Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	60506
Gene name	Nyctalopin
Gene symbol	NYX
Synonyms (NCBI Gene)	CLRPCSNB1CSNB1ACSNB4NBM1
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

Show/Hide all (17)

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

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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

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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

MIM	HGNC	e!Ensembl
300278	8082	ENSG00000188937

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

Interactions

View interactions

Show/Hide Causal Diseases (5)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Abnormality of the eye	Likely pathogenic	rs1555967263	RCV000504669
Congenital stationary night blindness	Likely pathogenic; Pathogenic	rs1555967281, rs1602180478, rs1602180791, rs1602181006, rs1602181043, rs1602181253	RCV000504858 RCV001003099 RCV001003100 RCV001003101 RCV001003102 RCV001003103
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
NYX-related disorder	Likely pathogenic; Pathogenic	rs1555967031	RCV003403381
Retinal dystrophy	Pathogenic; Likely pathogenic	rs62637025, rs281865194, rs2147025929, rs2147026037, rs2064376489, rs2064378728	RCV004815172 RCV001073621 RCV001591804 RCV004815726 RCV001075756 RCV001074015

Show/Hide Unknown Diseases (3)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Congenital stationary night blindness 1C	Uncertain significance	rs2064379837	RCV004765343
Retinitis pigmentosa	Uncertain significance	rs2147025940	RCV001591805
X-linked congenital stationary night blindness	Uncertain significance	rs201620180, rs762960396	RCV000293665 RCV000262785

Show/Hide Text Mining Associations (8)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Esophageal Squamous Cell Carcinoma	Associate	26330293
Myopia	Associate	17392683, 25802485, 37191617
Night Blindness	Associate	17392683
Night blindness congenital stationary	Associate	14609846, 15761389, 17392683, 18617546, 19896113, 23289809, 24715752, 25802485, 26234941, 34064005, 34781300, 36499293, 7966198, 8434607, 9529339
Nystagmus Pathologic	Associate	34064005
Retinal Diseases	Associate	37191617
Strabismus	Associate	34064005
Vision Disorders	Stimulate	8434607

NYX (nyctalopin)