Gene Gene information from NCBI Gene database.
Entrez ID 6496
Gene name SIX homeobox 3
Gene symbol SIX3
Synonyms (NCBI Gene)
HPE2
Chromosome 2
Chromosome location 2p21
Summary This gene encodes a member of the sine oculis homeobox transcription factor family. The encoded protein plays a role in eye development. Mutations in this gene have been associated with holoprosencephaly type 2. [provided by RefSeq, Oct 2009]
miRNA miRNA information provided by mirtarbase database.
541
miRTarBase ID miRNA Experiments Reference
MIRT612491 hsa-miR-339-5p HITS-CLIP 19536157
MIRT612490 hsa-miR-6748-3p HITS-CLIP 19536157
MIRT612489 hsa-miR-3679-3p HITS-CLIP 19536157
MIRT612488 hsa-miR-4446-5p HITS-CLIP 19536157
MIRT635884 hsa-miR-10a-3p HITS-CLIP 23824327
Transcription factors Transcription factors information provided by TRRUST V2 database.
2
Transcription factor Regulation Reference
PAX6 Activation 11554737
PROX1 Activation 11554737
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
80
GO ID Ontology Definition Evidence Reference
GO:0000785 Component Chromatin ISA
GO:0000978 Function RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
GO:0000978 Function RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA 18836447
GO:0000978 Function RNA polymerase II cis-regulatory region sequence-specific DNA binding IEA
GO:0000981 Function DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
603714 10889 ENSG00000138083
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
O95343
Protein name Homeobox protein SIX3 (Sine oculis homeobox homolog 3)
Protein function Transcriptional regulator which can act as both a transcriptional repressor and activator by binding a ATTA homeodomain core recognition sequence on these target genes. During forebrain development represses WNT1 expression allowing zona limitan
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF16878 SIX1_SD 87 201 Transcriptional regulator, SIX1, N-terminal SD domain Domain
PF00046 Homeodomain 207 263 Homeodomain Domain
Sequence
MVFRSPLDLYSSHFLLPNFADSHHRSILLASSGGGNGAGGGGGAGGGSGGGNGAGGGGAG
GAGGGGGGGSRAPPEELSMFQLPTLNFSPEQVASVCETLEETGDIERLGRFLWSLPVAPG
ACEAINKHESILRARAVVAFHTGNFRDLYHILENHKFTKESHGKLQAMWLEAHYQEAEKL
RGRPLGPVDKYRVRKKFPLPR
TIWDGEQKTHCFKERTRSLLREWYLQDPYPNPSKKRELA
QATGLTPTQVGNWFKNRRQRDRA
AAAKNRLQHQAIGPSGMRSLAEPGCPTHGSAESPSTA
ASPTTSVSSLTERADTGTSILSVTSSDSECDV
Sequence length 332
Interactions View interactions
Associated diseases Disease associations from ClinVar categorized as Causal (Pathogenic/Likely Pathogenic) or Unknown.
171
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Holoprosencephaly 2 Pathogenic; Likely pathogenic rs2103641880, rs2466514157, rs121917878, rs121917879, rs121917880, rs1572624159, rs137853021, rs1403385518, rs2466513762, rs387906867, rs753473749, rs1553337688, rs1558420022, rs397515502, rs1666605262 RCV001730118
RCV002819396
RCV000006466
RCV000006467
RCV000006468
RCV000006469
RCV000006472
RCV003508710
RCV003508821
RCV000023328
RCV002248753
RCV000656533
RCV000702708
RCV000055688
RCV001270879
Schizencephaly Pathogenic rs387906867 RCV000023329
SIX3-related disorder Likely pathogenic rs1572624326 RCV003416998
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Intellectual disability Uncertain significance rs121917881 RCV005625687
Solitary median maxillary central incisor syndrome Benign; Likely benign rs199823175 RCV000171135
Associations from Text MiningDisease associations identified through Pubtator
Disease Name Relationship Type References
Adenocarcinoma Bronchiolo Alveolar Associate 23977152
Adenocarcinoma of Lung Inhibit 23977152
Anophthalmia with pulmonary hypoplasia Associate 11826019
Astrocytoma Associate 33051600
Breast Neoplasms Inhibit 29463994
Carcinogenesis Associate 23977152
Carcinogenesis Inhibit 29463994
Carcinoma Non Small Cell Lung Associate 33264103
Central Nervous System Vascular Malformations Associate 22310223
Colorectal Neoplasms Associate 19723660