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    NYX nyctalopin [ Homo sapiens (human) ]

    Gene ID: 60506, updated on 10-Dec-2024

    Summary

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    Official Symbol
    NYXprovided by HGNC
    Official Full Name
    nyctalopinprovided by HGNC
    Primary source
    HGNC:HGNC:8082
    See related
    Ensembl:ENSG00000188937 MIM:300278; AllianceGenome:HGNC:8082
    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
    CLRP; NBM1; CSNB1; CSNB4; CSNB1A
    Summary
    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]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    mouse all
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    Genomic context

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    See NYX in Genome Data Viewer
    Location:
    Xp11.4
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (41447343..41475652)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (40851430..40879740)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (41306596..41334905)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 10897 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29554 Neighboring gene SHISA5 pseudogene 1 Neighboring gene RNA, 7SL, cytoplasmic 15, pseudogene Neighboring gene Sharpr-MPRA regulatory region 15169 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:41244756-41245273 Neighboring gene DEAD-box helicase 3 X-linked Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29555 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20775 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29556 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29557 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29559 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29558 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:41334409-41335000 Neighboring gene GEMIN7 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29560 Neighboring gene NANOG hESC enhancer GRCh37_chrX:41376070-41376571 Neighboring gene CASK antisense RNA 1 Neighboring gene calcium/calmodulin dependent serine protein kinase Neighboring gene RNA, U6 small nuclear 1321, pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. Assignment of the gene for complete X-linked congenital stationary night blindness (CSNB1) to Xp11.3. Musarella MA, et al. Genomics, 1989 Nov. PMID 2574143
    2. CSNB1 in Chinese families associated with novel mutations in NYX. Xiao X, et al. J Hum Genet, 2006. PMID 16670814
    3. Mutations in NYX of individuals with high myopia, but without night blindness. Zhang Q, et al. Mol Vis, 2007 Mar 1. PMID 17392683, Free PMC Article
    4. A common NYX mutation in Flemish patients with X linked CSNB. Leroy BP, et al. Br J Ophthalmol, 2009 May. PMID 18617546
    5. NYX-related Congenital Stationary Night Blindness in Two Siblings due to Probable Maternal Germline Mosaicism. Scanga HL, et al. Ophthalmic Genet, 2021 Oct. PMID 34165036

    See all (35) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Complete congenital stationary night blindness associated with a novel NYX variant (p.Asn216Lys) in middle-aged and older adult patients.
      Title: Complete congenital stationary night blindness associated with a novel NYX variant (p.Asn216Lys) in middle-aged and older adult patients.
    2. NYX-related Congenital Stationary Night Blindness in Two Siblings due to Probable Maternal Germline Mosaicism.
      Title: NYX-related Congenital Stationary Night Blindness in Two Siblings due to Probable Maternal Germline Mosaicism.
    3. Frameshift mutation in NYX gene is associated with congenital stationary night blindness.
      Title: Novel frameshift mutation in NYX gene in a Russian family with complete congenital stationary night blindness.
    4. Two Novel NYX Gene Mutations in the Chinese Families with X-linked Congenital Stationary Night Blindness were described.
      Title: Two Novel NYX Gene Mutations in the Chinese Families with X-linked Congenital Stationary Night Blindness.
    5. Four potential pathogenic variations in the NYX gene were found in four families with high myopia with or without CSNB1.
      Title: NYX mutations in four families with high myopia with or without CSNB1.
    6. Loss of ERG amplitude and apparent ON-pathway dysfunction at high temporal frequencies distinguish this patient with a Trp237Ter NYX mutation from those with other previously reported NYX mutations.
      Title: Electroretinographic findings in a patient with congenital stationary night blindness due to a novel NYX mutation.
    7. A missense mutation (c.529_530GC>AT or p.Ala177Met) was identified in one male subject with high myopia, but not in 200 male emmetropes.
      Title: A novel missense mutation in the NYX gene associated with high myopia.
    8. A mutation was identified in NYX in 20 male patients with Congenital Stationary Night Blindness 1.
      Title: Genotype and phenotype of 101 dutch patients with congenital stationary night blindness.
    9. The results expand the mutation spectrum of NYX, CACNA1F and GRM6. They also suggest that NYX mutations are a common cause of congenital stationary night blindness (CSNB).
      Title: Mutation screening of TRPM1, GRM6, NYX and CACNA1F genes in patients with congenital stationary night blindness.
    10. A proteomic search for proteins associated with nyctalopin in the retina identified TRPM1 as the binding partner and nyctalopin additionally interacts with mGluR6 receptor.
      Title: TRPM1 forms complexes with nyctalopin in vivo and accumulates in postsynaptic compartment of ON-bipolar neurons in mGluR6-dependent manner.
    Submit: New GeneRIF Correction See all GeneRIFs (23)

    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

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2020-01-22)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2020-01-22)

    ClinGen Genome Curation PagePubMed

    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

    Homology

    Clone Names

    • MGC138447

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in visual perception IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    nyctalopin
    Names
    leucine-rich repeat protein

    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

    1. NG_009112.1 RefSeqGene

      Range
      4884..33193
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001378477.3 → NP_001365406.2  nyctalopin precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) and variant 1 both encode the same protein.
      Source sequence(s)
      Z93015
      Consensus CDS
      CCDS14256.2
      UniProtKB/Swiss-Prot
      D3DWC0, Q2M1S4, Q5H983, Q9GZU5, Q9H4J0
      Related
      ENSP00000367465.2, ENST00000378220.3
      Conserved Domains (5) summary
      smart00082
      Location:331 → 365
      LRRCT; Leucine rich repeat C-terminal domain
      sd00031
      Location:323 → 335
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:63 → 82
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:61 → 115
      LRR_8; Leucine rich repeat
      cd21340
      Location:150 → 310
      PPP1R42; protein phosphatase 1 regulatory subunit 42

    2. NM_022567.3 → NP_072089.2  nyctalopin precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) and variant 2 both encode the same protein.
      Source sequence(s)
      Z93015
      Consensus CDS
      CCDS14256.2
      UniProtKB/Swiss-Prot
      D3DWC0, Q2M1S4, Q5H983, Q9GZU5, Q9H4J0
      Related
      ENSP00000340328.3, ENST00000342595.3
      Conserved Domains (5) summary
      smart00082
      Location:331 → 365
      LRRCT; Leucine rich repeat C-terminal domain
      sd00031
      Location:323 → 335
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:63 → 82
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:61 → 115
      LRR_8; Leucine rich repeat
      cd21340
      Location:150 → 310
      PPP1R42; protein phosphatase 1 regulatory subunit 42

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      41447343..41475652
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      40851430..40879740
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9GZU5.2 GenPept UniProtKB/Swiss-Prot:Q9GZU5

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