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 r... See more...

Aliases for NYX Gene

Aliases for NYX Gene

  • Nyctalopin 2 3 4 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, Type 1A and Congenital Stationary Night Blindness. An important paralog of this gene is LRRC4B.

Gene Wiki entry for NYX Gene

Additional gene information for NYX Gene

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NYX Gene

Genomics for NYX Gene

GeneHancer (GH) Regulatory Elements for NYX Gene

Promoters and enhancers for NYX Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ041446 Enhancer 0.6 Ensembl 500.7 +1.8 1763 1.2 RELA ZNF316 MAFK SCRT1 MAFG GLIS1 JUNB HLF NFIC GLIS2 NYX hsa-miR-5095-530 DDX3X RF00017-8326
GH0XJ041445 Enhancer 0.6 FANTOM5 Ensembl 500.7 -0.3 -336 0.2 EBF1 PKNOX1 NYX hsa-miR-5095-530 piR-38352-597 RF00017-8326
GH0XJ041447 Enhancer 0.4 Ensembl 500.7 +0.4 364 0.4 RFX1 NFIC NFIB BMI1 NYX hsa-miR-5095-530 RF00017-8326
GH0XJ041329 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 12 -111.0 -111031 9.6 FOXK2 HNRNPK ZBTB40 EP300 CTCF SIN3A NRF1 TCF12 USF1 POLR2G DDX3X NONHSAG054300.2 lnc-CASK-8 CASK-AS1 MED14 CXorf38 NYX RF00017-8327 RF00017-8323 RF00017-8326
GH0XJ041381 Enhancer 1.3 FANTOM5 Ensembl ENCODE 12.8 -62.6 -62636 5.2 TCF12 JUND FOS TRIM28 ZBTB25 EP300 JUN TEAD1 ZBTB26 CTBP1 piR-60051-110 piR-56759-602 piR-54764-666 NYX MED14 DDX3X piR-50444-492 RF00017-8326
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NYX on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NYX

Top Transcription factor binding sites by QIAGEN in the NYX gene promoter:
  • AML1a
  • Arnt
  • C/EBPalpha
  • E47
  • FOXJ2
  • HNF-3beta
  • Lhx3a
  • LHX3b
  • SRY
  • Tal-1beta

Genomic Locations for NYX Gene

Genomic Locations for NYX Gene
chrX:41,445,637-41,476,421
(GRCh38/hg38)
Size:
30,785 bases
Orientation:
Plus strand
chrX:41,306,687-41,334,963
(GRCh37/hg19)
Size:
28,277 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 Asn97, Asn183, Asn300, Asn393, Asn432, and Asn439
  • 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

Gene Families for NYX Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for NYX Gene

Blocks:
  • Cysteine-rich flanking region, C-terminal
  • Cysteine-rich flanking region, N-terminal
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for NYX Gene

GenScript: Design optimal peptide antigens:
  • Nyctalopin (NYX_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9GZU5

UniProtKB/Swiss-Prot:

NYX_HUMAN :
  • Belongs to the small leucine-rich proteoglycan (SLRP) family. SLRP class IV subfamily.
Family:
  • Belongs to the small leucine-rich proteoglycan (SLRP) family. SLRP class IV subfamily.
genes like me logo Genes that share domains with NYX: view

Function for NYX Gene

Phenotypes From GWAS Catalog 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:0005515 protein binding IEA --
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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NYX

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 4
plasma membrane 1
cytoskeleton 1
nucleus 1
endoplasmic reticulum 1
endosome 1
cytosol 1
golgi apparatus 1
lysosome 0

Gene Ontology (GO) - Cellular Components for NYX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space IBA 21873635
GO:0031012 extracellular matrix IBA 21873635
genes like me logo Genes that share ontologies with NYX: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for NYX Gene

Pathways & Interactions for NYX Gene

PathCards logo

SuperPathways for NYX Gene

No Data Available

Gene Ontology (GO) - Biological Process for NYX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007601 visual perception IEA --
GO:0008150 biological_process ND --
GO:0050896 response to stimulus IEA --
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

Drugs & Compounds for NYX Gene

No Compound Related Data Available

Transcripts for NYX Gene

mRNA/cDNA for NYX Gene

1 REFSEQ mRNAs :
3 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NYX

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

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).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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.

Evidence on tissue expression from TISSUES for NYX Gene

  • Nervous system(4.3)
  • Eye(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for NYX Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • immune
  • integumentary
  • nervous
  • skeletal muscle
Regions:
Head and neck:
  • brain
  • cranial nerve
  • eye
  • head
General:
  • blood
  • peripheral nervous system
  • skin
  • white blood cell
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 31 30
  • 99.65 (n)
OneToOne
dog
(Canis familiaris)
Mammalia NYX 31 30
  • 89.59 (n)
OneToOne
cow
(Bos Taurus)
Mammalia NYX 31 30
  • 88.7 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Nyx 17 31 30
  • 85.51 (n)
rat
(Rattus norvegicus)
Mammalia Nyx 30
  • 84.68 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia NYX 31
  • 56 (a)
OneToOne
chicken
(Gallus gallus)
Aves NYX 31 30
  • 63.08 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NYX 31
  • 53 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nyx 30
  • 55.91 (n)
zebrafish
(Danio rerio)
Actinopterygii nyx 31 30
  • 59.65 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG1504 31
  • 21 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea lron-12 31
  • 17 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for NYX: view image

Paralogs for NYX Gene

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

Variants for NYX Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NYX Gene

SNP ID Clinical significance and condition Chr 0X pos Variation AA Info Type
714923 Benign: not provided 41,474,226(+) C/T MISSENSE_VARIANT
716520 Benign: not provided 41,474,633(+) C/T MISSENSE_VARIANT
716521 Benign: not provided 41,474,704(+) C/T SYNONYMOUS_VARIANT
721566 Likely Benign: not provided 41,474,564(+) C/T SYNONYMOUS_VARIANT
723145 Likely Benign: not provided 41,474,539(+) C/T SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for NYX Gene

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)

Additional Variant Information for NYX Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for NYX Gene

MalaCards: The human disease database

(24) MalaCards diseases for NYX Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
night blindness, congenital stationary, type 1a
  • night blindness, congenital stationary, type 2a
congenital stationary night blindness
  • congenital essential nyctalopia
night blindness
x-linked congenital stationary night blindness
  • night blindness, congenital stationary, type 2a
myopia
  • near vision
- 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.

Additional Disease Information for NYX

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

No data available for Genatlas for NYX Gene

Publications for NYX Gene

  1. 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 CM … Meindl A (Nature genetics 2000) 2 3 4 23 54
  2. Mutations in NYX, encoding the leucine-rich proteoglycan nyctalopin, cause X-linked complete congenital stationary night blindness. (PMID: 11062471) Bech-Hansen NT … Weleber RG (Nature genetics 2000) 2 3 4 23 54
  3. Mutations in NYX of individuals with high myopia, but without night blindness. (PMID: 17392683) Zhang Q … Hejtmancik JF (Molecular vision 2007) 3 23 41 54
  4. Simultaneous mutation detection in 90 retinal disease genes in multiple patients using a custom-designed 300-kb retinal resequencing chip. (PMID: 20801516) Booij JC … Florijn RJ (Ophthalmology 2011) 3 41 54
  5. A common NYX mutation in Flemish patients with X linked CSNB. (PMID: 18617546) Leroy BP … Zeitz C (The British journal of ophthalmology 2009) 3 23 54

Products for NYX Gene

Sources for NYX Gene