Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Associated diseases
Entrez ID	338917
Gene name	Visual system homeobox 2
Gene symbol	VSX2
Synonyms (NCBI Gene)	CHX10HOX10MCOP2MCOPCB3RET1
Chromosome	14
Chromosome location	14q24.3
Summary	This gene encodes a homeobox protein originally described as a retina-specific transcription factor. Mutations in this gene are associated with microphthalmia, cataracts and iris abnormalities. [provided by RefSeq, Oct 2009]

Show/Hide all (10)

SNP ID	Visualize variation	Clinical significance	Consequence
rs121912543	G>A,C	Pathogenic	Missense variant, coding sequence variant
rs121912545	C>T	Pathogenic, uncertain-significance	Missense variant, coding sequence variant
rs189139917	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs375294678	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, missense variant
rs377107974	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs752313464	G>A	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs755799430	G>A	Pathogenic, uncertain-significance	Missense variant, coding sequence variant
rs869025268	->G	Pathogenic	Coding sequence variant, frameshift variant
rs1555387462	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs1566888340	G>A	Pathogenic	Stop gained, coding sequence variant

Show/Hide all (83)

miRTarBase ID	miRNA	Experiments
MIRT1487958	hsa-miR-1253	CLIP-seq
MIRT1487959	hsa-miR-145	CLIP-seq
MIRT1487960	hsa-miR-1910	CLIP-seq
MIRT1487961	hsa-miR-219-1-3p	CLIP-seq
MIRT1487962	hsa-miR-3135b	CLIP-seq
MIRT1487963	hsa-miR-3148	CLIP-seq
MIRT1487964	hsa-miR-3176	CLIP-seq
MIRT1487965	hsa-miR-3689a-3p	CLIP-seq
MIRT1487966	hsa-miR-3689c	CLIP-seq
MIRT1487967	hsa-miR-3922-3p	CLIP-seq
MIRT1487968	hsa-miR-4259	CLIP-seq
MIRT1487969	hsa-miR-4425	CLIP-seq
MIRT1487970	hsa-miR-4434	CLIP-seq
MIRT1487971	hsa-miR-4516	CLIP-seq
MIRT1487972	hsa-miR-4646-5p	CLIP-seq
MIRT1487973	hsa-miR-4653-3p	CLIP-seq
MIRT1487974	hsa-miR-4682	CLIP-seq
MIRT1487975	hsa-miR-4743	CLIP-seq
MIRT1487976	hsa-miR-4753-5p	CLIP-seq
MIRT1487977	hsa-miR-4755-3p	CLIP-seq
MIRT1487978	hsa-miR-4782-5p	CLIP-seq
MIRT1487979	hsa-miR-571	CLIP-seq
MIRT1487980	hsa-miR-661	CLIP-seq
MIRT2146855	hsa-miR-2467-3p	CLIP-seq
MIRT2146856	hsa-miR-3151	CLIP-seq
MIRT2146857	hsa-miR-485-5p	CLIP-seq
MIRT2146858	hsa-miR-486-3p	CLIP-seq
MIRT2367427	hsa-miR-1237	CLIP-seq
MIRT2367428	hsa-miR-128	CLIP-seq
MIRT2367429	hsa-miR-2861	CLIP-seq
MIRT2367430	hsa-miR-377	CLIP-seq
MIRT2367431	hsa-miR-412	CLIP-seq
MIRT2367432	hsa-miR-4318	CLIP-seq
MIRT2367433	hsa-miR-4446-5p	CLIP-seq
MIRT2367434	hsa-miR-4711-3p	CLIP-seq
MIRT1487964	hsa-miR-3176	CLIP-seq
MIRT1487967	hsa-miR-3922-3p	CLIP-seq
MIRT2463345	hsa-miR-3190	CLIP-seq
MIRT2367430	hsa-miR-377	CLIP-seq
MIRT2367431	hsa-miR-412	CLIP-seq
MIRT2367432	hsa-miR-4318	CLIP-seq
MIRT2367434	hsa-miR-4711-3p	CLIP-seq
MIRT2463346	hsa-miR-671-5p	CLIP-seq
MIRT2463345	hsa-miR-3190	CLIP-seq
MIRT2367430	hsa-miR-377	CLIP-seq
MIRT2367431	hsa-miR-412	CLIP-seq
MIRT2367432	hsa-miR-4318	CLIP-seq
MIRT2367434	hsa-miR-4711-3p	CLIP-seq
MIRT2463346	hsa-miR-671-5p	CLIP-seq
MIRT2660903	hsa-miR-1	CLIP-seq
MIRT2660904	hsa-miR-1321	CLIP-seq
MIRT2660905	hsa-miR-206	CLIP-seq
MIRT2660906	hsa-miR-2392	CLIP-seq
MIRT2146855	hsa-miR-2467-3p	CLIP-seq
MIRT2660907	hsa-miR-3605-5p	CLIP-seq
MIRT2660908	hsa-miR-3673	CLIP-seq
MIRT2660909	hsa-miR-4270	CLIP-seq
MIRT2660910	hsa-miR-4441	CLIP-seq
MIRT2660911	hsa-miR-4694-3p	CLIP-seq
MIRT2660912	hsa-miR-4728-5p	CLIP-seq
MIRT2660913	hsa-miR-4739	CLIP-seq
MIRT2660914	hsa-miR-4756-5p	CLIP-seq
MIRT2660915	hsa-miR-522	CLIP-seq
MIRT2660916	hsa-miR-587	CLIP-seq
MIRT2660917	hsa-miR-613	CLIP-seq
MIRT2660903	hsa-miR-1	CLIP-seq
MIRT2695099	hsa-miR-1293	CLIP-seq
MIRT2660904	hsa-miR-1321	CLIP-seq
MIRT2660905	hsa-miR-206	CLIP-seq
MIRT2660906	hsa-miR-2392	CLIP-seq
MIRT2146855	hsa-miR-2467-3p	CLIP-seq
MIRT2660907	hsa-miR-3605-5p	CLIP-seq
MIRT2660908	hsa-miR-3673	CLIP-seq
MIRT2660909	hsa-miR-4270	CLIP-seq
MIRT2660910	hsa-miR-4441	CLIP-seq
MIRT2695100	hsa-miR-4483	CLIP-seq
MIRT2660911	hsa-miR-4694-3p	CLIP-seq
MIRT2660912	hsa-miR-4728-5p	CLIP-seq
MIRT2660913	hsa-miR-4739	CLIP-seq
MIRT2660914	hsa-miR-4756-5p	CLIP-seq
MIRT2660915	hsa-miR-522	CLIP-seq
MIRT2660916	hsa-miR-587	CLIP-seq
MIRT2660917	hsa-miR-613	CLIP-seq

Show/Hide all (1)

Transcription factor	Regulation	Reference
NEUROG3	Activation	19028584

Show/Hide all (26)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IDA	15647262
GO:0000785	Component	Chromatin	ISA
GO:0000977	Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	IDA	15647262
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IEA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	ISA
GO:0001227	Function	DNA-binding transcription repressor activity, RNA polymerase II-specific	IDA	15647262
GO:0003677	Function	DNA binding	IEA
GO:0005515	Function	Protein binding	IPI	32814053
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0007405	Process	Neuroblast proliferation	IEA
GO:0007406	Process	Negative regulation of neuroblast proliferation	IEA
GO:0007601	Process	Visual perception	IEA
GO:0008283	Process	Cell population proliferation	IEA
GO:0008284	Process	Positive regulation of cell population proliferation	IEA
GO:0021953	Process	Central nervous system neuron differentiation	IEA
GO:0043010	Process	Camera-type eye development	IEA
GO:0045165	Process	Cell fate commitment	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0060040	Process	Retinal bipolar neuron differentiation	IEA
GO:0060042	Process	Retina morphogenesis in camera-type eye	IEA
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IBA
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536

MIM	HGNC	e!Ensembl
142993	1975	ENSG00000119614

P58304

Protein name

Visual system homeobox 2 (Ceh-10 homeodomain-containing homolog) (Homeobox protein CHX10)

Protein function

Acts as a transcriptional regulator through binding to DNA at the consensus sequence 5'-[TC]TAATT[AG][AG]-3' upstream of gene promoters (PubMed:27301076). Plays a significant role in the specification and morphogenesis of the sensory retina (By

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00046	Homeodomain	149 → 205	Homeodomain	Domain
PF03826	OAR	300 → 318	OAR motif	Motif

Tissue specificity

TISSUE SPECIFICITY: Abundantly expressed in retinal neuroblasts during eye development and in the inner nuclear layer of the adult retina. Within this layer, expression is stronger in the outer margin where bipolar cells predominate.

Sequence

MTGKAGEALSKPKSETVAKSTSGGAPARCTGFGIQEILGLNKEPPSSHPRAALDGLAPGH
LLAARSVLSPAGVGGMGLLGPGGLPGFYTQPTFLEVLSDPQSVHLQPLGRASGPLDTSQT
ASSDSEDVSSSDRKMSKSALNQTKKRKKRRHRTIFTSYQLEELEKAFNEAHYPDVYAREM
LAMKTELPEDRIQVWFQNRRAKWRKREKCWGRSSVMAEYGLYGAMVRHSIPLPESILKSA
KDGIMDSCAPWLLGMHKKSLEAAAESGRKPEGERQALPKLDKMEQDERGPDAQAAISQEE
LRENSIAVLRAKAQEHSTKVLGTVSGPDSLARSTEKPEEEEAMDEDRPAERLSPPQLEDM
A

Sequence length

361

Interactions

View interactions

547

Show/Hide Causal Diseases (9)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Anophthalmia	Likely pathogenic; Pathogenic	rs121912545	RCV000786019
Anophthalmia-microphthalmia syndrome	Pathogenic; Likely pathogenic	rs869025268, rs755799430	RCV000207414 RCV000207355
Isolated microphthalmia 2	Pathogenic; Likely pathogenic	rs768459071, rs755997898, rs1389175061, rs2139628331, rs2139628604, rs2139645825, rs2139628524, rs2139628344, rs2139645844, rs2139628382, rs1395124261, rs2504956615, rs2504945945, rs2504945051, rs2504948607 View all (14 more)	RCV001915878 RCV001384317 RCV001942909 RCV001925563 RCV001905978 RCV001931412 RCV001910499 RCV002000144 RCV001993138 RCV001879333 RCV001884138 RCV002756871 RCV002835089 RCV002852768 RCV002885006 RCV003026986 RCV003035344 RCV003517148 RCV001378265 RCV003517050 RCV003517658 RCV003630329 RCV003630373 RCV001851882 RCV000015987 RCV000015988 RCV003630776 RCV003831738 RCV003852133 RCV001052936 RCV001206613 RCV001201789
Microphthalmia	Likely pathogenic; Pathogenic	rs755799430, rs121912545	RCV001828043 RCV000786019
Microphthalmia, cataracts, and iris abnormalities	Pathogenic; Likely pathogenic	rs121912543	RCV000015985 RCV000015986
Microphthalmia, isolated, with coloboma 3	Likely pathogenic; Pathogenic	rs1389175061, rs1395124261, rs121912543, rs121912545, rs752288097	RCV005006213 RCV002077342 RCV001330573 RCV000714543 RCV005012495
Retinitis pigmentosa	Pathogenic	rs1566888340	RCV000678661
VSX2-related disorder	Likely pathogenic; Pathogenic	rs121912543	RCV004755737
VSX2-related Microphthalmia	Likely pathogenic; Pathogenic	rs755799430, rs121912545	RCV000778906 RCV004586011

Show/Hide Unknown Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Isolated microphthalmia 6	Uncertain significance; Likely benign	rs375426810, rs565380755, rs10592020, rs557085907	RCV000313331 RCV000333109 RCV000341114 RCV000285124

Show/Hide Text Mining Associations (15)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Adenoma	Associate	21636702
Anophthalmia with pulmonary hypoplasia	Associate	11826019
Anophthalmos	Associate	16113496, 18385794
Bipolar Disorder	Associate	36264558
Colorectal Neoplasms	Associate	21636702
Eye Abnormalities	Associate	31078532
Glaucoma Angle Closure	Associate	18648522
Lymphoma B Cell	Stimulate	23559850
Microphthalmos	Associate	16113496, 17167404, 18385794, 18648522, 31078532
Nanophthalmos 1	Associate	17167404
Neoplasms Squamous Cell	Associate	25115387
Night blindness congenital stationary	Associate	36264558
Retinal Diseases	Associate	10329014
Retinitis	Associate	27301076, 31078532
Zazam Sheriff Phillips syndrome	Associate	36264558

VSX2 (visual system homeobox 2)