NYX (nyctalopin)

Gene

• Entrez ID: 60506
• Gene name: Nyctalopin
• Gene symbol: NYX
• Synonyms (NCBI Gene): CLRP, CSNB1, CSNB1A, CSNB4, NBM1
• Chromosome: X
• Chromosome location: Xp11.4
• 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 (XLCS

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs62637021	C>A	Not-provided, pathogenic	Coding sequence variant, stop gained
rs62637027	GC>AA	Not-provided, pathogenic	Coding sequence variant, missense variant
rs62637035	A>G	Likely-pathogenic	Coding sequence variant, missense variant
rs62637037	G>A	Not-provided, pathogenic	Coding sequence variant, stop gained
rs104894910	G>C	Pathogenic	Coding sequence variant, missense variant
rs104894911	T>C	Pathogenic	Coding sequence variant, missense variant
rs281865194	CGCGCTTGTCCCGCCGCCTGCGCC>-	Pathogenic	Inframe deletion, coding sequence variant
rs764736358	G>T	Likely-pathogenic	Coding sequence variant, stop gained
rs1555967031	GC>TT	Pathogenic	Splice acceptor variant, coding sequence variant
rs1555967263	C>G	Likely-pathogenic	Missense variant, coding sequence variant
rs1555967281	TCTTCC>-	Likely-pathogenic	Inframe deletion, coding sequence variant
rs1602180352	T>A	Likely-pathogenic	Coding sequence variant, missense variant
rs1602180478	G>C	Likely-pathogenic	Coding sequence variant, missense variant
rs1602180791	T>C	Pathogenic	Coding sequence variant, missense variant
rs1602181006	T>G	Likely-pathogenic	Coding sequence variant, missense variant
rs1602181043	GT>-	Pathogenic	Coding sequence variant, frameshift variant
rs1602181253	->CT	Pathogenic	Coding sequence variant, frameshift variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT028759	hsa-miR-26b-5p	Microarray	19088304
MIRT488876	hsa-miR-500a-5p	PAR-CLIP	20371350
MIRT488875	hsa-miR-3917	PAR-CLIP	20371350
MIRT488874	hsa-miR-520d-5p	PAR-CLIP	20371350
MIRT488873	hsa-miR-524-5p	PAR-CLIP	20371350
MIRT488876	hsa-miR-500a-5p	PAR-CLIP	23592263
MIRT488875	hsa-miR-3917	PAR-CLIP	23592263
MIRT488874	hsa-miR-520d-5p	PAR-CLIP	23592263
MIRT488873	hsa-miR-524-5p	PAR-CLIP	23592263
MIRT488876	hsa-miR-500a-5p	PAR-CLIP	20371350
MIRT488875	hsa-miR-3917	PAR-CLIP	20371350
MIRT488874	hsa-miR-520d-5p	PAR-CLIP	20371350
MIRT488873	hsa-miR-524-5p	PAR-CLIP	20371350
MIRT488876	hsa-miR-500a-5p	PAR-CLIP	23592263
MIRT488875	hsa-miR-3917	PAR-CLIP	23592263
MIRT488874	hsa-miR-520d-5p	PAR-CLIP	23592263
MIRT488873	hsa-miR-524-5p	PAR-CLIP	23592263
MIRT2584413	hsa-miR-4504	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	32296183, 32814053
GO:0005576	Component	Extracellular region	IEA
GO:0007601	Process	Visual perception	IEA
GO:0007601	Process	Visual perception	IEA
GO:0007601	Process	Visual perception	IMP	11062471
GO:0031012	Component	Extracellular matrix	IBA
GO:0038023	Function	Signaling receptor activity	IBA

Other IDs

• MIM: 300278
• HGNC: 8082
• e!Ensembl: ENSG00000188937

Protein

• UniProt ID: Q9GZU5
• Protein name: Nyctalopin
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF01462	LRRNT	30 → 61	Leucine rich repeat N-terminal domain	Family
  PF00560	LRR_1	87 → 109	Leucine Rich Repeat	Repeat
  PF13855	LRR_8	231 → 290	Leucine rich repeat	Repeat

• Tissue specificity: 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. {ECO:0000269|PubMed:110624
• Sequence:

  MKGRGMLVLLLHAVVLGLPSAWAVGACARACPAACACSTVERGCSVRCDRAGLLRVPAEL
  PCEAVSIDLDRNGLRFLGERAFGTLPSLRRLSLRHNNLSFITPGAFKGLPRLAELRLAHN
  GDLRYLHARTFAALSRLRRLDLAACRLFSVPERLLAELPALRELAAFDNLFRRVPGALRG
  LANLTHAHLERGRIEAVASSSLQGLRRLRSLSLQANRVRAVHAGAFGDCGVLEHLLLNDN
  LLAELPADAFRGLRRLRTLNLGGNALDRVARAWFADLAELELLYLDRNSIAFVEEGAFQN
  LSGLLALHLNGNRLTVLAWVAFQPGFFLGRLFLFRNPWCCDCRLEWLRDWMEGSGRVTDV
  PCASPGSVAGLDLSQVTFGRSSDGLCVDPEELNLTTSSPGPSPEPAATTVSRFSSLLSKL
  LAPRVPVEEAANTTGGLANASLSDSLSSRGVGGAGRQPWFLLASCLLPSVAQHVVFGLQM
  D

• Sequence length: 481

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Abnormality of the eye	Likely pathogenic	rs1555967263	RCV000504669	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Congenital stationary night blindness	Likely pathogenic; Pathogenic	rs1555967281, rs1602180478, rs1602180791, rs1602181006, rs1602181043, rs1602181253	RCV000504858 RCV001003099 RCV001003100 RCV001003101 RCV001003102 RCV001003103	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Congenital stationary night blindness 1A	Pathogenic; Likely pathogenic	rs281865194, rs2147026677, rs2519607262, rs2519608394, rs62637021, rs62637027, rs104894910, rs104894911, rs1555967031, rs1602181043	RCV001847656 RCV001542515 RCV002290351 RCV003164458 RCV000012175 RCV000012176 RCV000012177 RCV000012178 RCV002289887 RCV005047187	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
NYX-related disorder	Likely pathogenic; Pathogenic	rs1555967031	RCV003403381	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinal dystrophy	Pathogenic; Likely pathogenic	rs62637025, rs281865194, rs2147025929, rs2147026037, rs2064376489, rs2064378728	RCV004815172 RCV001073621 RCV001591804 RCV004815726 RCV001075756 RCV001074015	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Congenital stationary night blindness 1C	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NIGHT BLINDNESS, CONGENITAL STATIONARY	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NIGHT BLINDNESS, CONGENITAL STATIONARY, TYPE 1A	—	Disgenet, HPO Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NIGHT BLINDNESS, CONGENITAL STATIONARY, TYPE 1C	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NIGHT BLINDNESS, CONGENITAL STATIONARY, TYPE 2A	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OGUCHI DISEASE	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Retinitis pigmentosa	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
RETINITIS PIGMENTOSA 1	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
X-linked congenital stationary night blindness	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Achromatopsia	Achromatopsia	BEFREE	12187427		★☆☆☆☆ Found in Text Mining only
Achromatopsia 3	Achromatopsia	BEFREE	12187427		★☆☆☆☆ Found in Text Mining only
Amaurosis congenita of Leber, type 1	Leber congenital amaurosis	BEFREE	12187427		★☆☆☆☆ Found in Text Mining only
CNS disorder	CNS Disorder	BEFREE	29099938		★☆☆☆☆ Found in Text Mining only
Cone Dystrophy	Cone Dystrophy	BEFREE	9418727		★☆☆☆☆ Found in Text Mining only
Cone-rod synaptic disorder, congenital nonprogressive	Congenital stationary night blindness	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Congenital stationary night blindness	Congenital stationary night blindness	Orphanet			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Disorder of eye	Disorder Of Eye	BEFREE	23406521		★☆☆☆☆ Found in Text Mining only
Disorder of eye	Disorder Of Eye	GENOMICS_ENGLAND_DG			★☆☆☆☆ Found in Text Mining only
Enhanced S-Cone Syndrome	Enhanced S-Cone Syndrome	BEFREE	12187427		★☆☆☆☆ Found in Text Mining only
Esophageal Squamous Cell Carcinoma	Esophageal squamous cell carcinoma	Pubtator	26330293	Associate	★☆☆☆☆ Found in Text Mining only
Hemeralopia	Hemeralopia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypoplasia of optic disc	Hypoplasia Of Optic Disc	HPO_DG			★☆☆☆☆ Found in Text Mining only
leukemia	Leukemia	BEFREE	20799951		★☆☆☆☆ Found in Text Mining only
Myopia	Myopia	BEFREE	16670814, 17392683, 23406521		★☆☆☆☆ Found in Text Mining only
Myopia	Myopia	LHGDN	17392683		★☆☆☆☆ Found in Text Mining only
Myopia	Myopia	Pubtator	17392683, 25802485, 37191617	Associate	★☆☆☆☆ Found in Text Mining only
Myopia	Myopia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Night blindness congenital stationary	Night blindness, congenital stationary	Pubtator	14609846, 15761389, 17392683, 18617546, 19896113, 23289809, 24715752, 25802485, 26234941, 34064005, 34781300, 36499293, 7966198, 8434607, 9529339	Associate	★☆☆☆☆ Found in Text Mining only
Night blindness, congenital stationary	Night blindness	BEFREE	11062471, 11581222, 14507859, 15331616, 15583843, 17392683, 17881478, 19666700, 20300565, 22735794, 23289809, 23714322, 26368928		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Night blindness, congenital stationary	Night blindness	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Night blindness, congenital stationary	Night blindness	HPO_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Night blindness, congenital stationary	Night blindness	GENOMICS_ENGLAND_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Night blindness, congenital stationary	Night blindness	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Night blindness, congenital stationary, type 1	Night blindness	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Night Blindness, Congenital Stationary, Type 1A	Night blindness	UNIPROT_DG	11062471, 11062472		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Night Blindness, Congenital Stationary, Type 1A	Night blindness	GENOMICS_ENGLAND_DG	11062472		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Night Blindness, Congenital Stationary, Type 1A	Night blindness	BEFREE	23406521, 31826698		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Night Blindness, Congenital Stationary, Type 1A	Night blindness	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Night Blindness, Congenital Stationary, Type 1A	Night blindness	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NIGHT BLINDNESS, CONGENITAL STATIONARY, TYPE 1B	Night blindness	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
NIGHT BLINDNESS, CONGENITAL STATIONARY, TYPE 2A	Night blindness	BEFREE	10439964, 10982042, 11172618, 11408949, 12187427, 12397430, 12552565, 12714669, 14507859, 14609846, 15583843, 15761389, 16670814, 17881478, 26234941, 30982101, 31826698, 8375106, 9418727, 9662400		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NIGHT BLINDNESS, CONGENITAL STATIONARY, TYPE 2A	Night blindness	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NIGHT BLINDNESS, CONGENITAL STATIONARY, TYPE 2B (disorder)	Night blindness	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Nyctalopia	Nyctalopia	LHGDN	12506099, 12552565, 15761389, 17392683		★☆☆☆☆ Found in Text Mining only
Nyctalopia	Nyctalopia	BEFREE	15331616, 15905181, 17392683, 23714322		★☆☆☆☆ Found in Text Mining only
Nyctalopia	Nyctalopia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nystagmus Pathologic	Nystagmus	Pubtator	34064005	Associate	★☆☆☆☆ Found in Text Mining only
Retinal Diseases	Retinal Diseases	BEFREE	10439964		★☆☆☆☆ Found in Text Mining only
Retinal Diseases	Retinal detachment	Pubtator	37191617	Associate	★☆☆☆☆ Found in Text Mining only
Retinitis Pigmentosa	Retinitis Pigmentosa	BEFREE	9418727		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Severe myopia	Myopia	BEFREE	17392683, 23406521, 25802485		★☆☆☆☆ Found in Text Mining only
Severe myopia	Myopia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Strabismus	Strabismus	Pubtator	34064005	Associate	★☆☆☆☆ Found in Text Mining only
Strabismus	Strabismus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Vision Disorders	Visual disorder	Pubtator	8434607	Stimulate	★☆☆☆☆ Found in Text Mining only
X-Linked Csnb	Congenital stationary night blindness, X-Linked	BEFREE	11062471, 18617546, 9529339, 9662400		★☆☆☆☆ Found in Text Mining only
X-Linked Csnb	Congenital stationary night blindness, X-Linked	CTD_human_DG			★☆☆☆☆ Found in Text Mining only