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VSX2 (visual system homeobox 2)

Gene
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.
338917
Gene nameGene Name - the full gene name approved by the HGNC.
Visual system homeobox 2
Gene symbolGene Symbol - the official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name.
VSX2
SynonymsGene synonyms aliases
CHX10, HOX10, MCOP2, MCOPCB3, RET1
ChromosomeChromosome number
14
Chromosome locationChromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.
14q24.3
SummarySummary of gene provided in NCBI Entrez Gene.
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]
SNPsSNP information provided by dbSNP.
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
miRNAmiRNA information provided by mirtarbase database.
miRTarBase ID miRNA Experiments Reference
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
Transcription factors
Transcription factor Regulation Reference
NEUROG3 Activation 19028584
Gene ontology (GO)Gene ontology information of associated ontologies with gene provided by GO database.
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 ISA
GO:0001227 Function DNA-binding transcription repressor activity, RNA polymerase II-specific IDA 15647262
Other IDsOther ids provides unique ids of gene in databases such as OMIM, HGNC, ENSEMBLE.
MIM
HGNC
e!Ensembl
Protein
UniProt ID 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
Sequence
MTGKAGEALSKPKSETVAKSTSGGAPARCTGFGIQEILGLNKEPPSSHPRAALDGLAPGH
LLAARSVLSPAGVGGMGLLGPGGLPGFYTQPTFLEVLSDPQSVHLQPLGRASGPLDTSQT
ASSDSEDVSSSDRKMSKSALNQTKKRKKRRHRTIFTSYQLEELEKAFNEAHYPDVYAREM
LAMKTELPEDRIQVWFQNRRAKWRK
REKCWGRSSVMAEYGLYGAMVRHSIPLPESILKSA
KDGIMDSCAPWLLGMHKKSLEAAAESGRKPEGERQALPKLDKMEQDERGPDAQAAISQEE
LRENSIAVLRAKAQEHST
KVLGTVSGPDSLARSTEKPEEEEAMDEDRPAERLSPPQLEDM
A
Sequence length 361
Interactions View interactions
Associated diseases
Causal
Disease name Disease term dbSNP ID References
Cataract Cataract rs118203965, rs118203966, rs104893685, rs121908938, rs104894175, rs121909048, rs28937573, rs121909049, rs121909050, rs74315488, rs80358200, rs80358203, rs121434643, rs56141211, rs132630322, rs121917775, rs121917735, rs121917736, rs137853199, rs137853200, rs121917867, rs121917869, rs121913555, rs104893736, rs121909595, rs121909596, rs121909597, rs28931605, rs121909598, rs104893618, rs1695062782, rs74315486, rs74315487, rs74315490, rs74315489, rs745938679, rs1566402656, rs74315439, rs74315441, rs121912973, rs121917823, rs1593332981, rs121917825, rs121917827, rs113994108, rs387906963, rs387906964, rs1240503246, rs387906965, rs387906966, rs750207077, rs387907336, rs387907337, rs387907342, rs140332366, rs397514703, rs398122937, rs398122378, rs398122392, rs398122944, rs137853924, rs398122947, rs397515623, rs397515624, rs397515625, rs397515626, rs398122948, rs587778872, rs398123066, rs587777601, rs370424081, rs786205221, rs786205222, rs864309684, rs864309688, rs864309701, rs864309689, rs864309690, rs864309681, rs864309686, rs864309696, rs864309693, rs864309687, rs864309691, rs864309692, rs864309695, rs864309678, rs864309685, rs864309700, rs864309698, rs864309683, rs864309682, rs864309679, rs111534978, rs864309680, rs864309702, rs864622780, rs756898971, rs869312732, rs775038545, rs878852983, rs1114167312, rs1114167313, rs1114167314, rs1114167315, rs1114167307, rs886041410, rs886041412, rs1057518738, rs1057517926, rs1057518878, rs1057519616, rs12799308, rs1064793935, rs1064797219, rs1085307126, rs1085307127, rs765628635, rs1114167427, rs1114167433, rs1554744860, rs1554743428, rs747093432, rs1411557416, rs1555179713, rs1481963503, rs1555549755, rs1456161420, rs1555547008, rs1555889308, rs1555888762, rs766522434, rs1264025914, rs1553585262, rs1567671947, rs1337897299, rs764945940, rs1307969607, rs949335475, rs1184095219, rs776129797, rs1569203234, rs1567668570, rs749141857, rs764098604, rs1184398243, rs1578956689, rs1568480054, rs1564745688, rs1564722302, rs1564723150, rs1571175950, rs1569602837, rs1576552712, rs1575369255, rs981126461, rs1570403798, rs200557771, rs1477743112, rs1651879427, rs1651881222, rs1651919374, rs2024441691, rs148284531, rs1246080692
Microphthalmia with coloboma Colobomatous microphthalmia, Microphthalmia, Isolated, with Coloboma 3 rs387906910, rs587776950, rs794726861, rs794726862, rs755000701, rs1243762658, rs919662130, rs753315599, rs2091986259 17919464, 27301076, 24033328, 10932181, 15257456
Congenital ocular coloboma Congenital ocular coloboma (disorder) rs587778875, rs587777249, rs767611891, rs2091986259, rs2091987023, rs2091988799
Microphthalmia MICROPHTHALMIA, ISOLATED 1, MICROPHTHALMIA, ISOLATED 2 rs587776595, rs121908189, rs587776596, rs104894663, rs121909127, rs1603388837, rs121909128, rs121912543, rs121912545, rs730882064, rs387907095, rs387907096, rs397514652, rs397514653, rs78931658, rs730882141, rs150232843, rs730882143, rs730882158, rs730882159, rs730882160, rs730882161, rs730882162, rs786205471, rs786205472, rs797045054, rs869025268, rs755799430, rs1555037395, rs770341402, rs1245503127, rs749156010, rs376898612, rs750894392, rs1359404443, rs1422497202, rs374823079, rs1565295426, rs145719998, rs1166512859, rs752288097, rs1226217440, rs1243587288 10932181, 15257456, 21976963
Unknown
Disease name Disease term dbSNP ID References
Disorder of eye Disorder of eye
Isolated microphthalmia-anophthalmia-coloboma Isolated microphthalmia-anophthalmia-coloboma
Microphthalmia, cataracts, and iris abnormalities Microphthalmia, Cataracts, and Iris Abnormalities

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