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NYX nyctalopin [ Homo sapiens (human) ]

Gene ID: 60506, updated on 5-Mar-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (41447343..41475652)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (40851430..40879740)
105.20220307 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 29558 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29559 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29557 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 calcium/calmodulin dependent serine protein kinase Neighboring gene RNA, U6 small nuclear 1321, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20776 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20777 Neighboring gene NANOG hESC enhancer GRCh37_chrX:41464273-41464774 Neighboring gene uncharacterized LOC124905180

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. 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
  2. Complete congenital stationary night blindness associated with a novel NYX variant (p.Asn216Lys) in middle-aged and older adult patients. Hayashi T, et al. Ophthalmic Genet, 2021 Aug. PMID 33769208
  3. Novel frameshift mutation in NYX gene in a Russian family with complete congenital stationary night blindness. Ivanova ME, et al. Ophthalmic Genet, 2019 Dec. PMID 31826698
  4. Two Novel NYX Gene Mutations in the Chinese Families with X-linked Congenital Stationary Night Blindness. Dai S, et al. Sci Rep, 2015 Aug 3. PMID 26234941, Free PMC Article
  5. NYX mutations in four families with high myopia with or without CSNB1. Zhou L, et al. Mol Vis, 2015. PMID 25802485, Free PMC Article

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)

Genotypes

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 molecular_function ND
No biological Data available
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
involved_in response to stimulus IEA
Inferred from Electronic Annotation
more info
  
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_2023_10

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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