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Aliases for NYX Gene

Aliases for NYX Gene

  • Nyctalopin 2 3 3 5
  • CLRP 3 4
  • Leucine-Rich Repeat Protein 3
  • CSNB1A 3
  • CSNB1 3
  • CSNB4 3
  • NBM1 3

External Ids for NYX Gene

Previous HGNC Symbols for NYX Gene

  • CSNB1
  • CSNB4

Previous GeneCards Identifiers for NYX Gene

  • GC0XP039333
  • GC0XP039555
  • GC0XP040151
  • GC0XP040337
  • GC0XP041062
  • GC0XP041191
  • GC0XP041306
  • GC0XP039038

Summaries for NYX Gene

Entrez Gene Summary for NYX Gene

  • The product of this gene belongs to the small leucine-rich proteoglycan (SLRP) family of proteins. Defects in this gene are the cause of congenital stationary night blindness type 1 (CSNB1), also called X-linked congenital stationary night blindness (XLCSNB). CSNB1 is a rare inherited retinal disorder characterized by impaired scotopic vision, myopia, hyperopia, nystagmus and reduced visual acuity. The role of other SLRP proteins suggests that mutations in this gene disrupt developing retinal interconnections involving the ON-bipolar cells, leading to the visual losses seen in patients with complete CSNB. [provided by RefSeq, Oct 2008]

GeneCards Summary for NYX Gene

NYX (Nyctalopin) is a Protein Coding gene. Diseases associated with NYX include Night Blindness, Congenital Stationary , 1A, X-Linked and Congenital Stationary Night Blindness. An important paralog of this gene is LRIG1.

Gene Wiki entry for NYX Gene

No data available for UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NYX Gene

Genomics for NYX Gene

Regulatory Elements for NYX Gene

Enhancers for NYX Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH0XF041381 1.6 FANTOM5 Ensembl ENCODE 12.7 -62.4 -62447 4.0 PKNOX1 ATF1 ARID4B DMAP1 BRCA1 YY1 FOS ZNF263 PPARG KAT8 NYX MED14 DDX3X PIR52979
GH0XF041329 1.6 FANTOM5 ENCODE 12 -112.2 -112164 7.3 HDGF PKNOX1 ARNT CREB3L1 WRNIP1 ARID4B SIN3A YBX1 FEZF1 DMAP1 DDX3X CASK-AS1 CXorf38 USP9X MED14 NYX PIR48586
GH0XF041491 1.1 Ensembl ENCODE 12.4 +46.0 45966 1.7 TBP SIN3A FEZF1 BMI1 CBX5 FOS ZNF263 PAF1 ZNF362 SMAD5 CASK-AS1 DDX3X USP9X MED14 NYX GPR34 LOC100506654
GH0XF041411 0.9 Ensembl ENCODE 13.4 -33.1 -33053 1.3 SOX13 CTCF ELF3 SOX5 NFIA SP5 RAD21 YY1 HNF4G SMC3 NYX PIR52979
GH0XF041389 0.8 ENCODE 12.4 -56.2 -56152 1.1 SAP130 ZMYM3 PTRF PYGO2 ZNF644 RAD21 YY1 ZNF121 HNF4G THAP11 NYX PIR52979
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around NYX on UCSC Golden Path with GeneCards custom track

Genomic Location for NYX Gene

Chromosome:
X
Start:
41,445,637 bp from pter
End:
41,476,421 bp from pter
Size:
30,785 bases
Orientation:
Plus strand

Genomic View for NYX Gene

Genes around NYX on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NYX Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NYX Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NYX Gene

Proteins for NYX Gene

  • Protein details for NYX Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9GZU5-NYX_HUMAN
    Recommended name:
    Nyctalopin
    Protein Accession:
    Q9GZU5
    Secondary Accessions:
    • D3DWC0
    • Q2M1S4
    • Q5H983
    • Q9H4J0

    Protein attributes for NYX Gene

    Size:
    481 amino acids
    Molecular mass:
    52000 Da
    Quaternary structure:
    No Data Available

neXtProt entry for NYX Gene

Post-translational modifications for NYX Gene

  • Glycosylation at Asn 97, Asn 183, Asn 300, Asn 393, Asn 432, and Asn 439
  • Modification sites at PhosphoSitePlus

Other Protein References for NYX Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for NYX Gene

Domains & Families for NYX Gene

Suggested Antigen Peptide Sequences for NYX Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9GZU5

UniProtKB/Swiss-Prot:

NYX_HUMAN :
  • Contains 1 LRRCT domain.
  • Belongs to the small leucine-rich proteoglycan (SLRP) family. SLRP class IV subfamily.
  • Contains 11 LRR (leucine-rich) repeats.
Domain:
  • Contains 1 LRRCT domain.
  • Contains 1 LRRNT domain.
Family:
  • Belongs to the small leucine-rich proteoglycan (SLRP) family. SLRP class IV subfamily.
Similarity:
  • Contains 11 LRR (leucine-rich) repeats.
genes like me logo Genes that share domains with NYX: view

No data available for Gene Families for NYX Gene

Function for NYX Gene

Gene Ontology (GO) - Molecular Function for NYX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0004860 protein kinase inhibitor activity IBA --
genes like me logo Genes that share ontologies with NYX: view
genes like me logo Genes that share phenotypes with NYX: view

Human Phenotype Ontology for NYX Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for NYX Gene

Localization for NYX Gene

Subcellular locations from UniProtKB/Swiss-Prot for NYX Gene

Secreted, extracellular space, extracellular matrix.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NYX gene
Compartment Confidence
extracellular 5
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for NYX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005578 proteinaceous extracellular matrix IEA --
GO:0005622 intracellular IDA 11062471
GO:0005737 cytoplasm IBA --
genes like me logo Genes that share ontologies with NYX: view

Pathways & Interactions for NYX Gene

No Data Available

Gene Ontology (GO) - Biological Process for NYX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006469 negative regulation of protein kinase activity IBA --
GO:0007601 visual perception IEA --
GO:0008150 biological_process ND --
GO:0019221 cytokine-mediated signaling pathway IBA --
GO:0046426 negative regulation of JAK-STAT cascade IBA --
genes like me logo Genes that share ontologies with NYX: view

No data available for Pathways by source and SIGNOR curated interactions for NYX Gene

Transcripts for NYX Gene

mRNA/cDNA for NYX Gene

(2) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(5) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for NYX Gene

Nyctalopin:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for NYX Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b
SP1: -
SP2:
SP3: -

Relevant External Links for NYX Gene

GeneLoc Exon Structure for
NYX
ECgene alternative splicing isoforms for
NYX

Expression for NYX Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for NYX Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for NYX Gene

This gene is overexpressed in Kidney - Cortex (x25.0) and Testis (x15.2).

NURSA nuclear receptor signaling pathways regulating expression of NYX Gene:

NYX

SOURCE GeneReport for Unigene cluster for NYX Gene:

Hs.302019

mRNA Expression by UniProt/SwissProt for NYX Gene:

Q9GZU5-NYX_HUMAN
Tissue specificity: Expressed in kidney and retina. Also at low levels in brain, testis and muscle. Within the retina, expressed in the inner segment of photoreceptors, outer and inner nuclear layers and the ganglion cell layer.
genes like me logo Genes that share expression patterns with NYX: view

No data available for Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners for NYX Gene

Orthologs for NYX Gene

This gene was present in the common ancestor of animals.

Orthologs for NYX Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NYX 34 35
  • 99.65 (n)
dog
(Canis familiaris)
Mammalia NYX 34 35
  • 89.59 (n)
cow
(Bos Taurus)
Mammalia NYX 34 35
  • 88.7 (n)
mouse
(Mus musculus)
Mammalia Nyx 34 16 35
  • 85.51 (n)
rat
(Rattus norvegicus)
Mammalia Nyx 34
  • 84.68 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia NYX 35
  • 56 (a)
OneToOne
chicken
(Gallus gallus)
Aves NYX 34 35
  • 63.08 (n)
lizard
(Anolis carolinensis)
Reptilia NYX 35
  • 53 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nyx 34
  • 55.91 (n)
zebrafish
(Danio rerio)
Actinopterygii nyx 34 35
  • 59.65 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG1504 35
  • 21 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea lron-12 35
  • 17 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 21 (a)
OneToMany
Species where no ortholog for NYX was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for NYX Gene

ENSEMBL:
Gene Tree for NYX (if available)
TreeFam:
Gene Tree for NYX (if available)

Paralogs for NYX Gene

genes like me logo Genes that share paralogs with NYX: view

Variants for NYX Gene

Sequence variations from dbSNP and Humsavar for NYX Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type
rs62637020 Night blindness, congenital stationary, 1A (CSNB1A) [MIM:310500], untested 41,473,545(+) CGCTT(C/G)TCCCG reference, missense
rs62637023 Night blindness, congenital stationary, 1A (CSNB1A) [MIM:310500], untested 41,473,880(+) ACCTA(C/G)CAGCC reference, missense
rs62637024 Night blindness, congenital stationary, 1A (CSNB1A) [MIM:310500], untested 41,473,905(+) CGTGC(C/T)CGAGC reference, missense
rs62637025 Night blindness, congenital stationary, 1A (CSNB1A) [MIM:310500], untested 41,473,977(+) CGTGC(C/G)GGGCG reference, missense
rs62637026 Night blindness, congenital stationary, 1A (CSNB1A) [MIM:310500], untested 41,474,004(+) CAACC(C/T)GACGC reference, missense

Structural Variations from Database of Genomic Variants (DGV) for NYX Gene

Variant ID Type Subtype PubMed ID
esv25432 CNV loss 19812545
esv33720 CNV loss 17666407
nsv508763 CNV insertion 20534489

Variation tolerance for NYX Gene

Gene Damage Index Score: 1.84; 34.54% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NYX Gene

Human Gene Mutation Database (HGMD)
NYX
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NYX

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NYX Gene

Disorders for NYX Gene

MalaCards: The human disease database

(13) MalaCards diseases for NYX Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search NYX in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

NYX_HUMAN
  • Night blindness, congenital stationary, 1A (CSNB1A) [MIM:310500]: A non-progressive retinal disorder characterized by impaired night vision. Congenital stationary night blindness type 1A is characterized by impaired scotopic vision, myopia, hyperopia, nystagmus and reduced visual acuity. {ECO:0000269 PubMed:11062471, ECO:0000269 PubMed:11062472}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for NYX

Genetic Association Database (GAD)
NYX
Human Genome Epidemiology (HuGE) Navigator
NYX
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
NYX
genes like me logo Genes that share disorders with NYX: view

No data available for Genatlas for NYX Gene

Publications for NYX Gene

  1. Mutations in NYX, encoding the leucine-rich proteoglycan nyctalopin, cause X-linked complete congenital stationary night blindness. (PMID: 11062471) Bech-Hansen N.T. … Weleber R.G. (Nat. Genet. 2000) 2 3 4 22 64
  2. The complete form of X-linked congenital stationary night blindness is caused by mutations in a gene encoding a leucine-rich repeat protein. (PMID: 11062472) Pusch C.M. … Meindl A. (Nat. Genet. 2000) 2 3 4 22 64
  3. Mutations in NYX of individuals with high myopia, but without night blindness. (PMID: 17392683) Zhang Q. … Hejtmancik J.F. (Mol. Vis. 2007) 3 22 46 64
  4. Simultaneous mutation detection in 90 retinal disease genes in multiple patients using a custom-designed 300-kb retinal resequencing chip. (PMID: 20801516) Booij J.C. … Florijn R.J. (Ophthalmology 2011) 3 46 64
  5. A common NYX mutation in Flemish patients with X linked CSNB. (PMID: 18617546) Leroy B.P. … Zeitz C. (Br J Ophthalmol 2009) 3 22 64

Products for NYX Gene

Sources for NYX Gene

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