SALL1 (spalt like transcription factor 1) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: SALL1 (spalt like transcription factor 1) Homo sapiens
Analyze
Symbol: SALL1
Name: spalt like transcription factor 1
RGD ID: 1320515
HGNC Page HGNC
Description: Exhibits beta-catenin binding activity. Involved in several processes, including animal organ development; embryonic digit morphogenesis; and regulation of transcription by RNA polymerase II. Localizes to several cellular components, including chromocenter; heterochromatin; and nucleus. Implicated in Townes-Brocks syndrome and middle lobe syndrome. Biomarker of hepatoblastoma.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: epididymis secretory protein Li 89; HEL-S-89; HSAL1; Sal-1; sal-like protein 1; spalt-like transcription factor 1; TBS; zinc finger protein 794; zinc finger protein SALL1; zinc finger protein Spalt-1; ZNF794
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: SALL1P1  
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1651,135,975 - 51,151,367 (-)EnsemblGRCh38hg38GRCh38
GRCh381651,135,982 - 51,151,270 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371651,169,893 - 51,185,181 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361649,727,387 - 49,742,684 (-)NCBINCBI36hg18NCBI36
Build 341649,727,829 - 49,742,653NCBI
Celera1635,686,254 - 35,701,557 (-)NCBI
Cytogenetic Map16q12.1NCBI
HuRef1637,057,983 - 37,073,288 (-)NCBIHuRef
CHM1_11652,577,216 - 52,592,517 (-)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adrenal gland development  (IEP)
branching involved in ureteric bud morphogenesis  (ISS)
embryonic digestive tract development  (IMP)
embryonic digit morphogenesis  (IMP)
forelimb morphogenesis  (ISO)
gonad development  (IEP)
heart development  (IMP)
hindlimb morphogenesis  (ISO)
inductive cell-cell signaling  (ISO,ISS)
kidney development  (IMP)
kidney epithelium development  (ISS)
limb development  (IMP)
mesenchymal stem cell maintenance involved in metanephric nephron morphogenesis  (ISO)
mesenchymal to epithelial transition involved in metanephros morphogenesis  (IEP)
negative regulation of ectoderm development  (ISO)
negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis  (ISO)
negative regulation of mesoderm development  (ISO)
negative regulation of smoothened signaling pathway  (ISO)
negative regulation of transcription by RNA polymerase II  (IDA,ISO)
negative regulation of transcription, DNA-templated  (IDA)
neural tube closure  (ISO)
neural tube development  (ISO)
olfactory bulb development  (ISO)
olfactory bulb interneuron differentiation  (ISS)
olfactory bulb mitral cell layer development  (IMP)
olfactory nerve development  (ISO,ISS)
pituitary gland development  (IEP)
positive regulation of branching involved in ureteric bud morphogenesis  (ISO)
positive regulation of neuron differentiation  (ISO)
positive regulation of transcription by RNA polymerase II  (IDA,ISO)
positive regulation of transcription, DNA-templated  (IDA)
positive regulation of Wnt signaling pathway  (IDA)
regulation of neural precursor cell proliferation  (ISO)
regulation of transcription by RNA polymerase II  (IBA)
somatic stem cell population maintenance  (TAS)
ureteric bud development  (ISO,ISS)
ureteric bud invasion  (ISO,ISS)
ventricular septum development  (ISO,ISS)

Cellular Component
chromocenter  (IDA)
cytoplasm  (IDA)
heterochromatin  (IDA)
nucleoplasm  (TAS)
nucleus  (IBA,IDA)
NuRD complex  (ISO)

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
2-3 toe syndactyly  (IAGP)
2-4 finger syndactyly  (IAGP)
3-4 finger syndactyly  (IAGP)
3-4 toe syndactyly  (IAGP)
Abnormal pulmonary valve morphology  (IAGP)
Abnormal vertebral morphology  (IAGP)
Abnormality of the ribs  (IAGP)
Abnormality of the tragus  (IAGP)
Abnormality of the uterus  (IAGP)
Abnormality of vision  (IAGP)
Agenesis of corpus callosum  (IAGP)
Anal atresia  (IAGP)
Anal stenosis  (IAGP)
Anteriorly placed anus  (IAGP)
Aplasia/Hypoplasia of the 3rd toe  (IAGP)
Arnold-Chiari malformation  (IAGP)
Atrial septal defect  (IAGP)
Autosomal dominant inheritance  (IAGP)
Bifid scrotum  (IAGP)
Bifid uterus  (IAGP)
Blepharophimosis  (IAGP)
Bowel incontinence  (IAGP)
Broad hallux phalanx  (IAGP)
Broad thumb  (IAGP)
Cataract  (IAGP)
Chorioretinal coloboma  (IAGP)
Clinodactyly of the 5th finger  (IAGP)
Clinodactyly of the 5th toe  (IAGP)
Constipation  (IAGP)
Cranial nerve paralysis  (IAGP)
Cryptorchidism  (IAGP)
Delayed puberty  (IAGP)
Duane anomaly  (IAGP)
Duodenal atresia  (IAGP)
Ectopic kidney  (IAGP)
External ear malformation  (IAGP)
Facial asymmetry  (IAGP)
Failure to thrive  (IAGP)
Gastroesophageal reflux  (IAGP)
Global developmental delay  (IAGP)
Hearing impairment  (IAGP)
Hypoplasia of penis  (IAGP)
Hypospadias  (IAGP)
Hypothyroidism  (IAGP)
Intellectual disability  (IAGP)
Iris coloboma  (IAGP)
Limbal dermoid  (IAGP)
Lower limb asymmetry  (IAGP)
Macrotia  (IAGP)
Metatarsal synostosis  (IAGP)
Microcephaly  (IAGP)
Microphthalmia  (IAGP)
Microtia  (IAGP)
Multicystic kidney dysplasia  (IAGP)
Multiple renal cysts  (IAGP)
Overfolded helix  (IAGP)
Overfolding of the superior helices  (IAGP)
Partial duplication of thumb phalanx  (IAGP)
Patent ductus arteriosus  (IAGP)
Pes planus  (IAGP)
Preauricular pit  (IAGP)
Preauricular skin tag  (IAGP)
Preaxial hand polydactyly  (IAGP)
Pseudoepiphyses of second metacarpal  (IAGP)
Rectoperineal fistula  (IAGP)
Rectovaginal fistula  (IAGP)
Renal dysplasia  (IAGP)
Renal hypoplasia  (IAGP)
Renal insufficiency  (IAGP)
Satyr ear  (IAGP)
Sensorineural hearing impairment  (IAGP)
Short metatarsal  (IAGP)
Short stature  (IAGP)
Stahl ear  (IAGP)
Strabismus  (IAGP)
Subcutaneous nodule  (IAGP)
Tetralogy of Fallot  (IAGP)
Toe clinodactyly  (IAGP)
Toe syndactyly  (IAGP)
Triphalangeal thumb  (IAGP)
Ulnar deviation of finger  (IAGP)
Umbilical hernia  (IAGP)
Urethral valve  (IAGP)
Ventricular septal defect  (IAGP)
Vesicoureteral reflux  (IAGP)
Wide mouth  (IAGP)
References

Additional References at PubMed
PMID:8975705   PMID:9425907   PMID:9973281   PMID:10533063   PMID:10928856   PMID:10965108   PMID:11484202   PMID:11511981   PMID:11751684   PMID:11836251   PMID:12065233   PMID:12200128  
PMID:12395297   PMID:12477932   PMID:15158448   PMID:15342556   PMID:16221172   PMID:16344560   PMID:16429401   PMID:16443351   PMID:16545361   PMID:16670092   PMID:16971658   PMID:17426652  
PMID:17910067   PMID:18000979   PMID:18024993   PMID:18280297   PMID:18297069   PMID:18470945   PMID:19005989   PMID:19213029   PMID:19247946   PMID:19274049   PMID:19440552   PMID:19942929  
PMID:20301618   PMID:20548946   PMID:20634891   PMID:21062744   PMID:21300955   PMID:21532573   PMID:21873635   PMID:22308078   PMID:22504420   PMID:23069192   PMID:23643386   PMID:24165912  
PMID:24292671   PMID:25241763   PMID:25609649   PMID:26186194   PMID:26687479   PMID:28514442   PMID:29395067   PMID:29395072   PMID:29507755   PMID:29625565   PMID:29844126   PMID:30385546  
PMID:31040265   PMID:32296183   PMID:32694731  


Genomics

Comparative Map Data
SALL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1651,135,975 - 51,151,367 (-)EnsemblGRCh38hg38GRCh38
GRCh381651,135,982 - 51,151,270 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371651,169,893 - 51,185,181 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361649,727,387 - 49,742,684 (-)NCBINCBI36hg18NCBI36
Build 341649,727,829 - 49,742,653NCBI
Celera1635,686,254 - 35,701,557 (-)NCBI
Cytogenetic Map16q12.1NCBI
HuRef1637,057,983 - 37,073,288 (-)NCBIHuRef
CHM1_11652,577,216 - 52,592,517 (-)NCBICHM1_1
Sall1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39889,753,867 - 89,770,790 (-)NCBIGRCm39mm39
GRCm39 Ensembl889,753,863 - 89,770,790 (-)Ensembl
GRCm38889,027,242 - 89,044,162 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl889,027,235 - 89,044,162 (-)EnsemblGRCm38mm10GRCm38
MGSCv37891,551,141 - 91,568,061 (-)NCBIGRCm37mm9NCBIm37
MGSCv36891,918,348 - 91,932,544 (-)NCBImm8
Celera893,321,670 - 93,338,514 (-)NCBICelera
Cytogenetic Map8C3NCBI
Sall1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21918,005,782 - 18,022,705 (+)NCBI
Rnor_6.0 Ensembl1923,389,375 - 23,405,039 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01923,387,737 - 23,405,025 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01934,377,838 - 34,395,131 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41919,277,337 - 19,293,298 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11919,283,733 - 19,298,618 (+)NCBI
Celera1917,896,753 - 17,911,869 (+)NCBICelera
Cytogenetic Map19p11NCBI
Sall1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554339,144,748 - 9,161,171 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554339,146,074 - 9,161,171 (-)NCBIChiLan1.0ChiLan1.0
SALL1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11650,274,081 - 50,280,239 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1650,274,090 - 50,284,819 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01631,396,399 - 31,412,753 (-)NCBIMhudiblu_PPA_v0panPan3
SALL1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1264,242,742 - 64,260,021 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl264,243,987 - 64,259,521 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha260,816,127 - 60,833,504 (+)NCBI
ROS_Cfam_1.0264,787,008 - 64,804,401 (+)NCBI
UMICH_Zoey_3.1261,612,959 - 61,630,321 (+)NCBI
UNSW_CanFamBas_1.0262,631,291 - 62,648,633 (+)NCBI
UU_Cfam_GSD_1.0263,519,257 - 63,536,638 (+)NCBI
Sall1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934955,465,986 - 55,483,143 (+)NCBI
SpeTri2.0NW_0049364754,106,663 - 4,121,356 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SALL1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl633,732,016 - 33,748,704 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1633,731,666 - 33,748,698 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2630,222,502 - 30,239,229 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SALL1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1536,928,711 - 36,944,158 (-)NCBI
ChlSab1.1 Ensembl536,927,990 - 36,943,630 (-)Ensembl
Sall1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247575,572,510 - 5,587,623 (+)NCBI

Position Markers
RH47686  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371651,169,976 - 51,170,124UniSTSGRCh37
Build 361649,727,477 - 49,727,625RGDNCBI36
Celera1635,686,344 - 35,686,492RGD
Cytogenetic Map16q12.1UniSTS
HuRef1637,058,073 - 37,058,221UniSTS
AF021116  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371651,175,610 - 51,175,771UniSTSGRCh37
Build 361649,733,111 - 49,733,272RGDNCBI36
Celera1635,691,981 - 35,692,142RGD
Cytogenetic Map16q12.1UniSTS
HuRef1637,063,710 - 37,063,871UniSTS
SHGC-9504  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371651,179,561 - 51,179,682UniSTSGRCh37
Build 361649,737,062 - 49,737,183RGDNCBI36
Celera1635,695,934 - 35,696,055RGD
Cytogenetic Map16q12.1UniSTS
HuRef1637,067,666 - 37,067,787UniSTS
TNG Radiation Hybrid Map1620489.0UniSTS
SALL1__5538  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371651,170,255 - 51,171,008UniSTSGRCh37
Build 361649,727,756 - 49,728,509RGDNCBI36
Celera1635,686,623 - 35,687,375RGD
HuRef1637,058,352 - 37,059,104UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1630
Count of miRNA genes:723
Interacting mature miRNAs:818
Transcripts:ENST00000251020, ENST00000440970, ENST00000541611, ENST00000562674, ENST00000566102, ENST00000570206
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system adipose tissue appendage entire extraembryonic component
High
Medium 10 4 1213 372 7 372 224 21 951 285 352 733
Low 852 247 226 112 178 78 803 44 2518 77 891 111 37 305 487 1
Below cutoff 1221 2067 249 134 742 6 2910 1694 225 35 137 457 131 816 1929 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NG_007990 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001127892 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_002968 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC009166 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF017654 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF017655 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF074949 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK295103 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK307835 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC113881 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC113906 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC131548 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BP229682 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471092 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DA318592 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU668343 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KT584341 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X98833 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Y18264 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Y18265 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000251020   ⟹   ENSP00000251020
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1651,135,982 - 51,151,270 (-)Ensembl
RefSeq Acc Id: ENST00000440970   ⟹   ENSP00000407914
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1651,135,975 - 51,150,597 (-)Ensembl
RefSeq Acc Id: ENST00000562674
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1651,143,204 - 51,151,367 (-)Ensembl
RefSeq Acc Id: ENST00000566102   ⟹   ENSP00000455582
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1651,137,064 - 51,151,241 (-)Ensembl
RefSeq Acc Id: ENST00000570206   ⟹   ENSP00000456777
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1651,137,332 - 51,150,597 (-)Ensembl
RefSeq Acc Id: NM_001127892   ⟹   NP_001121364
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381651,135,982 - 51,150,597 (-)NCBI
GRCh371651,169,886 - 51,185,183 (-)ENTREZGENE
HuRef1637,057,983 - 37,073,288 (-)ENTREZGENE
CHM1_11652,577,216 - 52,591,842 (-)NCBI
Sequence:
RefSeq Acc Id: NM_002968   ⟹   NP_002959
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381651,135,982 - 51,151,270 (-)NCBI
GRCh371651,169,886 - 51,185,183 (-)ENTREZGENE
Build 361649,727,387 - 49,742,684 (-)NCBI Archive
HuRef1637,057,983 - 37,073,288 (-)ENTREZGENE
CHM1_11652,577,216 - 52,592,517 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_002959   ⟸   NM_002968
- Peptide Label: isoform a
- UniProtKB: Q9NSC2 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001121364   ⟸   NM_001127892
- Peptide Label: isoform b
- UniProtKB: Q9NSC2 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000456777   ⟸   ENST00000570206
RefSeq Acc Id: ENSP00000407914   ⟸   ENST00000440970
RefSeq Acc Id: ENSP00000455582   ⟸   ENST00000566102
RefSeq Acc Id: ENSP00000251020   ⟸   ENST00000251020
Protein Domains
C2H2-type

Promoters
RGD ID:7232211
Promoter ID:EPDNEW_H21847
Type:initiation region
Name:SALL1_1
Description:spalt like transcription factor 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H21848  EPDNEW_H21849  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381651,151,270 - 51,151,330EPDNEW
RGD ID:7232203
Promoter ID:EPDNEW_H21848
Type:initiation region
Name:SALL1_2
Description:spalt like transcription factor 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H21849  EPDNEW_H21847  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381651,151,661 - 51,151,721EPDNEW
RGD ID:7232205
Promoter ID:EPDNEW_H21849
Type:initiation region
Name:SALL1_3
Description:spalt like transcription factor 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H21848  EPDNEW_H21847  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381651,152,334 - 51,152,394EPDNEW

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_002968.2(SALL1):c.1214dup (p.Leu406fs) duplication Townes syndrome [RCV000548925] Chr16:51141007..51141008 [GRCh38]
Chr16:51174918..51174919 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.3(SALL1):c.1270del (p.Gln424fs) deletion Townes-Brocks syndrome 1 [RCV000007851] Chr16:51140952 [GRCh38]
Chr16:51174863 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.2(SALL1):c.1115C>A (p.Ser372Ter) single nucleotide variant Townes-Brocks syndrome 1 [RCV000007852] Chr16:51141107 [GRCh38]
Chr16:51175018 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.2(SALL1):c.826C>T (p.Arg276Ter) single nucleotide variant Townes syndrome [RCV000792529]|Townes-Brocks syndrome 1 [RCV000007853] Chr16:51141396 [GRCh38]
Chr16:51175307 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.2(SALL1):c.1115C>G (p.Ser372Ter) single nucleotide variant Townes-Brocks syndrome 1 [RCV000007854] Chr16:51141107 [GRCh38]
Chr16:51175018 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.3(SALL1):c.1277_1278del (p.Arg426fs) deletion Townes-Brocks syndrome 1 [RCV000007855] Chr16:51140944..51140945 [GRCh38]
Chr16:51174855..51174856 [GRCh37]
Chr16:16q12.1
pathogenic
NM_001127892.1(SALL1):c.1054_1055CA[1] (p.His352fs) microsatellite Townes-Brocks syndrome 1 [RCV000007856] Chr16:51140874..51140875 [GRCh38]
Chr16:51174785..51174786 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.3(SALL1):c.1821del (p.Leu608fs) deletion Townes-Brocks-branchiootorenal-like syndrome [RCV000007857] Chr16:51140401 [GRCh38]
Chr16:51174312 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.3(SALL1):c.792_793del (p.Leu264fs) deletion Townes-Brocks syndrome 1 [RCV000007858] Chr16:51141429..51141430 [GRCh38]
Chr16:51175340..51175341 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.2(SALL1):c.967C>T (p.Gln323Ter) single nucleotide variant Townes syndrome [RCV000697040]|Townes-Brocks syndrome 1 [RCV000989601]|Townes-Brocks-branchiootorenal-like syndrome [RCV000007859] Chr16:51141255 [GRCh38]
Chr16:51175166 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.2(SALL1):c.1256T>A (p.Leu419Ter) single nucleotide variant Townes-Brocks syndrome 1 [RCV000007860] Chr16:51140966 [GRCh38]
Chr16:51174877 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.3(SALL1):c.995del (p.Pro332fs) deletion Townes-Brocks syndrome 1 [RCV000007862] Chr16:51141227 [GRCh38]
Chr16:51175138 [GRCh37]
Chr16:16q12.1
pathogenic
SALL1, 2-BP DEL, 3414AT deletion Townes-Brocks syndrome 1 [RCV000007863] Chr16:16q12.1 pathogenic
NM_001127892.1(SALL1):c.-39_-34del deletion not provided [RCV000722650] Chr16:51141964..51141969 [GRCh38]
Chr16:51175875..51175880 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.466_477dup (p.Ser159_Gly160insSerSerSerSer) microsatellite not provided [RCV000723051]|not specified [RCV000730806] Chr16:51141744..51141745 [GRCh38]
Chr16:51175655..51175656 [GRCh37]
Chr16:16q12.1
benign|uncertain significance
NM_002968.2(SALL1):c.2256del (p.Tyr753fs) deletion Townes syndrome [RCV000525061] Chr16:51139966 [GRCh38]
Chr16:51173877 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.2(SALL1):c.*714A>G single nucleotide variant Lung cancer [RCV000099970] Chr16:51136398 [GRCh38]
Chr16:51170309 [GRCh37]
Chr16:16q12.1
uncertain significance
GRCh38/hg38 16q11.2-12.1(chr16:46466829-52314178)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052404]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052404]|See cases [RCV000052404] Chr16:46466829..52314178 [GRCh38]
Chr16:46500741..52348090 [GRCh37]
Chr16:45058242..50905591 [NCBI36]
Chr16:16q11.2-12.1
pathogenic
GRCh38/hg38 16q11.2-12.1(chr16:46466829-51939304)x1 copy number loss See cases [RCV000053309] Chr16:46466829..51939304 [GRCh38]
Chr16:46500741..51973216 [GRCh37]
Chr16:45058242..50530717 [NCBI36]
Chr16:16q11.2-12.1
pathogenic
GRCh38/hg38 16q11.2-12.1(chr16:46466829-51673196)x1 copy number loss See cases [RCV000053310] Chr16:46466829..51673196 [GRCh38]
Chr16:46500741..51707107 [GRCh37]
Chr16:45058242..50264608 [NCBI36]
Chr16:16q11.2-12.1
pathogenic
GRCh38/hg38 16q11.2-12.1(chr16:46471520-52405956)x1 copy number loss See cases [RCV000053328] Chr16:46471520..52405956 [GRCh38]
Chr16:46505432..52439868 [GRCh37]
Chr16:45062933..50997369 [NCBI36]
Chr16:16q11.2-12.1
pathogenic
GRCh38/hg38 16q12.1-12.2(chr16:47250644-54121476)x1 copy number loss See cases [RCV000053329] Chr16:47250644..54121476 [GRCh38]
Chr16:47284555..54155388 [GRCh37]
Chr16:45842056..52712889 [NCBI36]
Chr16:16q12.1-12.2
pathogenic
GRCh38/hg38 16q12.1(chr16:48156593-52220374)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053330]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053330]|See cases [RCV000053330] Chr16:48156593..52220374 [GRCh38]
Chr16:48190504..52254286 [GRCh37]
Chr16:46748005..50811787 [NCBI36]
Chr16:16q12.1
pathogenic
GRCh38/hg38 16q12.1(chr16:49740807-51876620)x1 copy number loss See cases [RCV000053331] Chr16:49740807..51876620 [GRCh38]
Chr16:49774718..51910531 [GRCh37]
Chr16:48332219..50468032 [NCBI36]
Chr16:16q12.1
pathogenic
GRCh38/hg38 16q12.1-12.2(chr16:50784329-55566715)x1 copy number loss See cases [RCV000053332] Chr16:50784329..55566715 [GRCh38]
Chr16:50818240..55600627 [GRCh37]
Chr16:49375741..54158128 [NCBI36]
Chr16:16q12.1-12.2
pathogenic
NM_002968.2(SALL1):c.3629C>T (p.Pro1210Leu) single nucleotide variant Malignant melanoma [RCV000071152] Chr16:51137458 [GRCh38]
Chr16:51171369 [GRCh37]
Chr16:49728870 [NCBI36]
Chr16:16q12.1
not provided
NM_002968.2(SALL1):c.3356C>T (p.Ser1119Phe) single nucleotide variant Malignant melanoma [RCV000071153] Chr16:51138866 [GRCh38]
Chr16:51172777 [GRCh37]
Chr16:49730278 [NCBI36]
Chr16:16q12.1
not provided
NM_002968.2(SALL1):c.2395C>T (p.Pro799Ser) single nucleotide variant Malignant melanoma [RCV000071154] Chr16:51139827 [GRCh38]
Chr16:51173738 [GRCh37]
Chr16:49731239 [NCBI36]
Chr16:16q12.1
not provided
NM_002968.2(SALL1):c.3674C>T (p.Ser1225Leu) single nucleotide variant Malignant melanoma [RCV000063055] Chr16:51137413 [GRCh38]
Chr16:51171324 [GRCh37]
Chr16:49728825 [NCBI36]
Chr16:16q12.1
not provided
NM_002968.2(SALL1):c.3239C>T (p.Ser1080Leu) single nucleotide variant Malignant melanoma [RCV000063056] Chr16:51138983 [GRCh38]
Chr16:51172894 [GRCh37]
Chr16:49730395 [NCBI36]
Chr16:16q12.1
not provided
NM_002968.2(SALL1):c.3116C>T (p.Ser1039Phe) single nucleotide variant Malignant melanoma [RCV000063057] Chr16:51139106 [GRCh38]
Chr16:51173017 [GRCh37]
Chr16:49730518 [NCBI36]
Chr16:16q12.1
not provided
NM_002968.2(SALL1):c.1015C>T (p.Pro339Ser) single nucleotide variant Malignant melanoma [RCV000063058] Chr16:51141207 [GRCh38]
Chr16:51175118 [GRCh37]
Chr16:49732619 [NCBI36]
Chr16:16q12.1
not provided
NM_002968.2(SALL1):c.624C>T (p.Ala208=) single nucleotide variant Malignant melanoma [RCV000063059] Chr16:51141598 [GRCh38]
Chr16:51175509 [GRCh37]
Chr16:49733010 [NCBI36]
Chr16:16q12.1
not provided
NM_002968.2(SALL1):c.477_478insAGC (p.Ser159_Gly160insSer) insertion not specified [RCV000175746] Chr16:51141744..51141745 [GRCh38]
Chr16:51175655..51175656 [GRCh37]
Chr16:16q12.1
likely benign
GRCh38/hg38 16q11.2-12.1(chr16:46466829-52422170)x1 copy number loss See cases [RCV000137306] Chr16:46466829..52422170 [GRCh38]
Chr16:46500741..52456082 [GRCh37]
Chr16:45058242..51013583 [NCBI36]
Chr16:16q11.2-12.1
pathogenic
GRCh38/hg38 16q11.2-12.1(chr16:46466829-52355793)x3 copy number gain See cases [RCV000137170] Chr16:46466829..52355793 [GRCh38]
Chr16:46500741..52389705 [GRCh37]
Chr16:45058242..50947206 [NCBI36]
Chr16:16q11.2-12.1
pathogenic
NM_002968.2(SALL1):c.3872A>G (p.Asn1291Ser) single nucleotide variant Townes syndrome [RCV000540322]|Townes-Brocks syndrome 1 [RCV000292562]|not provided [RCV000992805]|not specified [RCV000202832] Chr16:51137215 [GRCh38]
Chr16:51171126 [GRCh37]
Chr16:16q12.1
benign|likely benign|conflicting interpretations of pathogenicity
GRCh38/hg38 16q12.1-12.2(chr16:49570553-53467065)x1 copy number loss See cases [RCV000137722] Chr16:49570553..53467065 [GRCh38]
Chr16:49604464..53500977 [GRCh37]
Chr16:48161965..52058478 [NCBI36]
Chr16:16q12.1-12.2
pathogenic
NM_002968.2(SALL1):c.1878G>C (p.Glu626Asp) single nucleotide variant Townes syndrome [RCV000871312]|not specified [RCV000203210] Chr16:51140344 [GRCh38]
Chr16:51174255 [GRCh37]
Chr16:16q12.1
benign|likely benign
GRCh38/hg38 16q12.1-22.1(chr16:49685521-68401712)x3 copy number gain See cases [RCV000143752] Chr16:49685521..68401712 [GRCh38]
Chr16:49719432..68435615 [GRCh37]
Chr16:48276933..66993116 [NCBI36]
Chr16:16q12.1-22.1
pathogenic
NM_002968.2(SALL1):c.2549G>C (p.Ser850Thr) single nucleotide variant not provided [RCV000175741] Chr16:51139673 [GRCh38]
Chr16:51173584 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.475_477delAGC microsatellite Townes-Brocks syndrome 1 [RCV000369147]|not specified [RCV000246493] Chr16:51141745..51141747 [GRCh38]
Chr16:51175656..51175658 [GRCh37]
Chr16:16q12.1
benign|conflicting interpretations of pathogenicity|uncertain significance
NM_002968.2(SALL1):c.1144A>G (p.Ser382Gly) single nucleotide variant not provided [RCV000175743] Chr16:51141078 [GRCh38]
Chr16:51174989 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.2283G>C (p.Pro761=) single nucleotide variant not provided [RCV000175744] Chr16:51139939 [GRCh38]
Chr16:51173850 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.3120A>G (p.Thr1040=) single nucleotide variant Townes syndrome [RCV000634155]|not specified [RCV000175745] Chr16:51139102 [GRCh38]
Chr16:51173013 [GRCh37]
Chr16:16q12.1
likely benign|uncertain significance
NM_002968.2(SALL1):c.3794G>A (p.Gly1265Glu) single nucleotide variant Townes syndrome [RCV000870809]|Townes-Brocks syndrome 1 [RCV000387972]|not specified [RCV000348679] Chr16:51137293 [GRCh38]
Chr16:51171204 [GRCh37]
Chr16:16q12.1
benign|likely benign
NM_002968.2(SALL1):c.1322C>A (p.Thr441Asn) single nucleotide variant not provided [RCV000864422]|not specified [RCV000301654] Chr16:51140900 [GRCh38]
Chr16:51174811 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.2(SALL1):c.809C>T (p.Pro270Leu) single nucleotide variant Townes syndrome [RCV001087010]|not provided [RCV000514663]|not specified [RCV000320758] Chr16:51141413 [GRCh38]
Chr16:51175324 [GRCh37]
Chr16:16q12.1
benign|likely benign
NM_001127892.1(SALL1):c.157_159AGC[7] (p.Ser60_Ser62del) microsatellite Townes-Brocks syndrome 1 [RCV000269733]|not provided [RCV000871207]|not specified [RCV000322345] Chr16:51141745..51141753 [GRCh38]
Chr16:51175656..51175664 [GRCh37]
Chr16:16q12.1
benign|likely benign|conflicting interpretations of pathogenicity|uncertain significance
NM_002968.2(SALL1):c.235G>C (p.Ala79Pro) single nucleotide variant not specified [RCV000304067] Chr16:51141987 [GRCh38]
Chr16:51175898 [GRCh37]
Chr16:16q12.1
benign
NM_002968.2(SALL1):c.3915C>T (p.Asn1305=) single nucleotide variant Townes syndrome [RCV000872592]|not specified [RCV000331240] Chr16:51137172 [GRCh38]
Chr16:51171083 [GRCh37]
Chr16:16q12.1
benign|likely benign|conflicting interpretations of pathogenicity
NM_002968.2(SALL1):c.949C>T (p.Pro317Ser) single nucleotide variant Townes-Brocks syndrome 1 [RCV000205374] Chr16:51141273 [GRCh38]
Chr16:51175184 [GRCh37]
Chr16:16q12.1
pathogenic|conflicting interpretations of pathogenicity
NM_002968.2(SALL1):c.3160C>T (p.Arg1054Ter) single nucleotide variant Townes syndrome [RCV000634152]|Townes-Brocks syndrome 1 [RCV000203506] Chr16:51139062 [GRCh38]
Chr16:51172973 [GRCh37]
Chr16:16q12.1
pathogenic|uncertain significance
GRCh37/hg19 16q11.2-24.3(chr16:46615804-90142285)x1 copy number loss Ductal breast carcinoma [RCV000207138] Chr16:46615804..90142285 [GRCh37]
Chr16:16q11.2-24.3
uncertain significance
GRCh38/hg38 16q12.1-12.2(chr16:48543083-53879916)x1 copy number loss Ductal breast carcinoma [RCV000207292] Chr16:48543083..53879916 [GRCh38]
Chr16:48576994..53913828 [GRCh37]
Chr16:16q12.1-12.2
uncertain significance
NM_002968.2(SALL1):c.292A>G (p.Met98Val) single nucleotide variant Townes syndrome [RCV001088967]|not provided [RCV000224272]|not specified [RCV000246370] Chr16:51141930 [GRCh38]
Chr16:51175841 [GRCh37]
Chr16:16q12.1
benign
NM_002968.2(SALL1):c.814C>T (p.Gln272Ter) single nucleotide variant not provided [RCV000579178] Chr16:51141408 [GRCh38]
Chr16:51175319 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.2(SALL1):c.3601G>A (p.Gly1201Ser) single nucleotide variant not provided [RCV000519326] Chr16:51137486 [GRCh38]
Chr16:51171397 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.2343G>C (p.Leu781=) single nucleotide variant Townes syndrome [RCV000549967]|not provided [RCV000712996]|not specified [RCV000246046] Chr16:51139879 [GRCh38]
Chr16:51173790 [GRCh37]
Chr16:16q12.1
benign
NM_002968.2(SALL1):c.478G>A (p.Gly160Ser) single nucleotide variant not specified [RCV000248435] Chr16:51141744 [GRCh38]
Chr16:51175655 [GRCh37]
Chr16:16q12.1
benign|likely benign
NM_002968.2(SALL1):c.379G>C (p.Val127Leu) single nucleotide variant Townes syndrome [RCV001089030]|not provided [RCV000439131]|not specified [RCV000250871] Chr16:51141843 [GRCh38]
Chr16:51175754 [GRCh37]
Chr16:16q12.1
benign|likely benign|conflicting interpretations of pathogenicity
NM_002968.2(SALL1):c.2544A>G (p.Gln848=) single nucleotide variant Townes syndrome [RCV001088388]|not provided [RCV000525845]|not specified [RCV000250989] Chr16:51139678 [GRCh38]
Chr16:51173589 [GRCh37]
Chr16:16q12.1
benign|likely benign
NM_002968.2(SALL1):c.3199C>T (p.Leu1067Phe) single nucleotide variant Townes syndrome [RCV000550746] Chr16:51139023 [GRCh38]
Chr16:51172934 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.2(SALL1):c.472A>G (p.Ser158Gly) single nucleotide variant Townes syndrome [RCV000865465]|not specified [RCV000244001] Chr16:51141750 [GRCh38]
Chr16:51175661 [GRCh37]
Chr16:16q12.1
benign|likely benign|conflicting interpretations of pathogenicity
NM_002968.3(SALL1):c.448_450AGC[11] (p.Ser159dup) microsatellite Townes syndrome [RCV000552954]|Townes-Brocks syndrome 1 [RCV000612233]|not specified [RCV000251431] Chr16:51141744..51141745 [GRCh38]
Chr16:51175655..51175656 [GRCh37]
Chr16:16q12.1
benign|likely benign|conflicting interpretations of pathogenicity
NM_001127892.1(SALL1):c.187_189GGC[5] (p.Gly66dup) microsatellite Townes syndrome [RCV000533357]|Townes-Brocks syndrome 1 [RCV000356333]|not specified [RCV000254222] Chr16:51141732..51141733 [GRCh38]
Chr16:51175643..51175644 [GRCh37]
Chr16:16q12.1
benign|likely benign|conflicting interpretations of pathogenicity|uncertain significance
NM_002968.2(SALL1):c.3823G>A (p.Val1275Ile) single nucleotide variant Townes-Brocks syndrome 1 [RCV000349793]|not specified [RCV000242039] Chr16:51137264 [GRCh38]
Chr16:51171175 [GRCh37]
Chr16:16q12.1
benign
NM_002968.3(SALL1):c.76+26AC[5] microsatellite not specified [RCV000244594] Chr16:51151129..51151130 [GRCh38]
Chr16:51185040..51185041 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.2(SALL1):c.390G>A (p.Pro130=) single nucleotide variant Townes syndrome [RCV001087416]|not provided [RCV000634154]|not specified [RCV000251993] Chr16:51141832 [GRCh38]
Chr16:51175743 [GRCh37]
Chr16:16q12.1
benign|likely benign
NM_002968.2(SALL1):c.1904C>T (p.Pro635Leu) single nucleotide variant Townes syndrome [RCV000864308]|not specified [RCV000244926] Chr16:51140318 [GRCh38]
Chr16:51174229 [GRCh37]
Chr16:16q12.1
benign|likely benign
NM_002968.2(SALL1):c.3456C>T (p.His1152=) single nucleotide variant not specified [RCV000242543] Chr16:51138766 [GRCh38]
Chr16:51172677 [GRCh37]
Chr16:16q12.1
benign
NM_002968.3(SALL1):c.3535-44CT[6] microsatellite not specified [RCV000247523] Chr16:51137583..51137584 [GRCh38]
Chr16:51171494..51171495 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.2(SALL1):c.2574C>T (p.Leu858=) single nucleotide variant Townes-Brocks syndrome 1 [RCV000391169]|not specified [RCV000242992] Chr16:51139648 [GRCh38]
Chr16:51173559 [GRCh37]
Chr16:16q12.1
benign
NM_002968.2(SALL1):c.129C>T (p.His43=) single nucleotide variant not specified [RCV000252927] Chr16:51142093 [GRCh38]
Chr16:51176004 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.2(SALL1):c.2967C>T (p.Leu989=) single nucleotide variant not specified [RCV000250570] Chr16:51139255 [GRCh38]
Chr16:51173166 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.2(SALL1):c.475A>G (p.Ser159Gly) single nucleotide variant not specified [RCV000243488] Chr16:51141747 [GRCh38]
Chr16:51175658 [GRCh37]
Chr16:16q12.1
benign
NM_002968.2(SALL1):c.2178G>A (p.Arg726=) single nucleotide variant not provided [RCV000992804]|not specified [RCV000248259] Chr16:51140044 [GRCh38]
Chr16:51173955 [GRCh37]
Chr16:16q12.1
benign|likely benign
NM_002968.2(SALL1):c.2310C>T (p.Ile770=) single nucleotide variant Townes syndrome [RCV000537361]|not specified [RCV000253246] Chr16:51139912 [GRCh38]
Chr16:51173823 [GRCh37]
Chr16:16q12.1
benign
NM_002968.2(SALL1):c.44A>C (p.Asp15Ala) single nucleotide variant Townes-Brocks syndrome 1 [RCV000283494] Chr16:51151198 [GRCh38]
Chr16:51185109 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.*45C>A single nucleotide variant Townes-Brocks syndrome 1 [RCV000266009] Chr16:51137067 [GRCh38]
Chr16:51170978 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.3222G>A (p.Ala1074=) single nucleotide variant Townes syndrome [RCV000871349] Chr16:51139000 [GRCh38]
Chr16:51172911 [GRCh37]
Chr16:16q12.1
benign|likely benign
NM_002968.2(SALL1):c.220G>A (p.Val74Ile) single nucleotide variant Townes-Brocks syndrome 1 [RCV000287135] Chr16:51142002 [GRCh38]
Chr16:51175913 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.2(SALL1):c.*922T>G single nucleotide variant Townes-Brocks syndrome 1 [RCV000287374] Chr16:51136190 [GRCh38]
Chr16:51170101 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.2(SALL1):c.*192T>C single nucleotide variant Townes-Brocks syndrome 1 [RCV000271928] Chr16:51136920 [GRCh38]
Chr16:51170831 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.2(SALL1):c.3942C>T (p.Phe1314=) single nucleotide variant Townes syndrome [RCV000872924] Chr16:51137145 [GRCh38]
Chr16:51171056 [GRCh37]
Chr16:16q12.1
benign|likely benign
NM_002968.2(SALL1):c.2557T>G (p.Ser853Ala) single nucleotide variant Townes-Brocks syndrome 1 [RCV000297267] Chr16:51139665 [GRCh38]
Chr16:51173576 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.2399A>G (p.Asp800Gly) single nucleotide variant Townes-Brocks syndrome 1 [RCV000261863] Chr16:51139823 [GRCh38]
Chr16:51173734 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.537C>T (p.Leu179=) single nucleotide variant not provided [RCV000878015] Chr16:51141685 [GRCh38]
Chr16:51175596 [GRCh37]
Chr16:16q12.1
benign|likely benign
NM_002968.2(SALL1):c.351C>T (p.Asn117=) single nucleotide variant Townes syndrome [RCV000877917] Chr16:51141871 [GRCh38]
Chr16:51175782 [GRCh37]
Chr16:16q12.1
likely benign|uncertain significance
NM_002968.2(SALL1):c.3277G>A (p.Val1093Met) single nucleotide variant Townes-Brocks syndrome 1 [RCV000391161] Chr16:51138945 [GRCh38]
Chr16:51172856 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.1006G>A (p.Gly336Ser) single nucleotide variant Townes-Brocks syndrome 1 [RCV000390281] Chr16:51141216 [GRCh38]
Chr16:51175127 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.2(SALL1):c.*1016T>C single nucleotide variant Townes-Brocks syndrome 1 [RCV000264916] Chr16:51136096 [GRCh38]
Chr16:51170007 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.3305A>G (p.Asp1102Gly) single nucleotide variant not provided [RCV000271174] Chr16:51138917 [GRCh38]
Chr16:51172828 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.*705_*706del deletion Townes-Brocks syndrome 1 [RCV000281493] Chr16:51136406..51136407 [GRCh38]
Chr16:51170317..51170318 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.676G>A (p.Val226Ile) single nucleotide variant not provided [RCV000513820] Chr16:51141546 [GRCh38]
Chr16:51175457 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.2(SALL1):c.3099_3105dup (p.Arg1036fs) duplication not provided [RCV000287226] Chr16:51139116..51139117 [GRCh38]
Chr16:51173027..51173028 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.2(SALL1):c.*997C>A single nucleotide variant Townes-Brocks syndrome 1 [RCV000322324] Chr16:51136115 [GRCh38]
Chr16:51170026 [GRCh37]
Chr16:16q12.1
benign
NM_002968.2(SALL1):c.3947A>G (p.Glu1316Gly) single nucleotide variant Townes-Brocks syndrome 1 [RCV000323365] Chr16:51137140 [GRCh38]
Chr16:51171051 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.1398C>A (p.Ile466=) single nucleotide variant not provided [RCV000272933] Chr16:51140824 [GRCh38]
Chr16:51174735 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.727C>T (p.Gln243Ter) single nucleotide variant not provided [RCV000302939] Chr16:51141495 [GRCh38]
Chr16:51175406 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.2(SALL1):c.3768G>A (p.Gln1256=) single nucleotide variant Townes-Brocks syndrome 1 [RCV000296006] Chr16:51137319 [GRCh38]
Chr16:51171230 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.2825C>A (p.Pro942His) single nucleotide variant not provided [RCV001288382]|not specified [RCV000276120] Chr16:51139397 [GRCh38]
Chr16:51173308 [GRCh37]
Chr16:16q12.1
likely benign|uncertain significance
NM_002968.2(SALL1):c.1715C>T (p.Thr572Met) single nucleotide variant not provided [RCV000311105] Chr16:51140507 [GRCh38]
Chr16:51174418 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.1731C>G (p.Pro577=) single nucleotide variant Townes-Brocks syndrome 1 [RCV000326701] Chr16:51140491 [GRCh38]
Chr16:51174402 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.2(SALL1):c.1903C>T (p.Pro635Ser) single nucleotide variant not specified [RCV000315235] Chr16:51140319 [GRCh38]
Chr16:51174230 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.2(SALL1):c.*550G>T single nucleotide variant Townes-Brocks syndrome 1 [RCV000307202] Chr16:51136562 [GRCh38]
Chr16:51170473 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.2(SALL1):c.76+10C>G single nucleotide variant Townes-Brocks syndrome 1 [RCV000400596] Chr16:51151156 [GRCh38]
Chr16:51185067 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.2(SALL1):c.3711T>C (p.Tyr1237=) single nucleotide variant Townes-Brocks syndrome 1 [RCV000400930] Chr16:51137376 [GRCh38]
Chr16:51171287 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.2(SALL1):c.649G>A (p.Gly217Ser) single nucleotide variant Townes-Brocks syndrome 1 [RCV000401428] Chr16:51141573 [GRCh38]
Chr16:51175484 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_001127892.1(SALL1):c.577_578TC[3] (p.Gln194fs) microsatellite not provided [RCV000335508] Chr16:51141350..51141351 [GRCh38]
Chr16:51175261..51175262 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.2(SALL1):c.*1112dup duplication Townes-Brocks syndrome 1 [RCV000327970] Chr16:51135999..51136000 [GRCh38]
Chr16:51169910..51169911 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.2(SALL1):c.477_478insAGCGGC (p.Gly160_Gly161insSerGly) insertion not provided [RCV000766499]|not specified [RCV000350628] Chr16:51141744..51141745 [GRCh38]
Chr16:51175655..51175656 [GRCh37]
Chr16:16q12.1
likely benign|conflicting interpretations of pathogenicity|uncertain significance
NM_002968.2(SALL1):c.389C>T (p.Pro130Leu) single nucleotide variant Townes-Brocks syndrome 1 [RCV000330479] Chr16:51141833 [GRCh38]
Chr16:51175744 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.2(SALL1):c.3424A>G (p.Thr1142Ala) single nucleotide variant Townes-Brocks syndrome 1 [RCV000347610] Chr16:51138798 [GRCh38]
Chr16:51172709 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.2008T>C (p.Phe670Leu) single nucleotide variant Townes-Brocks syndrome 1 [RCV000332787] Chr16:51140214 [GRCh38]
Chr16:51174125 [GRCh37]
Chr16:16q12.1
likely benign
NM_001127892.1(SALL1):c.*920_*922CTT[2] microsatellite Townes-Brocks syndrome 1 [RCV000379240] Chr16:51136184..51136186 [GRCh38]
Chr16:51170095..51170097 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.3947A>C (p.Glu1316Ala) single nucleotide variant Townes-Brocks syndrome 1 [RCV000380134] Chr16:51137140 [GRCh38]
Chr16:51171051 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.*1033dup duplication Townes-Brocks syndrome 1 [RCV000385156] Chr16:51136078..51136079 [GRCh38]
Chr16:51169989..51169990 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.1911G>A (p.Ala637=) single nucleotide variant not specified [RCV000287936] Chr16:51140311 [GRCh38]
Chr16:51174222 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.2(SALL1):c.1329T>A (p.Asp443Glu) single nucleotide variant not provided [RCV000289286] Chr16:51140893 [GRCh38]
Chr16:51174804 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.*588del deletion Townes-Brocks syndrome 1 [RCV000312169] Chr16:51136524 [GRCh38]
Chr16:51170435 [GRCh37]
Chr16:16q12.1
benign
NM_002968.2(SALL1):c.*592G>A single nucleotide variant Townes-Brocks syndrome 1 [RCV000398604] Chr16:51136520 [GRCh38]
Chr16:51170431 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_001127892.1(SALL1):c.*83_*87GCCCC[1] microsatellite Townes-Brocks syndrome 1 [RCV000358349] Chr16:51137020..51137024 [GRCh38]
Chr16:51170931..51170935 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.2(SALL1):c.1502A>G (p.Glu501Gly) single nucleotide variant Townes-Brocks syndrome 1 [RCV000383660] Chr16:51140720 [GRCh38]
Chr16:51174631 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.*558A>G single nucleotide variant Townes-Brocks syndrome 1 [RCV000408040] Chr16:51136554 [GRCh38]
Chr16:51170465 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.*646C>T single nucleotide variant Townes-Brocks syndrome 1 [RCV000337827] Chr16:51136466 [GRCh38]
Chr16:51170377 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.2(SALL1):c.3929G>A (p.Arg1310His) single nucleotide variant Townes-Brocks syndrome 1 [RCV000317442] Chr16:51137158 [GRCh38]
Chr16:51171069 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.263G>A (p.Ser88Asn) single nucleotide variant Townes-Brocks syndrome 1 [RCV000317519] Chr16:51141959 [GRCh38]
Chr16:51175870 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.2(SALL1):c.1025A>C (p.Asn342Thr) single nucleotide variant not provided [RCV000331820] Chr16:51141197 [GRCh38]
Chr16:51175108 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.484G>A (p.Gly162Ser) single nucleotide variant not provided [RCV000405577] Chr16:51141738 [GRCh38]
Chr16:51175649 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.*437C>A single nucleotide variant Townes-Brocks syndrome 1 [RCV000364171] Chr16:51136675 [GRCh38]
Chr16:51170586 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.2(SALL1):c.986C>T (p.Thr329Ile) single nucleotide variant Inborn genetic diseases [RCV000624031]|not provided [RCV000334683] Chr16:51141236 [GRCh38]
Chr16:51175147 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.2373C>A (p.Gly791=) single nucleotide variant not provided [RCV000336180] Chr16:51139849 [GRCh38]
Chr16:51173760 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.1108_1109del (p.Val370fs) deletion Townes-Brocks syndrome 1 [RCV000489064] Chr16:51141113..51141114 [GRCh38]
Chr16:51175024..51175025 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.2(SALL1):c.3938G>A (p.Arg1313His) single nucleotide variant Townes syndrome [RCV001212454]|not provided [RCV000489514] Chr16:51137149 [GRCh38]
Chr16:51171060 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.3180C>A (p.Leu1060=) single nucleotide variant not provided [RCV000951923]|not specified [RCV000597625] Chr16:51139042 [GRCh38]
Chr16:51172953 [GRCh37]
Chr16:16q12.1
benign|likely benign
NM_002968.2(SALL1):c.2909T>C (p.Leu970Ser) single nucleotide variant not provided [RCV000723151] Chr16:51139313 [GRCh38]
Chr16:51173224 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.43G>A (p.Asp15Asn) single nucleotide variant Townes-Brocks syndrome 1 [RCV000347818] Chr16:51151199 [GRCh38]
Chr16:51185110 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.*904C>T single nucleotide variant Townes-Brocks syndrome 1 [RCV000335422] Chr16:51136208 [GRCh38]
Chr16:51170119 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.*563del deletion Townes-Brocks syndrome 1 [RCV000350691] Chr16:51136549 [GRCh38]
Chr16:51170460 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.3(SALL1):c.448_450AGC[12] (p.Ser158_Ser159dup) microsatellite Townes syndrome [RCV000872954]|Townes-Brocks syndrome 1 [RCV000393511]|not specified [RCV000403758] Chr16:51141744..51141745 [GRCh38]
Chr16:51175655..51175656 [GRCh37]
Chr16:16q12.1
benign|uncertain significance
NM_002968.2(SALL1):c.*865A>C single nucleotide variant Townes-Brocks syndrome 1 [RCV000373606] Chr16:51136247 [GRCh38]
Chr16:51170158 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.*125C>T single nucleotide variant Townes-Brocks syndrome 1 [RCV000310540] Chr16:51136987 [GRCh38]
Chr16:51170898 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.1321A>G (p.Thr441Ala) single nucleotide variant Townes-Brocks syndrome 1 [RCV000339917] Chr16:51140901 [GRCh38]
Chr16:51174812 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.3713C>A (p.Ala1238Glu) single nucleotide variant Townes-Brocks syndrome 1 [RCV000344108] Chr16:51137374 [GRCh38]
Chr16:51171285 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.3750C>T (p.Asn1250=) single nucleotide variant not provided [RCV000592828] Chr16:51137337 [GRCh38]
Chr16:51171248 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.361A>G (p.Arg121Gly) single nucleotide variant not provided [RCV000593129] Chr16:51141861 [GRCh38]
Chr16:51175772 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.3021C>G (p.Gly1007=) single nucleotide variant not provided [RCV000591086] Chr16:51139201 [GRCh38]
Chr16:51173112 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.855A>G (p.Leu285=) single nucleotide variant not provided [RCV000541405] Chr16:51141367 [GRCh38]
Chr16:51175278 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.2(SALL1):c.411C>T (p.Ser137=) single nucleotide variant not provided [RCV000734381] Chr16:51141811 [GRCh38]
Chr16:51175722 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.3270C>T (p.Asn1090=) single nucleotide variant not provided [RCV000728506] Chr16:51138952 [GRCh38]
Chr16:51172863 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.3222G>C (p.Ala1074=) single nucleotide variant not provided [RCV000728508] Chr16:51139000 [GRCh38]
Chr16:51172911 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.2223G>A (p.Arg741=) single nucleotide variant not provided [RCV000730177] Chr16:51139999 [GRCh38]
Chr16:51173910 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_001127892.1(SALL1):c.-117C>T single nucleotide variant not provided [RCV000729023] Chr16:51142047 [GRCh38]
Chr16:51175958 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.2590G>A (p.Ala864Thr) single nucleotide variant not provided [RCV000733436] Chr16:51139632 [GRCh38]
Chr16:51173543 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.3154C>T (p.Gln1052Ter) single nucleotide variant not provided [RCV000413349] Chr16:51139068 [GRCh38]
Chr16:51172979 [GRCh37]
Chr16:16q12.1
likely pathogenic
NM_002968.2(SALL1):c.1393C>T (p.Gln465Ter) single nucleotide variant not provided [RCV000414232] Chr16:51140829 [GRCh38]
Chr16:51174740 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.2(SALL1):c.1763dup (p.Gly589fs) duplication not provided [RCV000414487] Chr16:51140458..51140459 [GRCh38]
Chr16:51174369..51174370 [GRCh37]
Chr16:16q12.1
pathogenic
GRCh37/hg19 16q11.2-24.3(chr16:46464488-90155062)x3 copy number gain See cases [RCV000446110] Chr16:46464488..90155062 [GRCh37]
Chr16:16q11.2-24.3
pathogenic
GRCh37/hg19 16p13.3-q24.3(chr16:69193-90274381)x3 copy number gain See cases [RCV000446684] Chr16:69193..90274381 [GRCh37]
Chr16:16p13.3-q24.3
pathogenic
NM_002968.2(SALL1):c.1950C>T (p.Gly650=) single nucleotide variant not specified [RCV000428044] Chr16:51140272 [GRCh38]
Chr16:51174183 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.2(SALL1):c.3534+5C>T single nucleotide variant not specified [RCV000436189] Chr16:51138683 [GRCh38]
Chr16:51172594 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.2(SALL1):c.3157A>C (p.Met1053Leu) single nucleotide variant not provided [RCV000430109] Chr16:51139065 [GRCh38]
Chr16:51172976 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.3771C>T (p.Asn1257=) single nucleotide variant not specified [RCV000436838] Chr16:51137316 [GRCh38]
Chr16:51171227 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.2(SALL1):c.1405C>T (p.Arg469Cys) single nucleotide variant not provided [RCV000440800] Chr16:51140817 [GRCh38]
Chr16:51174728 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.130G>A (p.Val44Ile) single nucleotide variant Townes-Brocks syndrome 1 [RCV000416591] Chr16:51142092 [GRCh38]
Chr16:51176003 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.3326C>T (p.Pro1109Leu) single nucleotide variant not provided [RCV000480807] Chr16:51138896 [GRCh38]
Chr16:51172807 [GRCh37]
Chr16:16q12.1
likely pathogenic
NM_002968.2(SALL1):c.1380_1381del (p.Ser460fs) deletion not provided [RCV000479335] Chr16:51140841..51140842 [GRCh38]
Chr16:51174752..51174753 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.2(SALL1):c.3414_3415del (p.Cys1139fs) deletion Townes syndrome [RCV000526857]|not provided [RCV000486755] Chr16:51138807..51138808 [GRCh38]
Chr16:51172718..51172719 [GRCh37]
Chr16:16q12.1
pathogenic
GRCh37/hg19 16p11.2-q21(chr16:34197492-64509054)x3 copy number gain See cases [RCV000511791] Chr16:34197492..64509054 [GRCh37]
Chr16:16p11.2-q21
pathogenic
GRCh37/hg19 16p13.2-q24.3(chr16:9273328-89548493)x3 copy number gain See cases [RCV000511622] Chr16:9273328..89548493 [GRCh37]
Chr16:16p13.2-q24.3
uncertain significance
GRCh37/hg19 16q11.2-12.1(chr16:46737110-51838691)x1 copy number loss See cases [RCV000511950] Chr16:46737110..51838691 [GRCh37]
Chr16:16q11.2-12.1
pathogenic
GRCh37/hg19 16q11.2-24.3(chr16:46497599-90354753)x1 copy number loss PARP Inhibitor response [RCV000626429] Chr16:46497599..90354753 [GRCh37]
Chr16:16q11.2-24.3
drug response
NM_002968.2(SALL1):c.264C>T (p.Ser88=) single nucleotide variant Townes syndrome [RCV000634157] Chr16:51141958 [GRCh38]
Chr16:51175869 [GRCh37]
Chr16:16q12.1
benign
NC_000016.10:g.(?_51137092)_(51151261_?)del deletion Townes syndrome [RCV000634158] Chr16:51137092..51151261 [GRCh38]
Chr16:51171003..51185172 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.2(SALL1):c.477_478insAGCAGCGGC (p.Gly160_Gly161insSerSerGly) insertion Townes-Brocks syndrome 1 [RCV000626257] Chr16:51141744..51141745 [GRCh38]
Chr16:51175655..51175656 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.572T>C (p.Ile191Thr) single nucleotide variant not provided [RCV000585096] Chr16:51141650 [GRCh38]
Chr16:51175561 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.387C>T (p.Ala129=) single nucleotide variant not specified [RCV000609960] Chr16:51141835 [GRCh38]
Chr16:51175746 [GRCh37]
Chr16:16q12.1
likely benign
GRCh37/hg19 16p13.3-q24.3(chr16:85881-90155062) copy number gain See cases [RCV000511296] Chr16:85881..90155062 [GRCh37]
Chr16:16p13.3-q24.3
pathogenic
NM_002968.2(SALL1):c.2278C>T (p.Pro760Ser) single nucleotide variant not provided [RCV000594770] Chr16:51139944 [GRCh38]
Chr16:51173855 [GRCh37]
Chr16:16q12.1
uncertain significance
GRCh37/hg19 16q11.2-24.3(chr16:46455960-90354753)x1 copy number loss PARP Inhibitor response [RCV000626435] Chr16:46455960..90354753 [GRCh37]
Chr16:16q11.2-24.3
drug response
NM_002968.2(SALL1):c.866T>A (p.Leu289Ter) single nucleotide variant Townes syndrome [RCV000634150] Chr16:51141356 [GRCh38]
Chr16:51175267 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.2(SALL1):c.958C>T (p.Gln320Ter) single nucleotide variant Townes syndrome [RCV000634151] Chr16:51141264 [GRCh38]
Chr16:51175175 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.2(SALL1):c.2356del (p.Arg786fs) deletion Townes syndrome [RCV000634153] Chr16:51139866 [GRCh38]
Chr16:51173777 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.2(SALL1):c.1014T>G (p.Ser338=) single nucleotide variant Townes syndrome [RCV000634156] Chr16:51141208 [GRCh38]
Chr16:51175119 [GRCh37]
Chr16:16q12.1
likely benign
GRCh37/hg19 16p13.3-q24.3(chr16:85881-90155062)x3 copy number gain See cases [RCV000512138] Chr16:85881..90155062 [GRCh37]
Chr16:16p13.3-q24.3
pathogenic
NM_002968.2(SALL1):c.712C>T (p.Gln238Ter) single nucleotide variant not provided [RCV000681840] Chr16:51141510 [GRCh38]
Chr16:51175421 [GRCh37]
Chr16:16q12.1
likely pathogenic
NM_002968.2(SALL1):c.3584G>A (p.Arg1195Gln) single nucleotide variant Townes syndrome [RCV000696783] Chr16:51137503 [GRCh38]
Chr16:51171414 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.3(SALL1):c.3322G>A (p.Val1108Ile) single nucleotide variant not specified [RCV001002753] Chr16:51138900 [GRCh38]
Chr16:51172811 [GRCh37]
Chr16:16q12.1
likely benign
GRCh37/hg19 16p13.3-q24.3(chr16:88165-90163275)x3 copy number gain not provided [RCV000738917] Chr16:88165..90163275 [GRCh37]
Chr16:16p13.3-q24.3
pathogenic
GRCh37/hg19 16p13.3-q24.3(chr16:88165-90274695)x3 copy number gain not provided [RCV000738918] Chr16:88165..90274695 [GRCh37]
Chr16:16p13.3-q24.3
pathogenic
GRCh37/hg19 16p13.3-q24.3(chr16:61451-90294632)x3 copy number gain not provided [RCV000738915] Chr16:61451..90294632 [GRCh37]
Chr16:16p13.3-q24.3
pathogenic
NM_002968.3(SALL1):c.1022T>C (p.Met341Thr) single nucleotide variant not provided [RCV000904128] Chr16:51141200 [GRCh38]
Chr16:51175111 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.3(SALL1):c.703G>A (p.Ala235Thr) single nucleotide variant Townes-Brocks syndrome 1 [RCV001254690]|not provided [RCV000951173] Chr16:51141519 [GRCh38]
Chr16:51175430 [GRCh37]
Chr16:16q12.1
likely benign|uncertain significance
NM_002968.3(SALL1):c.1485C>T (p.His495=) single nucleotide variant not provided [RCV000905621] Chr16:51140737 [GRCh38]
Chr16:51174648 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.3(SALL1):c.3957G>A (p.Lys1319=) single nucleotide variant not provided [RCV000883832] Chr16:51137130 [GRCh38]
Chr16:51171041 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.3(SALL1):c.1200G>A (p.Ser400=) single nucleotide variant not provided [RCV000946230] Chr16:51141022 [GRCh38]
Chr16:51174933 [GRCh37]
Chr16:16q12.1
benign
NM_002968.3(SALL1):c.3964G>A (p.Val1322Ile) single nucleotide variant not provided [RCV000996269] Chr16:51137123 [GRCh38]
Chr16:51171034 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.3(SALL1):c.2686_2689dup (p.Val897fs) duplication Townes-Brocks syndrome 1 [RCV000995629] Chr16:51139532..51139533 [GRCh38]
Chr16:51173443..51173444 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.3(SALL1):c.3759C>T (p.Ser1253=) single nucleotide variant Townes syndrome [RCV000874421] Chr16:51137328 [GRCh38]
Chr16:51171239 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.3(SALL1):c.3084A>G (p.Pro1028=) single nucleotide variant not provided [RCV000871943] Chr16:51139138 [GRCh38]
Chr16:51173049 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.3(SALL1):c.3836C>T (p.Thr1279Met) single nucleotide variant Townes-Brocks syndrome 1 [RCV001029863] Chr16:51137251 [GRCh38]
Chr16:51171162 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.3(SALL1):c.2050C>T (p.Gln684Ter) single nucleotide variant Townes-Brocks syndrome 1 [RCV001029950] Chr16:51140172 [GRCh38]
Chr16:51174083 [GRCh37]
Chr16:16q12.1
likely pathogenic|uncertain significance
NM_002968.2(SALL1):c.3005_3008del (p.Ala1002fs) deletion Townes syndrome [RCV000821059] Chr16:51139214..51139217 [GRCh38]
Chr16:51173125..51173128 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.3(SALL1):c.448_450AGC[13] (p.Ser157_Ser159dup) microsatellite Townes syndrome [RCV000871313] Chr16:51141744..51141745 [GRCh38]
Chr16:51175655..51175656 [GRCh37]
Chr16:16q12.1
benign
NM_002968.3(SALL1):c.2287dup (p.Arg763fs) duplication Townes-Brocks syndrome 1 [RCV001029980] Chr16:51139934..51139935 [GRCh38]
Chr16:51173845..51173846 [GRCh37]
Chr16:16q12.1
likely pathogenic
NM_002968.2(SALL1):c.3535-207G>A single nucleotide variant not provided [RCV000826350] Chr16:51137759 [GRCh38]
Chr16:51171670 [GRCh37]
Chr16:16q12.1
benign
NM_002968.3(SALL1):c.1324del (p.Ser442fs) deletion Townes syndrome [RCV000803639] Chr16:51140898 [GRCh38]
Chr16:51174809 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.2(SALL1):c.1738A>G (p.Ile580Val) single nucleotide variant not provided [RCV000782252] Chr16:51140484 [GRCh38]
Chr16:51174395 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.602A>G (p.Gln201Arg) single nucleotide variant VACTERL association with hydrocephalus [RCV001007926]|not provided [RCV000782264] Chr16:51141620 [GRCh38]
Chr16:51175531 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.2(SALL1):c.548C>A (p.Thr183Lys) single nucleotide variant Townes syndrome [RCV000810771] Chr16:51141674 [GRCh38]
Chr16:51175585 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.3(SALL1):c.2409dup (p.Glu804Ter) duplication not provided [RCV001008730] Chr16:51139812..51139813 [GRCh38]
Chr16:51173723..51173724 [GRCh37]
Chr16:16q12.1
likely pathogenic
NM_002968.3(SALL1):c.1873G>T (p.Glu625Ter) single nucleotide variant Townes-Brocks syndrome 1 [RCV001249670] Chr16:51140349 [GRCh38]
Chr16:51174260 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.3(SALL1):c.3787A>G (p.Ile1263Val) single nucleotide variant Townes-Brocks syndrome 1 [RCV001199084] Chr16:51137300 [GRCh38]
Chr16:51171211 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.3(SALL1):c.3847G>A (p.Glu1283Lys) single nucleotide variant Townes-Brocks syndrome 1 [RCV001250545] Chr16:51137240 [GRCh38]
Chr16:51171151 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.3(SALL1):c.1514A>G (p.His505Arg) single nucleotide variant Townes-Brocks syndrome 1 [RCV000855402] Chr16:51140708 [GRCh38]
Chr16:51174619 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.3(SALL1):c.2752G>A (p.Ala918Thr) single nucleotide variant not provided [RCV000983808] Chr16:51139470 [GRCh38]
Chr16:51173381 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.3(SALL1):c.2798_2803dup (p.Asn933_Ser934dup) duplication not provided [RCV000897197] Chr16:51139418..51139419 [GRCh38]
Chr16:51173329..51173330 [GRCh37]
Chr16:16q12.1
likely benign
NM_002968.3(SALL1):c.420del (p.Ser141fs) deletion Townes syndrome [RCV001203386] Chr16:51141802 [GRCh38]
Chr16:51175713 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.3(SALL1):c.2712_2715del (p.Gly906fs) deletion not provided [RCV001008523] Chr16:51139507..51139510 [GRCh38]
Chr16:51173418..51173421 [GRCh37]
Chr16:16q12.1
likely pathogenic
NM_002968.3(SALL1):c.2801del (p.Ser934fs) deletion Townes-Brocks syndrome 1 [RCV001029827] Chr16:51139421 [GRCh38]
Chr16:51173332 [GRCh37]
Chr16:16q12.1
likely pathogenic
NM_002968.3(SALL1):c.750dup (p.Arg251fs) duplication Townes syndrome [RCV001218743] Chr16:51141471..51141472 [GRCh38]
Chr16:51175382..51175383 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.3(SALL1):c.871C>T (p.Gln291Ter) single nucleotide variant Townes syndrome [RCV001205091] Chr16:51141351 [GRCh38]
Chr16:51175262 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.3(SALL1):c.412G>A (p.Gly138Ser) single nucleotide variant Townes syndrome [RCV001069839] Chr16:51141810 [GRCh38]
Chr16:51175721 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.3(SALL1):c.424G>A (p.Gly142Ser) single nucleotide variant Townes syndrome [RCV001059302] Chr16:51141798 [GRCh38]
Chr16:51175709 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.3(SALL1):c.1762C>T (p.Pro588Ser) single nucleotide variant Microcephaly [RCV001252901] Chr16:51140460 [GRCh38]
Chr16:51174371 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.3(SALL1):c.3782C>T (p.Pro1261Leu) single nucleotide variant Townes-Brocks syndrome 1 [RCV001262006] Chr16:51137305 [GRCh38]
Chr16:51171216 [GRCh37]
Chr16:16q12.1
uncertain significance
GRCh37/hg19 16q12.1(chr16:51025932-51360215)x3 copy number gain not provided [RCV001259854] Chr16:51025932..51360215 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.3(SALL1):c.1365_1366insGCAG (p.Lys456fs) insertion Townes-Brocks syndrome 1 [RCV001290092] Chr16:51140856..51140857 [GRCh38]
Chr16:51174767..51174768 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.3(SALL1):c.477C>A (p.Ser159Arg) single nucleotide variant Congenital anomalies of kidney and urinary tract [RCV001328262] Chr16:51141745 [GRCh38]
Chr16:51175656 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.3(SALL1):c.3088A>G (p.Ile1030Val) single nucleotide variant Townes syndrome [RCV001303592] Chr16:51139134 [GRCh38]
Chr16:51173045 [GRCh37]
Chr16:16q12.1
uncertain significance
NM_002968.3(SALL1):c.824T>A (p.Leu275Ter) single nucleotide variant not provided [RCV001311449] Chr16:51141398 [GRCh38]
Chr16:51175309 [GRCh37]
Chr16:16q12.1
pathogenic
NM_002968.3(SALL1):c.2846A>G (p.Gln949Arg) single nucleotide variant Congenital anomalies of kidney and urinary tract [RCV001328263] Chr16:51139376 [GRCh38]
Chr16:51173287 [GRCh37]
Chr16:16q12.1
uncertain significance

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:10524 AgrOrtholog
COSMIC SALL1 COSMIC
Ensembl Genes ENSG00000103449 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSP00000251020 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000407914 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000455582 UniProtKB/TrEMBL
  ENSP00000456777 UniProtKB/TrEMBL
Ensembl Transcript ENST00000251020 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000440970 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000566102 UniProtKB/TrEMBL
  ENST00000570206 UniProtKB/TrEMBL
GTEx ENSG00000103449 GTEx
HGNC ID HGNC:10524 ENTREZGENE
Human Proteome Map SALL1 Human Proteome Map
InterPro Znf_C2H2_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_C2H2_type UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:6299 UniProtKB/Swiss-Prot
NCBI Gene 6299 ENTREZGENE
OMIM 107480 OMIM
  602218 OMIM
Pfam zf-C2H2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA34932 PharmGKB
PROSITE ZINC_FINGER_C2H2_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART ZnF_C2H2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF57667 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt H3BQ32_HUMAN UniProtKB/TrEMBL
  H3BSM9_HUMAN UniProtKB/TrEMBL
  Q14CE9_HUMAN UniProtKB/TrEMBL
  Q9NSC2 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q99881 UniProtKB/Swiss-Prot
  Q9NSC3 UniProtKB/Swiss-Prot
  Q9P1R0 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-05-31 SALL1  spalt like transcription factor 1  SALL1  spalt-like transcription factor 1  Symbol and/or name change 5135510 APPROVED
2013-10-22 SALL1  spalt-like transcription factor 1  SALL1  sal-like 1 (Drosophila)  Symbol and/or name change 5135510 APPROVED