID: 57167
• Gene name: Spalt like transcription factor 4
• Gene symbol: SALL4
• Synonyms: DRRS, HSAL4, IVIC, ZNF797
• 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

SNPs

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

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT016935	hsa-miR-335-5p	Microarray	18185580
MIRT438578	hsa-miR-107	Immunofluorescence, Luciferase reporter assay, qRT-PCR, Western blot	23811124
MIRT438578	hsa-miR-107	Immunofluorescence, Luciferase reporter assay, qRT-PCR, Western blot	23811124
MIRT438578	hsa-miR-107	Immunofluorescence, Luciferase reporter assay, qRT-PCR, Western blot	23811124
MIRT438578	hsa-miR-107	Immunofluorescence, Luciferase reporter assay, qRT-PCR, Western blot	23811124
MIRT731777	hsa-miR-219a-5p	Luciferase reporter assay, qRT-PCR, Western blot	26238082
MIRT731777	hsa-miR-219a-5p	Luciferase reporter assay, qRT-PCR, Western 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

Transcription factors

Transcription factor	Regulation	Reference
SALL4	Unknown	20505821
STAT3	Activation	19151334

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IEA
GO:0000792	Component	Heterochromatin	IEA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA	21873635
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA	21873635
GO:0001833	Process	Inner cell mass cell proliferation	IEA
GO:0001843	Process	Neural tube closure	IEA
GO:0003281	Process	Ventricular septum development	IEA
GO:0005515	Function	Protein binding	IPI	21914818
GO:0005634	Component	Nucleus	IBA	21873635
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	21873635
GO:0008134	Function	Transcription factor binding	IEA
GO:0030326	Process	Embryonic limb morphogenesis	IEA
GO:0032991	Component	Protein-containing complex	IEA
GO:0035019	Process	Somatic stem cell population maintenance	TAS
GO:0043231	Component	Intracellular membrane-bounded organelle	IDA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0046872	Function	Metal ion binding	IEA

Other IDs

• MIM: 607343
• HGNC: 15924
• e!Ensembl: ENSG00000101115

Protein

• UniProt ID: 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

• Sequence:

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

• Sequence length: 1053

Pathways

Reactome:

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

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Duane-radial ray syndrome	Acro-renal-ocular syndrome, Okihiro Syndrome, Okihiro syndrome due to 20q13 microdeletion, Okihiro syndrome due to a point mutation	rs74315424, rs1601170510, rs1601170799, rs1601168967, rs74315425, rs1601168015, rs1601171949, rs74315426, rs74315427, rs74315428, rs74315429, rs879255537, rs1555850961, rs1568864697, rs1568865283, rs1568866374, rs2078031226	26791099, 16402211, 12395297, 6426304, 12393809, 16086360, 12843316, 30067223
Atrial septal defect	Atrial Septal Defects	rs137852951, rs137852953, rs137852955, rs267607106, rs104893900, rs104893901, rs104893903, rs606231358, rs606231359, rs137852683, rs606231360, rs104893907, rs104894073, rs1585703301, rs104894074, rs267606903, rs121912677, rs387906585, rs387906773, rs72554028, rs587782928, rs587782929, rs587782930, rs587784067, rs1555226315, rs879253754, rs1114167356, rs773922431, rs1554093487, rs1554093433, rs1554093461, rs1561621507, rs1561619801, rs766692577, rs1581108237, rs1581111034, rs1579663872, rs1583066622, rs1456289029, rs1761430125
Cataract	Cataract	rs118203965, rs118203966, rs104893685, rs121908938, rs104894175, rs121909048, rs28937573, rs121909049, rs121909050, rs74315488, rs80358200, rs80358203, rs121434643, rs56141211, rs132630322, rs121917775, rs121917735, rs121917736, rs137853199, rs137853200, rs121917867, rs121917869, rs121913555, rs104893736, rs121909595, rs121909596, rs121909597, rs28931605, rs121909598, rs104893618, rs1695062782, rs74315486, rs74315487, rs74315490, rs74315489, rs745938679, rs1566402656, rs74315439, rs74315441, rs121912973, rs121917823, rs1593332981, rs121917825, rs121917827, rs113994108, rs387906963, rs387906964, rs1240503246, rs387906965, rs387906966, rs750207077, rs387907336, rs387907337, rs387907342, rs140332366, rs397514703, rs398122937, rs398122378, rs398122392, rs398122944, rs137853924, rs398122947, rs397515623, rs397515624, rs397515625, rs397515626, rs398122948, rs587778872, rs398123066, rs587777601, rs370424081, rs786205221, rs786205222, rs864309684, rs864309688, rs864309701, rs864309689, rs864309690, rs864309681, rs864309686, rs864309696, rs864309693, rs864309687, rs864309691, rs864309692, rs864309695, rs864309678, rs864309685, rs864309700, rs864309698, rs864309683, rs864309682, rs864309679, rs111534978, rs864309680, rs864309702, rs864622780, rs756898971, rs869312732, rs775038545, rs878852983, rs1114167312, rs1114167313, rs1114167314, rs1114167315, rs1114167307, rs886041410, rs886041412, rs1057518738, rs1057517926, rs1057518878, rs1057519616, rs12799308, rs1064793935, rs1064797219, rs1085307126, rs1085307127, rs765628635, rs1114167427, rs1114167433, rs1554744860, rs1554743428, rs747093432, rs1411557416, rs1555179713, rs1481963503, rs1555549755, rs1456161420, rs1555547008, rs1555889308, rs1555888762, rs766522434, rs1264025914, rs1553585262, rs1567671947, rs1337897299, rs764945940, rs1307969607, rs949335475, rs1184095219, rs776129797, rs1569203234, rs1567668570, rs749141857, rs764098604, rs1184398243, rs1578956689, rs1568480054, rs1564745688, rs1564722302, rs1564723150, rs1571175950, rs1569602837, rs1576552712, rs1575369255, rs981126461, rs1570403798, rs200557771, rs1477743112, rs1651879427, rs1651881222, rs1651919374, rs2024441691, rs148284531, rs1246080692
Duane syndrome	Duane Retraction Syndrome, Type 2, Duane Retraction Syndrome, Type 3	rs121912792, rs121912793, rs121912794, rs121912795, rs121912796, rs121912797, rs121912798, rs387906599	30067223, 16402211
Esophagus neoplasm	Squamous cell carcinoma of esophagus	rs28934578, rs121918714, rs1567556006, rs1575166666	30431698
External ophthalmoplegia	External Ophthalmoplegia	rs1569484022
Hearing loss	Conductive hearing loss, Sensorineural Hearing Loss (disorder)	rs267607135, rs267606855, rs779841884, rs267606854, rs28942097, rs121908073, rs121908076, rs74315289, rs121908144, rs111033313, rs74315437, rs121908348, rs121908349, rs121908350, rs397515359, rs180177151, rs180177154, rs180177153, rs35689081, rs35887622, rs80338944, rs104894396, rs104894398, rs80338947, rs80338948, rs80338942, rs104894402, rs104894403, rs80338945, rs28931594, rs80338940, rs80338941, rs80356590, rs80338950, rs387906706, rs387906707, rs387906708, rs398122848, rs387907016, rs587776894, rs387907088, rs397515411, rs370965183, rs398122930, rs199897298, rs111033187, rs111033448, rs199606180, rs111033284, rs397516413, rs111033305, rs111033220, rs111033256, rs111033297, rs111033253, rs104894408, rs111033295, rs397516874, rs76434661, rs111033335, rs397517323, rs111033247, rs367928692, rs374793617, rs143939430, rs397515605, rs80338939, rs200656442, rs779748859, rs587781261, rs587781262, rs143343083, rs200147906, rs730880338, rs797044491, rs146281367, rs756484720, rs869025593, rs201306709, rs540895576, rs777777359, rs879255246, rs1554358720, rs142498437, rs377145777, rs1057517519, rs779077039, rs952741388, rs1060499797, rs764139009, rs1060499590, rs1064794012, rs1064797115, rs756790858, rs775633137, rs1554952443, rs1554952193, rs782063761, rs1199012623, rs756147087, rs1555648043, rs1555661490, rs1553196233, rs781546107, rs111033190, rs775428246, rs782539587, rs537227442, rs148695069, rs1554835827, rs953422571, rs1554834186, rs1554834161, rs1554835103, rs1554577339, rs1554577402, rs768471577, rs782279338, rs781951909, rs998045226, rs375759781, rs755804651, rs1557458426, rs767797828, rs538027448, rs1559366084, rs367688416, rs1558480402, rs1558490542, rs1559870857, rs1560690591, rs1561299289, rs1562817224, rs1562817529, rs1562822565, rs1562835391, rs1564113368, rs1564554255, rs773851192, rs1564555240, rs761261855, rs1564805114, rs1565522273, rs1565127413, rs781790246, rs1565430886, rs1565469959, rs746667217, rs1565819402, rs1565855932, rs150529554, rs1567939793, rs201866631, rs754472294, rs1559372512, rs1558464965, rs1558488902, rs775062249, rs1226171550, rs1561590396, rs765574676, rs762876554, rs757327146, rs1564949059, rs1565519673, rs368050948, rs1565541888, rs781989117, rs1565402473, rs750358148, rs1386887007, rs1209665716, rs1567641234, rs1237955948, rs1569042782, rs752672077, rs146689036, rs1560070780, rs149712664, rs1564556995, rs762226905, rs773573968, rs1568528171, rs1198256157, rs377267777, rs370564476, rs1577876794, rs747787770, rs759432278, rs1043716893, rs1581138934, rs2033773650, rs1421964916, rs771766431, rs780917129, rs1895773215, rs1895769400, rs761543680, rs1565920060
Hirschsprung disease	Hirschsprung Disease	rs104893891, rs76262710, rs75075748, rs75996173, rs79014735, rs77316810, rs75076352, rs76087194, rs76534745, rs76764689, rs76449634, rs78098482, rs79661516, rs104894389, rs769735757, rs267606780, rs1568823467, rs377767412, rs193922699, rs75030001, rs606231342, rs1553540620, rs759944122, rs1057519322, rs1057519323, rs1057519052, rs1588873476, rs1588866040, rs1838178869
Holt-oram syndrome	Holt-Oram syndrome	rs104894377, rs104894378, rs104894381, rs104894382, rs1593880204, rs104894383, rs104894384, rs104894379, rs863223778, rs863223788, rs1555226315, rs863223776, rs886041247, rs1057516042, rs1555225344, rs1064795870, rs1565941587, rs1565927747, rs756049331, rs377649723, rs765204502, rs1565923887, rs1565927645, rs1565927664, rs1565927740, rs1565927794, rs1565935314, rs1565935397, rs1565935410, rs1565935426, rs1565935432, rs1565935458, rs1565939303, rs1565939337, rs1555226301, rs1565940841, rs1565941422, rs1565941529, rs767197919, rs1565941579, rs1555226575, rs1565942511, rs903933027, rs1565943328, rs1593876058, rs1869529188	30067223
Oculootoradial syndrome	IVIC syndrome, Oculootoradial syndrome	rs1601166963, rs1568866374	17256792
Microphthalmos	Microphthalmos	rs794726862, rs1329285216
Nystagmus	Nystagmus	rs137852207, rs137852208, rs1928435502, rs137852209, rs137852210, rs1929191668, rs137852211, rs137852212, rs2124209414, rs387906720, rs387906721, rs1602791884, rs786205896
Polydactyly	Polydactyly, Polydactyly preaxial type 1	rs1583729398, rs121917709, rs1583734240, rs121917714, rs397507422, rs398122899, rs587776959, rs386833752, rs1057518698, rs1060499558, rs755938967, rs1375768446, rs1309855392, rs1565601979, rs748321474, rs368652620, rs1562587032, rs760694987
Radioulnar synostosis	Radioulnar Synostosis	rs1595756416, rs1595756703, rs1231501584, rs1595756962, rs1595757203, rs1595763070, rs1595766210
Scoliosis	Scoliosis, unspecified	rs1057518828, rs147296805, rs758163506, rs1555613564, rs1596852902, rs1596853067, rs1596853085
Syndactyly	Syndactyly	rs878854345, rs104893635, rs28931600, rs587777050, rs587777051, rs606231304
Tetralogy of fallot	Tetralogy of Fallot	rs28939668, rs727504412, rs864321649, rs774966208, rs876660981, rs886044220, rs1114167357, rs1569484126, rs1569484164, rs1569484122, rs1569484124, rs1569484042, rs1569484120, rs1569484299, rs1569484301, rs1569484288
Ventricular septal defect	Ventricular Septal Defects	rs104894073, rs387906775	30067223
Vesicoureteral reflux	Vesico-Ureteral Reflux	rs587777684, rs148731211

Unknown
Disease name	Disease term	dbSNP ID	References
Abnormal dermatoglyphic pattern	Abnormal dermatoglyphic pattern
Bladder diverticulum	Bladder Diverticulum
Carpal synostosis	Carpal synostosis
Choanal atresia	Choanal Atresia
Coloboma of optic disc	Coloboma of optic disc
Congenital anomaly of limb	Limb Deformities, Congenital		30067223
Congenital coloboma of iris	Congenital coloboma of iris
Congenital epicanthus	Congenital Epicanthus
Congenital hypoplasia of radius	Congenital hypoplasia of radius
Congenital malrotation of intestine	Congenital malrotation of intestine
Convergence insufficiency	Convergence Insufficiency
Duane retraction syndrome	Duane Retraction Syndrome, Type 1 Duane Retraction Syndrome	rs121912838, rs574270883, rs375494218, rs886055152, rs547068631, rs66480716	16402211, 30067223, 30067223, 16402211
Dwarfism	Dwarfism
Facial paralysis	Facial paralysis
Fundus coloboma	Fundus coloboma
Horseshoe kidney	Horseshoe Kidney
Hydronephrosis	Hydronephrosis
Hypoplasia of optic disc	Hypoplasia of optic disc
Hypoplasia of thumb	Hypoplasia of thumb
Imperforate anus	Anus, Imperforate
Malrotation of kidney	Malrotation of kidney
Microcornea	Microcornea
Ptosis	Blepharoptosis, Ptosis	rs139920573
Radial polydactyly	Radial polydactyly
Renal agenesis	Congenital absence of kidneys syndrome
Renal hypoplasia	Congenital hypoplasia of kidney	rs561111097
Retinal coloboma	Coloboma of the Retina
Spina bifida occulta	Spina Bifida Occulta
Strabismus	Strabismus
Syndactyly of fingers	Syndactyly of fingers
Syndactyly of the toes	Syndactyly of the toes
Talipes	Talipes
Thumb aplasia	Thumb aplasia
Wildervanck`s syndrome	Wildervanck`s syndrome		30067223