SIX3 (SIX homeobox 3) - Rat Genome Database

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Gene: SIX3 (SIX homeobox 3) Homo sapiens
Analyze
Symbol: SIX3
Name: SIX homeobox 3
RGD ID: 733474
HGNC Page HGNC
Description: Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and transcription corepressor binding activity. Involved in eye development; forebrain dorsal/ventral pattern formation; and negative regulation of transcription, DNA-templated. Predicted to be part of chromatin and transcription regulator complex. Predicted to be active in nucleus. Implicated in holoprosencephaly and holoprosencephaly 2.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: homeobox protein SIX3; HPE2; sine oculis homeobox homolog 3; sine oculis homeobox-like protein 3; truncated SIX3
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl244,941,702 - 44,946,071 (+)EnsemblGRCh38hg38GRCh38
GRCh38244,941,702 - 44,946,071 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37245,168,841 - 45,173,210 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36245,022,541 - 45,025,894 (+)NCBINCBI36hg18NCBI36
Build 34245,080,511 - 45,084,092NCBI
Celera245,007,709 - 45,011,888 (+)NCBI
Cytogenetic Map2p21NCBI
HuRef244,885,400 - 44,910,885 (+)NCBIHuRef
CHM1_1245,098,943 - 45,103,122 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
Abnormal aortic morphology  (IAGP)
Abnormal brainstem morphology  (IAGP)
Abnormal corpus callosum morphology  (IAGP)
Abnormal facial shape  (IAGP)
Abnormal form of the vertebral bodies  (IAGP)
Abnormal heart morphology  (IAGP)
Abnormal heart rate variability  (IAGP)
Abnormal hypothalamus physiology  (IAGP)
Abnormal midbrain morphology  (IAGP)
Abnormal morphology of the olfactory bulb  (IAGP)
Abnormal pulmonary valve morphology  (IAGP)
Abnormal vertebral morphology  (IAGP)
Abnormality of neuronal migration  (IAGP)
Abnormality of the antihelix  (IAGP)
Abnormality of the autonomic nervous system  (IAGP)
Abnormality of the genitourinary system  (IAGP)
Abnormality of the ribs  (IAGP)
Abnormality of the septum pellucidum  (IAGP)
Abnormality of the spleen  (IAGP)
Absent nares  (IAGP)
Absent nasal septal cartilage  (IAGP)
Absent speech  (IAGP)
Adrenal hypoplasia  (IAGP)
Agenesis of corpus callosum  (IAGP)
Ambiguous genitalia  (IAGP)
Anophthalmia  (IAGP)
Anosmia  (IAGP)
Anterior hypopituitarism  (IAGP)
Anterior pituitary agenesis  (IAGP)
Anteriorly placed anus  (IAGP)
Anteverted nares  (IAGP)
Anxiety  (IAGP)
Apathy  (IAGP)
Aplasia of the falx cerebri  (IAGP)
Aplasia of the nose  (IAGP)
Aplasia/Hypoplasia involving the nose  (IAGP)
Aplasia/Hypoplasia of the corpus callosum  (IAGP)
Aplasia/Hypoplasia of the lungs  (IAGP)
Arrhythmia  (IAGP)
Aspiration pneumonia  (IAGP)
Asthma  (IAGP)
Attention deficit hyperactivity disorder  (IAGP)
Autosomal dominant inheritance  (IAGP)
Bifid uvula  (IAGP)
Bilateral cleft lip  (IAGP)
Blepharophimosis  (IAGP)
Brachydactyly  (IAGP)
Branchial anomaly  (IAGP)
Broad philtrum  (IAGP)
Central apnea  (IAGP)
Central diabetes insipidus  (IAGP)
Central hypothyroidism  (IAGP)
Cerebellar hypoplasia  (IAGP)
Cerebral cortical atrophy  (IAGP)
Cerebral visual impairment  (IAGP)
Choanal atresia  (IAGP)
Chorea  (IAGP)
Chorioretinal coloboma  (IAGP)
Chronic lung disease  (IAGP)
Cleft palate  (IAGP)
Coarctation of aorta  (IAGP)
Cognitive impairment  (IAGP)
Congenital diaphragmatic hernia  (IAGP)
Constipation  (IAGP)
Cryptorchidism  (IAGP)
Cyclopia  (IAGP)
Dandy-Walker malformation  (IAGP)
Decreased response to growth hormone stimulation test  (IAGP)
Deep philtrum  (IAGP)
Deeply set eye  (IAGP)
Depressed nasal ridge  (IAGP)
Depressed nasal tip  (IAGP)
Depression  (IAGP)
Diabetes insipidus  (IAGP)
Diabetes mellitus  (IAGP)
Duodenal atresia  (IAGP)
Dysphagia  (IAGP)
Dystonia  (IAGP)
EMG: myopathic abnormalities  (IAGP)
Encephalocele  (IAGP)
Epicanthus  (IAGP)
Ethmoidal encephalocele  (IAGP)
Expressive language delay  (IAGP)
External ear malformation  (IAGP)
Failure to thrive  (IAGP)
Failure to thrive in infancy  (IAGP)
Feeding difficulties in infancy  (IAGP)
Flat occiput  (IAGP)
Flexion contracture  (IAGP)
Frontal bossing  (IAGP)
Gastroesophageal reflux  (IAGP)
Gastrostomy tube feeding in infancy  (IAGP)
Generalized hypotonia  (IAGP)
Global developmental delay  (IAGP)
Hand polydactyly  (IAGP)
Hemangioma  (IAGP)
Heterogeneous  (IAGP)
High palate  (IAGP)
Highly arched eyebrow  (IAGP)
Hip dislocation  (IAGP)
Holoprosencephaly  (IAGP)
Hydrocephalus  (IAGP)
Hypertelorism  (IAGP)
Hypoglycemia  (IAGP)
Hyponatremia  (IAGP)
Hypoplasia of penis  (IAGP)
Hypoplasia of the pons  (IAGP)
Hypoplasia of the zygomatic bone  (IAGP)
Hyposmia  (IAGP)
Hypotelorism  (IAGP)
Hypothyroidism  (IAGP)
Hypotonia  (IAGP)
Impulsivity  (IAGP)
Inability to walk  (IAGP)
Incomplete penetrance  (IAGP)
Infantile axial hypotonia  (IAGP)
Intellectual disability  (IAGP)
Intestinal atresia  (IAGP)
Intrauterine growth retardation  (IAGP)
Iris coloboma  (IAGP)
Irritability  (IAGP)
Joint hyperflexibility  (IAGP)
Lethargy  (IAGP)
Limb dystonia  (IAGP)
Macrocephaly  (IAGP)
Macrotia  (IAGP)
Malar flattening  (IAGP)
Maternal diabetes  (IAGP)
Median cleft lip  (IAGP)
Median cleft lip and palate  (IAGP)
Megalencephaly  (IAGP)
Microcephaly  (IAGP)
Microphthalmia  (IAGP)
Midface retrusion  (IAGP)
Midnasal stenosis  (IAGP)
Morphological abnormality of the gastrointestinal tract  (IAGP)
Muscle weakness  (IAGP)
Narrow nasal bridge  (IAGP)
Neural tube defect  (IAGP)
Omphalocele  (IAGP)
Optic atrophy  (IAGP)
Oromotor apraxia  (IAGP)
Panhypopituitarism  (IAGP)
Perisylvian polymicrogyria  (IAGP)
Poor speech  (IAGP)
Poor suck  (IAGP)
Precocious puberty  (IAGP)
Premature birth  (IAGP)
Proboscis  (IAGP)
Proteinuria  (IAGP)
Ptosis  (IAGP)
Renal agenesis  (IAGP)
Respiratory insufficiency  (IAGP)
Retinopathy  (IAGP)
Rhombencephalosynapsis  (IAGP)
Schizencephaly  (IAGP)
Scoliosis  (IAGP)
Seizure  (IAGP)
Sensorineural hearing impairment  (IAGP)
Short attention span  (IAGP)
Short neck  (IAGP)
Short nose  (IAGP)
Short philtrum  (IAGP)
Short stature  (IAGP)
Single naris  (IAGP)
Single ventricle  (IAGP)
Sleep-wake cycle disturbance  (IAGP)
Solitary median maxillary central incisor  (IAGP)
Spasticity  (IAGP)
Specific learning disability  (IAGP)
Spinal cord tumor  (IAGP)
Spinal dysraphism  (IAGP)
Sporadic  (IAGP)
Strabismus  (IAGP)
Submucous cleft hard palate  (IAGP)
Synophrys  (IAGP)
Talipes  (IAGP)
Temperature instability  (IAGP)
Tented upper lip vermilion  (IAGP)
Tetralogy of Fallot  (IAGP)
Thick eyebrow  (IAGP)
Tooth agenesis  (IAGP)
Upslanted palpebral fissure  (IAGP)
Variable expressivity  (IAGP)
Ventricular septal defect  (IAGP)
Vomiting  (IAGP)
References

Additional References at PubMed
PMID:1887845   PMID:8889548   PMID:9889003   PMID:10415461   PMID:10490620   PMID:11069920   PMID:11173923   PMID:11554737   PMID:12050133   PMID:12107413   PMID:12441302   PMID:12477932  
PMID:12543801   PMID:14973488   PMID:15221788   PMID:15635066   PMID:16323008   PMID:17576749   PMID:17666527   PMID:18791198   PMID:18836447   PMID:19274049   PMID:19346217   PMID:19353631  
PMID:19921650   PMID:20057906   PMID:20157829   PMID:20201926   PMID:20301552   PMID:20301702   PMID:20531442   PMID:20634891   PMID:20682799   PMID:21873635   PMID:21909109   PMID:21940735  
PMID:22310223   PMID:22488850   PMID:23977152   PMID:25187374   PMID:27501229   PMID:27821176   PMID:28473536   PMID:28595628   PMID:28643150   PMID:28670735   PMID:29463994   PMID:30242153  
PMID:30672777   PMID:32051553   PMID:33264103   PMID:33961781  


Genomics

Comparative Map Data
SIX3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl244,941,702 - 44,946,071 (+)EnsemblGRCh38hg38GRCh38
GRCh38244,941,702 - 44,946,071 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37245,168,841 - 45,173,210 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36245,022,541 - 45,025,894 (+)NCBINCBI36hg18NCBI36
Build 34245,080,511 - 45,084,092NCBI
Celera245,007,709 - 45,011,888 (+)NCBI
Cytogenetic Map2p21NCBI
HuRef244,885,400 - 44,910,885 (+)NCBIHuRef
CHM1_1245,098,943 - 45,103,122 (+)NCBICHM1_1
Six3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391785,921,036 - 85,933,619 (+)NCBIGRCm39mm39
GRCm39 Ensembl1785,921,036 - 85,936,730 (+)Ensembl
GRCm381785,613,608 - 85,626,191 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1785,613,608 - 85,629,302 (+)EnsemblGRCm38mm10GRCm38
MGSCv371786,020,174 - 86,025,531 (+)NCBIGRCm37mm9NCBIm37
MGSCv361785,529,160 - 85,532,488 (+)NCBImm8
Celera1789,974,811 - 89,987,580 (+)NCBICelera
Cytogenetic Map17E4NCBI
cM Map1755.42NCBI
Six3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.269,040,123 - 9,043,336 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl69,036,434 - 9,053,301 (-)Ensembl
Rnor_6.068,886,730 - 8,891,094 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl68,886,591 - 8,889,925 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.068,778,756 - 8,815,903 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.468,981,995 - 9,019,365 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.169,015,373 - 9,019,374 (+)NCBI
Celera68,770,011 - 8,793,533 (-)NCBICelera
Cytogenetic Map6q12NCBI
Six3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544111,966,389 - 11,979,466 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544111,966,389 - 11,978,545 (+)NCBIChiLan1.0ChiLan1.0
SIX3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A45,978,828 - 45,988,078 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v02A45,038,634 - 45,072,867 (+)NCBIMhudiblu_PPA_v0panPan3
SIX3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11047,332,875 - 47,369,359 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1047,332,888 - 47,343,635 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1047,190,442 - 47,227,035 (+)NCBI
ROS_Cfam_1.01048,209,368 - 48,245,952 (+)NCBI
UMICH_Zoey_3.11047,917,957 - 47,954,541 (+)NCBI
UNSW_CanFamBas_1.01048,207,086 - 48,217,927 (+)NCBI
UU_Cfam_GSD_1.01048,389,961 - 48,426,595 (+)NCBI
Six3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629235,674,153 - 35,677,974 (-)NCBI
SpeTri2.0NW_0049365087,103,578 - 7,106,588 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SIX3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl395,521,333 - 95,525,436 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1395,521,330 - 95,527,004 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
SIX3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11462,278,124 - 62,292,942 (-)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604549,599,060 - 49,626,248 (+)NCBIVero_WHO_p1.0
Six3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473826,379,172 - 26,391,669 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH94877  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37245,170,233 - 45,170,465UniSTSGRCh37
Build 36245,023,737 - 45,023,969RGDNCBI36
Celera245,008,905 - 45,009,137RGD
Cytogenetic Map2p21UniSTS
HuRef244,907,902 - 44,908,134UniSTS
G65690  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37245,172,806 - 45,173,049UniSTSGRCh37
Build 36245,026,310 - 45,026,553RGDNCBI36
Celera245,011,478 - 45,011,721RGD
Cytogenetic Map2p21UniSTS
HuRef244,910,475 - 44,910,718UniSTS
D2S4014  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37245,147,423 - 45,147,701UniSTSGRCh37
Build 36245,000,927 - 45,001,205RGDNCBI36
Celera244,986,098 - 44,986,376RGD
Cytogenetic Map2p21UniSTS
HuRef244,885,323 - 44,885,601UniSTS
RH143896  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37245,169,875 - 45,170,000UniSTSGRCh37
Build 36245,023,379 - 45,023,504RGDNCBI36
Celera245,008,547 - 45,008,672RGD
Cytogenetic Map2p21UniSTS
HuRef244,907,544 - 44,907,669UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:711
Count of miRNA genes:463
Interacting mature miRNAs:521
Transcripts:ENST00000260653
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 visual system adipose tissue appendage
High
Medium 4 286 2 79 2 46 11 1069 5 43 47 2 1
Low 62 11 26 12 297 13 177 44 1086 21 480 187 3 21 33
Below cutoff 1215 1365 531 203 622 77 2670 1327 1329 172 437 790 130 730 1767

Sequence

Nucleotide Sequences
RefSeq Transcripts NG_016222 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_005413 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC012354 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF049339 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF083891 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF092047 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ012611 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL162671 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC030289 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BF569811 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BF570321 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BM668514 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CD673488 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471053 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EL952320 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KM609548 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KM609549 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KM609550 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KM609551 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KM609552 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KP061153 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KT585110 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KU342029 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KU342030 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KX710183 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  LC106310 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  LC106314 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000260653   ⟹   ENSP00000260653
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl244,941,702 - 44,946,071 (+)Ensembl
RefSeq Acc Id: NM_005413   ⟹   NP_005404
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38244,941,702 - 44,946,071 (+)NCBI
GRCh37245,169,037 - 45,173,216 (+)ENTREZGENE
Build 36245,022,541 - 45,025,894 (+)NCBI Archive
HuRef244,885,400 - 44,910,885 (+)ENTREZGENE
CHM1_1245,098,943 - 45,103,122 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_005404   ⟸   NM_005413
- UniProtKB: O95343 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000260653   ⟸   ENST00000260653
Protein Domains
Homeobox   SIX1_SD

Promoters
RGD ID:6860212
Promoter ID:EPDNEW_H3271
Type:initiation region
Name:SIX3_1
Description:SIX homeobox 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H3272  EPDNEW_H3273  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38244,941,702 - 44,941,762EPDNEW
RGD ID:6860214
Promoter ID:EPDNEW_H3272
Type:initiation region
Name:SIX3_2
Description:SIX homeobox 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H3271  EPDNEW_H3273  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38244,941,842 - 44,941,902EPDNEW
RGD ID:6860216
Promoter ID:EPDNEW_H3273
Type:initiation region
Name:SIX3_3
Description:SIX homeobox 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H3271  EPDNEW_H3272  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38244,942,075 - 44,942,135EPDNEW
RGD ID:6798168
Promoter ID:HG_KWN:32476
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Lymphoblastoid
Transcripts:OTTHUMT00000326192
Position:
Human AssemblyChrPosition (strand)Source
Build 36245,022,416 - 45,023,317 (+)MPROMDB

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_005413.4(SIX3):c.385G>T (p.Glu129Ter) single nucleotide variant Holoprosencephaly 2 [RCV000023328]|Schizencephaly [RCV000023329] Chr2:44942489 [GRCh38]
Chr2:45169628 [GRCh37]
Chr2:2p21
pathogenic
NM_005413.4(SIX3):c.109G>T (p.Gly37Cys) single nucleotide variant Holoprosencephaly 2 [RCV000023330]|Schizencephaly [RCV000023331]|Solitary median maxillary central incisor syndrome [RCV000171135]|not provided [RCV000713302]|not specified [RCV000173372] Chr2:44942213 [GRCh38]
Chr2:45169352 [GRCh37]
Chr2:2p21
pathogenic|benign|likely benign
NM_005413.4(SIX3):c.499G>T (p.Ala167Ser) single nucleotide variant Schizencephaly [RCV000023332] Chr2:44942603 [GRCh38]
Chr2:45169742 [GRCh37]
Chr2:2p21
pathogenic
NM_005413.4(SIX3):c.676C>G (p.Leu226Val) single nucleotide variant Holoprosencephaly 2 [RCV000006466] Chr2:44942780 [GRCh38]
Chr2:45169919 [GRCh37]
Chr2:2p21
pathogenic
NM_005413.4(SIX3):c.770G>C (p.Arg257Pro) single nucleotide variant Holoprosencephaly 2 [RCV000006467] Chr2:44942874 [GRCh38]
Chr2:45170013 [GRCh37]
Chr2:2p21
pathogenic|likely pathogenic
NM_005413.4(SIX3):c.749T>C (p.Val250Ala) single nucleotide variant Holoprosencephaly 2 [RCV000006468] Chr2:44942853 [GRCh38]
Chr2:45169992 [GRCh37]
Chr2:2p21
pathogenic
NM_005413.4(SIX3):c.556_557dup (p.Pro187fs) duplication Holoprosencephaly 2 [RCV000006469] Chr2:44942659..44942660 [GRCh38]
Chr2:45169798..45169799 [GRCh37]
Chr2:2p21
pathogenic
NM_005413.3(SIX3):c.406_407dup (p.Val137Profs) duplication Holoprosencephaly 2 [RCV000006470] Chr2:44942510..44942511 [GRCh38]
Chr2:45169649..45169650 [GRCh37]
Chr2:2p21
pathogenic
NM_005413.4(SIX3):c.206G>A (p.Gly69Asp) single nucleotide variant Holoprosencephaly 2 [RCV000812876] Chr2:44942310 [GRCh38]
Chr2:45169449 [GRCh37]
Chr2:2p21
pathogenic|uncertain significance
NM_005413.4(SIX3):c.339G>T (p.Trp113Cys) single nucleotide variant Holoprosencephaly 2 [RCV000006472]|not specified [RCV000506131] Chr2:44942443 [GRCh38]
Chr2:45169582 [GRCh37]
Chr2:2p21
pathogenic
NM_005413.4(SIX3):c.169G>T (p.Gly57Cys) single nucleotide variant Holoprosencephaly 2 [RCV000656534] Chr2:44942273 [GRCh38]
Chr2:45169412 [GRCh37]
Chr2:2p21
uncertain significance
NM_005413.4(SIX3):c.219C>T (p.Pro73=) single nucleotide variant Holoprosencephaly 2 [RCV000055680]|not provided [RCV000878695]|not specified [RCV000304572] Chr2:44942323 [GRCh38]
Chr2:45169462 [GRCh37]
Chr2:2p21
benign|likely benign
NM_005413.4(SIX3):c.576C>T (p.Arg192=) single nucleotide variant Holoprosencephaly 2 [RCV000055687]|none provided [RCV001283570]|not provided [RCV000713305]|not specified [RCV000245285] Chr2:44942680 [GRCh38]
Chr2:45169819 [GRCh37]
Chr2:2p21
benign
NM_005413.4(SIX3):c.696_705del (p.Asn232fs) deletion Holoprosencephaly 2 [RCV000055688] Chr2:44942800..44942809 [GRCh38]
Chr2:45169939..45169948 [GRCh37]
Chr2:2p21
pathogenic
NM_005413.4(SIX3):c.90G>T (p.Ala30=) single nucleotide variant Holoprosencephaly 2 [RCV000055692]|not provided [RCV000713306]|not specified [RCV000245820] Chr2:44942194 [GRCh38]
Chr2:45169333 [GRCh37]
Chr2:2p21
benign
GRCh38/hg38 2p25.3-16.1(chr2:66097-55570637)x3 copy number gain See cases [RCV000052933] Chr2:66097..55570637 [GRCh38]
Chr2:66097..55797773 [GRCh37]
Chr2:56097..55651277 [NCBI36]
Chr2:2p25.3-16.1
pathogenic
GRCh38/hg38 2p22.3-21(chr2:32849247-45016061)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052942]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052942]|See cases [RCV000052942] Chr2:32849247..45016061 [GRCh38]
Chr2:33074314..45243200 [GRCh37]
Chr2:32927818..45096704 [NCBI36]
Chr2:2p22.3-21
pathogenic
GRCh38/hg38 2p22.1-16.1(chr2:40738282-57863821)x3 copy number gain See cases [RCV000052943] Chr2:40738282..57863821 [GRCh38]
Chr2:40965422..58090956 [GRCh37]
Chr2:40818926..57944460 [NCBI36]
Chr2:2p22.1-16.1
pathogenic
NM_005413.4(SIX3):c.525G>A (p.Gln175=) single nucleotide variant Holoprosencephaly 2 [RCV001084820]|not provided [RCV000713304]|not specified [RCV000173373] Chr2:44942629 [GRCh38]
Chr2:45169768 [GRCh37]
Chr2:2p21
benign|likely benign|conflicting interpretations of pathogenicity
NM_005413.4(SIX3):c.187GGC[8] (p.Gly69dup) microsatellite not provided [RCV000173374] Chr2:44942290..44942291 [GRCh38]
Chr2:45169429..45169430 [GRCh37]
Chr2:2p21
uncertain significance
NM_005413.4(SIX3):c.-2C>G single nucleotide variant not provided [RCV000173375] Chr2:44942103 [GRCh38]
Chr2:45169242 [GRCh37]
Chr2:2p21
uncertain significance
GRCh38/hg38 2p21(chr2:44942723-45431847)x3 copy number gain See cases [RCV000133760] Chr2:44942723..45431847 [GRCh38]
Chr2:45169862..45658986 [GRCh37]
Chr2:45023366..45512490 [NCBI36]
Chr2:2p21
uncertain significance
GRCh38/hg38 2p21(chr2:43762375-44960289)x3 copy number gain See cases [RCV000135631] Chr2:43762375..44960289 [GRCh38]
Chr2:43989514..45187428 [GRCh37]
Chr2:43843018..45040932 [NCBI36]
Chr2:2p21
pathogenic|uncertain significance
GRCh38/hg38 2p21(chr2:44944718-44945255)x3 copy number gain See cases [RCV000137014] Chr2:44944718..44945255 [GRCh38]
Chr2:45171857..45172394 [GRCh37]
Chr2:45025361..45025898 [NCBI36]
Chr2:2p21
benign
GRCh38/hg38 2p21(chr2:44945067-44945255)x3 copy number gain See cases [RCV000137043] Chr2:44945067..44945255 [GRCh38]
Chr2:45172206..45172394 [GRCh37]
Chr2:45025710..45025898 [NCBI36]
Chr2:2p21
benign
GRCh38/hg38 2p21(chr2:43676810-45016061)x3 copy number gain See cases [RCV000137089] Chr2:43676810..45016061 [GRCh38]
Chr2:43903949..45243200 [GRCh37]
Chr2:43757453..45096704 [NCBI36]
Chr2:2p21
uncertain significance
GRCh38/hg38 2p21(chr2:44893684-45016061)x3 copy number gain See cases [RCV000137573] Chr2:44893684..45016061 [GRCh38]
Chr2:45120823..45243200 [GRCh37]
Chr2:44974327..45096704 [NCBI36]
Chr2:2p21
uncertain significance
GRCh38/hg38 2p21(chr2:44868615-44944763)x1 copy number loss See cases [RCV000137186] Chr2:44868615..44944763 [GRCh38]
Chr2:45095754..45171902 [GRCh37]
Chr2:44949258..45025406 [NCBI36]
Chr2:2p21
benign
GRCh38/hg38 2p21(chr2:44941697-44942746)x3 copy number gain See cases [RCV000141473] Chr2:44941697..44942746 [GRCh38]
Chr2:45168836..45169885 [GRCh37]
Chr2:45022340..45023389 [NCBI36]
Chr2:2p21
benign
GRCh38/hg38 2p21(chr2:44944704-44945255)x3 copy number gain See cases [RCV000141474] Chr2:44944704..44945255 [GRCh38]
Chr2:45171843..45172394 [GRCh37]
Chr2:45025347..45025898 [NCBI36]
Chr2:2p21
benign
GRCh38/hg38 2p25.1-11.2(chr2:7495123-87705899)x3 copy number gain See cases [RCV000141494] Chr2:7495123..87705899 [GRCh38]
Chr2:7635254..88005418 [GRCh37]
Chr2:7552705..87786533 [NCBI36]
Chr2:2p25.1-11.2
benign
GRCh38/hg38 2p21(chr2:44941697-44942175)x3 copy number gain See cases [RCV000142377] Chr2:44941697..44942175 [GRCh38]
Chr2:45168836..45169314 [GRCh37]
Chr2:45022340..45022818 [NCBI36]
Chr2:2p21
benign
GRCh38/hg38 2p25.3-21(chr2:236816-45983232)x3 copy number gain See cases [RCV000143682] Chr2:236816..45983232 [GRCh38]
Chr2:236816..46210371 [GRCh37]
Chr2:226816..46063875 [NCBI36]
Chr2:2p25.3-21
pathogenic
NM_005413.4(SIX3):c.942A>G (p.Ala314=) single nucleotide variant Holoprosencephaly 2 [RCV001520367]|not provided [RCV000713307]|not specified [RCV000153953] Chr2:44944703 [GRCh38]
Chr2:45171842 [GRCh37]
Chr2:2p21
benign
NC_000002.12:g.44950068T>A single nucleotide variant Lung cancer [RCV000092091] Chr2:44950068 [GRCh38]
Chr2:45177207 [GRCh37]
Chr2:2p21
uncertain significance
NM_005413.4(SIX3):c.831G>A (p.Pro277=) single nucleotide variant not specified [RCV000253592] Chr2:44944592 [GRCh38]
Chr2:45171731 [GRCh37]
Chr2:2p21
likely benign
NM_004820.5(CYP7B1):c.90C>T (p.Leu30=) single nucleotide variant Holoprosencephaly 2 [RCV000872928]|not provided [RCV001636789]|not specified [RCV000248820] Chr2:44942824 [GRCh38]
Chr2:45169963 [GRCh37]
Chr2:2p21
benign|likely benign
NM_005413.4(SIX3):c.406_407del (p.Ala136fs) microsatellite not provided [RCV000520730] Chr2:44942500..44942501 [GRCh38]
Chr2:45169639..45169640 [GRCh37]
Chr2:2p21
pathogenic
NM_005413.4(SIX3):c.369G>A (p.Glu123=) single nucleotide variant Holoprosencephaly 2 [RCV001078601]|not provided [RCV000273668] Chr2:44942473 [GRCh38]
Chr2:45169612 [GRCh37]
Chr2:2p21
benign|conflicting interpretations of pathogenicity|uncertain significance
NM_005413.4(SIX3):c.180C>T (p.Gly60=) single nucleotide variant not provided [RCV000274505] Chr2:44942284 [GRCh38]
Chr2:45169423 [GRCh37]
Chr2:2p21
uncertain significance
NM_005413.4(SIX3):c.357del (p.Ala121fs) deletion not provided [RCV000351427] Chr2:44942457 [GRCh38]
Chr2:45169596 [GRCh37]
Chr2:2p21
pathogenic
NM_005413.4(SIX3):c.947C>T (p.Thr316Ile) single nucleotide variant Holoprosencephaly 2 [RCV001394388]|not provided [RCV000354705] Chr2:44944708 [GRCh38]
Chr2:45171847 [GRCh37]
Chr2:2p21
likely benign|uncertain significance
NM_005413.4(SIX3):c.375C>A (p.Ile125=) single nucleotide variant not provided [RCV000363582] Chr2:44942479 [GRCh38]
Chr2:45169618 [GRCh37]
Chr2:2p21
uncertain significance
NM_005413.4(SIX3):c.876C>G (p.Gly292=) single nucleotide variant not provided [RCV000400778] Chr2:44944637 [GRCh38]
Chr2:45171776 [GRCh37]
Chr2:2p21
uncertain significance
NM_005413.4(SIX3):c.613G>C (p.Asp205His) single nucleotide variant not provided [RCV000269190] Chr2:44942717 [GRCh38]
Chr2:45169856 [GRCh37]
Chr2:2p21
uncertain significance
NM_005413.4(SIX3):c.824T>C (p.Ile275Thr) single nucleotide variant not provided [RCV000514708] Chr2:44944585 [GRCh38]
Chr2:45171724 [GRCh37]
Chr2:2p21
likely benign
NM_005413.4(SIX3):c.127G>T (p.Gly43Cys) single nucleotide variant Holoprosencephaly 2 [RCV000764416]|not provided [RCV000594169] Chr2:44942231 [GRCh38]
Chr2:45169370 [GRCh37]
Chr2:2p21
uncertain significance
NM_005413.4(SIX3):c.777G>T (p.Gln259His) single nucleotide variant not provided [RCV000489818] Chr2:44942881 [GRCh38]
Chr2:45170020 [GRCh37]
Chr2:2p21
likely pathogenic
NM_005413.4(SIX3):c.168C>T (p.Gly56=) single nucleotide variant not provided [RCV000591655] Chr2:44942272 [GRCh38]
Chr2:45169411 [GRCh37]
Chr2:2p21
uncertain significance
NM_005413.4(SIX3):c.441_451del (p.Leu148fs) deletion Holoprosencephaly 2 [RCV000656533] Chr2:44942544..44942554 [GRCh38]
Chr2:45169683..45169693 [GRCh37]
Chr2:2p21
pathogenic
NM_005413.4(SIX3):c.288T>A (p.Cys96Ter) single nucleotide variant not provided [RCV000578945] Chr2:44942392 [GRCh38]
Chr2:45169531 [GRCh37]
Chr2:2p21
pathogenic
NM_005413.4(SIX3):c.1A>G (p.Met1Val) single nucleotide variant not provided [RCV000599004] Chr2:44942105 [GRCh38]
Chr2:45169244 [GRCh37]
Chr2:2p21
likely pathogenic
NM_005413.4(SIX3):c.786C>A (p.Arg262=) single nucleotide variant not provided [RCV000593691] Chr2:44942890 [GRCh38]
Chr2:45170029 [GRCh37]
Chr2:2p21
uncertain significance
NM_005413.4(SIX3):c.887C>G (p.Ser296Trp) single nucleotide variant Holoprosencephaly 2 [RCV000639734] Chr2:44944648 [GRCh38]
Chr2:45171787 [GRCh37]
Chr2:2p21
uncertain significance
NM_005413.4(SIX3):c.105G>T (p.Gly35=) single nucleotide variant not provided [RCV000728660] Chr2:44942209 [GRCh38]
Chr2:45169348 [GRCh37]
Chr2:2p21
uncertain significance
NM_005413.4(SIX3):c.594G>C (p.Pro198=) single nucleotide variant not provided [RCV000734680] Chr2:44942698 [GRCh38]
Chr2:45169837 [GRCh37]
Chr2:2p21
uncertain significance
GRCh37/hg19 2p25.3-q37.3(chr2:14238-243048760)x3 copy number gain not provided [RCV000752802] Chr2:14238..243048760 [GRCh37]
Chr2:2p25.3-q37.3
pathogenic
GRCh37/hg19 2p23.3-16.1(chr2:27861707-60790985)x3 copy number gain See cases [RCV000454271] Chr2:27861707..60790985 [GRCh37]
Chr2:2p23.3-16.1
pathogenic
GRCh37/hg19 2p21(chr2:44914980-45172628)x1 copy number loss See cases [RCV000446138] Chr2:44914980..45172628 [GRCh37]
Chr2:2p21
pathogenic
NM_005413.4(SIX3):c.306G>A (p.Thr102=) single nucleotide variant not provided [RCV001698266] Chr2:44942410 [GRCh38]
Chr2:45169549 [GRCh37]
Chr2:2p21
likely benign
GRCh37/hg19 2p25.3-q37.3(chr2:12771-242783384) copy number gain See cases [RCV000512056] Chr2:12771..242783384 [GRCh37]
Chr2:2p25.3-q37.3
pathogenic
SIX3, 2-BP DUP, 406GC AND GLY69ASP duplication Holoprosencephaly 2 [RCV000006470] Chr2:2p21 pathogenic
NC_000002.11:g.38121110_47669522inv inversion Lynch syndrome [RCV000494356] Chr2:38121110..47669522 [GRCh37]
Chr2:2p22.2-21
pathogenic
Single allele inversion not provided [RCV000714264] Chr2:40608411..146900718 [GRCh37]
Chr2:2p22.1-q22.3
likely pathogenic
GRCh37/hg19 2p25.3-q37.3(chr2:12771-242783384)x3 copy number gain See cases [RCV000511212] Chr2:12771..242783384 [GRCh37]
Chr2:2p25.3-q37.3
pathogenic
NM_005413.4(SIX3):c.602G>A (p.Arg201His) single nucleotide variant not provided [RCV000658046] Chr2:44942706 [GRCh38]
Chr2:45169845 [GRCh37]
Chr2:2p21
uncertain significance
NM_005413.4(SIX3):c.52A>T (p.Asn18Tyr) single nucleotide variant Holoprosencephaly 2 [RCV000686110] Chr2:44942156 [GRCh38]
Chr2:45169295 [GRCh37]
Chr2:2p21
uncertain significance
GRCh37/hg19 2p22.3-16.1(chr2:34792916-56676541)x3 copy number gain not provided [RCV000682169] Chr2:34792916..56676541 [GRCh37]
Chr2:2p22.3-16.1
pathogenic
NM_005413.4(SIX3):c.507G>A (p.Trp169Ter) single nucleotide variant Holoprosencephaly 2 [RCV000702708] Chr2:44942611 [GRCh38]
Chr2:45169750 [GRCh37]
Chr2:2p21
pathogenic
NM_005413.4(SIX3):c.348C>T (p.Pro116=) single nucleotide variant Holoprosencephaly 2 [RCV001078552]|not provided [RCV000713303] Chr2:44942452 [GRCh38]
Chr2:45169591 [GRCh37]
Chr2:2p21
benign
GRCh37/hg19 2p24.1-16.3(chr2:22665048-52850368)x3 copy number gain not provided [RCV000752875] Chr2:22665048..52850368 [GRCh37]
Chr2:2p24.1-16.3
pathogenic
GRCh37/hg19 2p25.3-q37.3(chr2:15672-243101834)x3 copy number gain not provided [RCV000752804] Chr2:15672..243101834 [GRCh37]
Chr2:2p25.3-q37.3
pathogenic
NM_005413.4(SIX3):c.831G>C (p.Pro277=) single nucleotide variant Holoprosencephaly 2 [RCV001496270]|not provided [RCV000937703] Chr2:44944592 [GRCh38]
Chr2:45171731 [GRCh37]
Chr2:2p21
likely benign
NM_005413.4(SIX3):c.807-7C>T single nucleotide variant Holoprosencephaly 2 [RCV000872803] Chr2:44944561 [GRCh38]
Chr2:45171700 [GRCh37]
Chr2:2p21
likely benign
null single nucleotide variant not provided [RCV001709237] Chr2:44943053 [GRCh38]
Chr2:45170192 [GRCh37]
Chr2:2p21
benign
NM_005413.4(SIX3):c.830C>A (p.Pro277Gln) single nucleotide variant not provided [RCV000964681] Chr2:44944591 [GRCh38]
Chr2:45171730 [GRCh37]
Chr2:2p21
benign
NM_005413.4(SIX3):c.43T>C (p.Leu15=) single nucleotide variant not provided [RCV000928810] Chr2:44942147 [GRCh38]
Chr2:45169286 [GRCh37]
Chr2:2p21
likely benign
NM_005413.4(SIX3):c.363G>T (p.Ala121=) single nucleotide variant not provided [RCV000919811] Chr2:44942467 [GRCh38]
Chr2:45169606 [GRCh37]
Chr2:2p21
likely benign
NM_005413.4(SIX3):c.855G>A (p.Glu285=) single nucleotide variant not provided [RCV000924464] Chr2:44944616 [GRCh38]
Chr2:45171755 [GRCh37]
Chr2:2p21
likely benign
NM_005413.4(SIX3):c.58G>T (p.Ala20Ser) single nucleotide variant not provided [RCV000878187] Chr2:44942162 [GRCh38]
Chr2:45169301 [GRCh37]
Chr2:2p21
benign
NM_005413.4(SIX3):c.961C>T (p.Leu321Phe) single nucleotide variant Holoprosencephaly 2 [RCV001037917] Chr2:44944722 [GRCh38]
Chr2:45171861 [GRCh37]
Chr2:2p21
uncertain significance
NM_005413.4(SIX3):c.96C>T (p.Ser32=) single nucleotide variant Holoprosencephaly 2 [RCV000864825] Chr2:44942200 [GRCh38]
Chr2:45169339 [GRCh37]
Chr2:2p21
likely benign
NM_005413.4(SIX3):c.216C>T (p.Ala72=) single nucleotide variant not provided [RCV000879247] Chr2:44942320 [GRCh38]
Chr2:45169459 [GRCh37]
Chr2:2p21
likely benign
NM_005413.4(SIX3):c.435C>T (p.Phe145=) single nucleotide variant not provided [RCV000951777] Chr2:44942539 [GRCh38]
Chr2:45169678 [GRCh37]
Chr2:2p21
likely benign
NM_005413.4(SIX3):c.338G>C (p.Trp113Ser) single nucleotide variant Holoprosencephaly 2 [RCV000822509] Chr2:44942442 [GRCh38]
Chr2:45169581 [GRCh37]
Chr2:2p21
uncertain significance
NM_005413.4(SIX3):c.807-161C>T single nucleotide variant not provided [RCV000826369] Chr2:44944407 [GRCh38]
Chr2:45171546 [GRCh37]
Chr2:2p21
benign
NM_005413.4(SIX3):c.806+104G>A single nucleotide variant not provided [RCV000834278] Chr2:44943014 [GRCh38]
Chr2:45170153 [GRCh37]
Chr2:2p21
benign
NM_005413.4(SIX3):c.351G>A (p.Val117=) single nucleotide variant not provided [RCV000842199] Chr2:44942455 [GRCh38]
Chr2:45169594 [GRCh37]
Chr2:2p21
likely benign
NM_005413.4(SIX3):c.208T>C (p.Ser70Pro) single nucleotide variant Schizencephaly [RCV001197116] Chr2:44942312 [GRCh38]
Chr2:45169451 [GRCh37]
Chr2:2p21
uncertain significance
NM_005413.4(SIX3):c.806+145A>G single nucleotide variant not provided [RCV001534006] Chr2:44943055 [GRCh38]
Chr2:45170194 [GRCh37]
Chr2:2p21
benign
NM_005413.4(SIX3):c.-323C>T single nucleotide variant not provided [RCV001561092] Chr2:44941782 [GRCh38]
Chr2:45168921 [GRCh37]
Chr2:2p21
likely benign
NM_005413.4(SIX3):c.324G>A (p.Leu108=) single nucleotide variant not provided [RCV000938720] Chr2:44942428 [GRCh38]
Chr2:45169567 [GRCh37]
Chr2:2p21
likely benign
NM_005413.4(SIX3):c.909G>C (p.Pro303=) single nucleotide variant Holoprosencephaly 2 [RCV000896830] Chr2:44944670 [GRCh38]
Chr2:45171809 [GRCh37]
Chr2:2p21
benign
NM_005413.4(SIX3):c.300G>A (p.Glu100=) single nucleotide variant not provided [RCV000897018] Chr2:44942404 [GRCh38]
Chr2:45169543 [GRCh37]
Chr2:2p21
likely benign
NM_005413.4(SIX3):c.42C>T (p.Phe14=) single nucleotide variant not provided [RCV000952671] Chr2:44942146 [GRCh38]
Chr2:45169285 [GRCh37]
Chr2:2p21
likely benign
NM_005413.4(SIX3):c.108C>T (p.Asn36=) single nucleotide variant Holoprosencephaly 2 [RCV001485215]|not provided [RCV000934906] Chr2:44942212 [GRCh38]
Chr2:45169351 [GRCh37]
Chr2:2p21
likely benign
NM_005529.7(HSPG2):c.6141T>C (p.Asp2047=) microsatellite not provided [RCV001644026] Chr2:44941808..44941813 [GRCh38]
Chr2:45168947..45168952 [GRCh37]
Chr2:2p21
benign
NM_005413.4(SIX3):c.419T>C (p.Phe140Ser) single nucleotide variant not provided [RCV001268497] Chr2:44942523 [GRCh38]
Chr2:45169662 [GRCh37]
Chr2:2p21
likely pathogenic
NM_005413.4(SIX3):c.581G>C (p.Arg194Pro) single nucleotide variant Holoprosencephaly 2 [RCV001270879] Chr2:44942685 [GRCh38]
Chr2:45169824 [GRCh37]
Chr2:2p21
likely pathogenic
NM_005413.4(SIX3):c.385G>A (p.Glu129Lys) single nucleotide variant not provided [RCV001358645] Chr2:44942489 [GRCh38]
Chr2:45169628 [GRCh37]
Chr2:2p21
uncertain significance
NM_005413.4(SIX3):c.573C>T (p.Tyr191=) single nucleotide variant Holoprosencephaly 2 [RCV001497219] Chr2:44942677 [GRCh38]
Chr2:45169816 [GRCh37]
Chr2:2p21
likely benign
NM_201596.3(CACNB2):c.121-3_121-2insTGT deletion Holoprosencephaly 2 [RCV001730118] Chr2:44942503..44942517 [GRCh38]
Chr2:45169642..45169656 [GRCh37]
Chr2:2p21
pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:10889 AgrOrtholog
COSMIC SIX3 COSMIC
Ensembl Genes ENSG00000138083 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSP00000260653 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000260653 ENTREZGENE, UniProtKB/Swiss-Prot
GTEx ENSG00000138083 GTEx
HGNC ID HGNC:10889 ENTREZGENE
Human Proteome Map SIX3 Human Proteome Map
InterPro Homeobox-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HTH_motif UniProtKB/TrEMBL
  SIX1_SD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SIX3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:6496 UniProtKB/Swiss-Prot
NCBI Gene 6496 ENTREZGENE
OMIM 157170 OMIM
  269160 OMIM
  603714 OMIM
PANTHER PTHR10390:SF31 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Homeodomain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SIX1_SD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA35789 PharmGKB
PRINTS HTHREPRESSR UniProtKB/TrEMBL
PROSITE HOMEOBOX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART HOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0D3RS46_HUMAN UniProtKB/TrEMBL
  A0A127AXB2_HUMAN UniProtKB/TrEMBL
  A0A127AXF1_HUMAN UniProtKB/TrEMBL
  A0A1Y0ZN85_HUMAN UniProtKB/TrEMBL
  A0A1Y0ZVZ1_HUMAN UniProtKB/TrEMBL
  A0PJI2_HUMAN UniProtKB/TrEMBL
  O95343 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary D6W5A5 UniProtKB/Swiss-Prot
  Q53T42 UniProtKB/Swiss-Prot