SIX6 SIX homeobox 6 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SIX6provided by HGNC
Official Full Name: SIX homeobox 6provided by HGNC
Primary source: HGNC:HGNC:10892
See related: Ensembl:ENSG00000184302 MIM:606326; AllianceGenome:HGNC:10892
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: Six9; ODRMD; OPTX2; MCOPCT2
Summary: The protein encoded by this gene is a homeobox protein that is similar to the Drosophila 'sine oculis' gene product. This gene is found in a cluster of related genes on chromosome 14 and is thought to be involved in eye development. Defects in this gene are a cause of isolated microphthalmia with cataract type 2 (MCOPCT2). [provided by RefSeq, Jul 2008]
Expression: Low expression observed in reference dataset See more
Orthologs: mouse all
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Genomic context

Location:: 14q23.1

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	14	NC_000014.9 (60509146..60512850)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	14	NC_060938.1 (54715467..54719149)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	14	NC_000014.8 (60975864..60979568)

Chromosome 14 - NC_000014.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Association of SIX1-SIX6 polymorphisms with peripapillary retinal nerve fibre layer thickness in children.
Title: Association of SIX1-SIX6 polymorphisms with peripapillary retinal nerve fibre layer thickness in children.
Lack of association between SIX1/SIX6 locus polymorphisms and pseudoexfoliation syndrome in a population from the Republic of Korea.
Title: Lack of association between SIX1/SIX6 locus polymorphisms and pseudoexfoliation syndrome in a population from the Republic of Korea.
Association of Polymorphisms at the SIX1/SIX6 Locus With Normal Tension Glaucoma in a Korean Population.
Title: Association of Polymorphisms at the SIX1/SIX6 Locus With Normal Tension Glaucoma in a Korean Population.
Mutually exclusive epigenetic modification on SIX6 with hypermethylation for precancerous stage and metastasis emergence tracing.
Title: Mutually exclusive epigenetic modification on SIX6 with hypermethylation for precancerous stage and metastasis emergence tracing.
Novel SIX6 mutations cause recessively inherited congenital cataract, microcornea, and corneal opacification with or without coloboma and microphthalmia.
Title: Novel SIX6 mutations cause recessively inherited congenital cataract, microcornea, and corneal opacification with or without coloboma and microphthalmia.
SIX6-related anophthalmia/microphthalmia: second report on a deletion in a consanguineous family.
Title: SIX6-related anophthalmia/microphthalmia: second report on a deletion in a consanguineous family.
SIX6 is a TAL1-regulated transcription factor in T-ALL and associated with inferior outcome.
Title: SIX6 is a TAL1-regulated transcription factor in T-ALL and associated with inferior outcome.
Age-dependent regional retinal nerve fibre changes in SIX1/SIX6 polymorphism.
Title: Age-dependent regional retinal nerve fibre changes in SIX1/SIX6 polymorphism.
Genetic prediction models for primary open-angle glaucoma: translational research.
Title: Genetic prediction models for primary open-angle glaucoma: translational research.
Results uncover the mechanism through which ceRNET_CC is regulated, identify novel roles for the six2/ceRNET_CC axis in regulating the stemness of breast cancer cells, and propose the possibility of targeting the six2/ceRNET_CC axis to inhibit breast cancer stem cell (CSC) traits.
Title: Transcriptional factor six2 promotes the competitive endogenous RNA network between CYP4Z1 and pseudogene CYP4Z2P responsible for maintaining the stemness of breast cancer cells.

Submit: New GeneRIF Correction See all GeneRIFs (32)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Anophthalmia/microphthalmia-esophageal atresia syndrome MedGen: C1859773 OMIM: 206900 GeneReviews: SOX2 Disorder	Compare labs
Colobomatous optic disc-macular atrophy-chorioretinopathy syndrome MedGen: C4225424 OMIM: 212550 GeneReviews: Not available	Compare labs

Copy number response

Description
Copy number response Haploinsufficency No evidence available (Last evaluated 2012-03-22) ClinGen Genome Curation Page Triplosensitivity No evidence available (Last evaluated 2012-03-22) ClinGen Genome Curation Page

EBI GWAS Catalog

Description
A genome-wide association study in the Japanese population confirms 9p21 and 14q23 as susceptibility loci for primary open angle glaucoma. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common variants at 9p21 and 8q22 are associated with increased susceptibility to optic nerve degeneration in glaucoma. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common variants near ABCA1, AFAP1 and GMDS confer risk of primary open-angle glaucoma. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analyses of multiancestry cohorts identify multiple new susceptibility loci for refractive error and myopia. EBI GWAS Catalog EBI GWAS CatalogPubMed
Hundreds of variants clustered in genomic loci and biological pathways affect human height. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis of genome-wide association studies identifies novel loci that influence cupping and the glaucomatous process. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:481851

NoName (e-PCR)
- UniSTS:486210

G62930 (e-PCR)
- UniSTS:139905

Six6 (e-PCR), detects polymorphism
- UniSTS:527037

RH106539 (e-PCR)
- UniSTS:86228

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in animal organ morphogenesis	TAS Traceable Author Statement more info	PubMed
involved_in eye development	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in visual perception	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
part_of chromatin	ISA Inferred from Sequence Alignment more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
part_of transcription regulator complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: homeobox protein SIX6

Names: homeodomain protein OPTX2; optic homeobox 2; sine oculis homeobox homolog 6; sine oculis homeobox protein 6; sine oculis homeobox-like protein 6

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_008203.1 RefSeqGene

Range

4927..8631

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_007374.3 → NP_031400.2 homeobox protein SIX6

See identical proteins and their annotated locations for NP_031400.2

Status: REVIEWED

Source sequence(s)

AL049874, BC065831

Consensus CDS

CCDS9747.1

UniProtKB/Swiss-Prot

O95475, Q6NT42, Q9P1X8

UniProtKB/TrEMBL

Q5M8S8

Related

ENSP00000328596.5, ENST00000327720.6

Conserved Domains (2) summary

cd00086
Location:130 → 178

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

pfam16878
Location:9 → 122

SIX1_SD; Transcriptional regulator, SIX1, N-terminal SD domain