NYX

Summary

NYX (nyctalopin, HGNC:8082) is a protein-coding gene on chromosome Xp11.4, encoding Nyctalopin (Q9GZU5). Required for normal vision. It is haploinsufficient (ClinGen: sufficient evidence).

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.

Source: NCBI Gene 60506 — RefSeq curated summary.

At a glance

• Gene–disease (curated): NYX-related retinopathy (Definitive, ClinGen) — +2 more curated relationships
• Clinical variants (ClinVar): 484 total — 35 pathogenic, 17 likely-pathogenic
• Phenotypes (HPO): 5
• Dosage sensitivity (ClinGen): haploinsufficiency sufficient evidence, triplosensitivity no evidence
• MANE Select transcript: NM_001378477

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:8082
Approved symbol	NYX
Name	nyctalopin
Location	Xp11.4
Locus type	gene with protein product
Status	Approved
Aliases	CLRP, CSNB1A
Ensembl gene	ENSG00000188937
Ensembl biotype	protein_coding
OMIM	300278
Entrez	60506

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000342595, ENST00000378220, ENST00000486842, ENST00000938151

RefSeq mRNA: 2 — MANE Select: NM_001378477 NM_001378477, NM_022567

CCDS: CCDS14256

Canonical transcript exons

ENST00000378220 — 3 exons

Exon	Start	End
ENSE00001476691	41473491	41475652
ENSE00001476695	41447849	41447926
ENSE00001476697	41447343	41447516

Expression profiles

Bgee: expression breadth broad, 20 present calls, max score 87.10.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0112 / max 6.3616, expressed in 5 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
196038	0.0112	5

Top tissues by expression

221 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
tendon of biceps brachii	UBERON:0008188	87.10	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.73	gold quality
pancreatic ductal cell	CL:0002079	86.35	silver quality
pigmented layer of retina	UBERON:0001782	74.74	gold quality
gingival epithelium	UBERON:0001949	70.30	silver quality
heart right ventricle	UBERON:0002080	68.93	silver quality
vena cava	UBERON:0004087	68.54	silver quality
biceps brachii	UBERON:0001507	68.03	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	66.39	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	66.37	gold quality
medial globus pallidus	UBERON:0002477	66.28	silver quality
secondary oocyte	CL:0000655	66.04	gold quality
cartilage tissue	UBERON:0002418	64.52	silver quality
esophagus squamous epithelium	UBERON:0006920	64.02	gold quality
buccal mucosa cell	CL:0002336	63.94	gold quality
mucosa of sigmoid colon	UBERON:0004993	63.23	gold quality
squamous epithelium	UBERON:0006914	63.09	gold quality
globus pallidus	UBERON:0001875	62.93	silver quality
cerebellar vermis	UBERON:0004720	62.35	silver quality
epithelium of esophagus	UBERON:0001976	62.23	gold quality
germinal epithelium of ovary	UBERON:0001304	61.21	gold quality
vastus lateralis	UBERON:0001379	60.68	gold quality
oral cavity	UBERON:0000167	60.46	gold quality
quadriceps femoris	UBERON:0001377	60.34	gold quality
pleura	UBERON:0000977	60.09	gold quality
parietal pleura	UBERON:0002400	59.86	gold quality
deltoid	UBERON:0001476	59.85	gold quality
visceral pleura	UBERON:0002401	59.65	gold quality
decidua	UBERON:0002450	59.32	gold quality
tibia	UBERON:0000979	58.44	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.97

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

30 targeting NYX, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-11181-3P	99.75	66.38	2205
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-3202	99.66	67.70	2737
HSA-MIR-3612	99.45	66.02	1333
HSA-MIR-650	99.45	65.77	1309
HSA-MIR-542-3P	99.34	67.58	1270
HSA-MIR-4504	99.10	69.14	1328
HSA-MIR-661	99.09	65.94	2062
HSA-MIR-4650-3P	99.01	68.39	1062
HSA-MIR-6895-3P	98.79	65.69	996
HSA-MIR-4290	98.51	65.17	907
HSA-MIR-4536-5P	98.47	64.39	657
HSA-MIR-374C-3P	98.47	67.93	451
HSA-MIR-6511B-5P	97.98	65.64	823
HSA-MIR-6811-5P	97.98	64.96	848
HSA-MIR-6514-3P	97.52	66.50	808
HSA-MIR-3116	97.07	65.78	1324
HSA-MIR-1913	97.07	66.20	1417
HSA-MIR-4474-3P	96.97	65.87	870
HSA-MIR-6894-3P	96.73	65.64	798
HSA-MIR-6734-5P	95.70	65.56	950
HSA-MIR-4423-5P	95.24	64.42	454
HSA-MIR-1281	92.96	65.73	260

Functional genomics

ClinGen dosage: haploinsufficiency 3 (sufficient evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 21)

• Phenotypic expression of the complete type of X-linked congenital stationary night blindness in patients with different mutations in the NYX gene. (PMID:12397430)
• The nob (no b-wave) mouse model of CSNB1 (complete form of human X-linked congenital stationary night blindness) involves an 85-bp deletion in the nyx gene. (PMID:12506099)
• Seven in-frame deletion, splicing, missense, nonsense, and frameshift mutations were identified segregating with X-linked congenital stationary night blindness in the NYX gene. (PMID:12552565)
• Human and mouse nyctalopin are membrane-bound extracellular proteins and are functionally conserved. (PMID:14507859)
• The results implicated a specific on-pathway signaling deficiency in CSNB1-NYX males with no evidence of off-pathway involvement. Likewise, rapid-on/off ramping stimuli also indicated that the functional deficit was localized to the on pathway. (PMID:15331616)
• In a pool of eight diagnosed XLCSNB (X-linked congenital stationary night blindness) patients, five showed a sequence variation in the CACNA1F and two in the NYX gene. (PMID:15761389)
• Results support a role for nyctalopin in synaptic transmission and/or synapse formation at ribbon synapses in the retina. (PMID:16553780)
• Novel mutations of NYX were identified in two Chinese families with CSNB1 and myopia. (PMID:16670814)
• X-linked congenital night blindness mutations are reported in Chinese males in two families. (PMID:16670814)
• Mutations in NYX may cause high myopia without congenital stationary night blindness. (PMID:17392683)
• The c.855delG deletion in NYX seems to be a common mutation associated with CSNB in the Flemish population from Belgium. (PMID:18617546)
• A proteomic search for proteins associated with nyctalopin in the retina identified TRPM1 as the binding partner and nyctalopin additionally interacts with mGluR6 receptor. (PMID:21832182)
• 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). (PMID:22735794)
• 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. (PMID:23289809)
• 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. (PMID:23406521)
• A mutation was identified in NYX in 20 male patients with Congenital Stationary Night Blindness 1. (PMID:23714322)
• Four potential pathogenic variations in the NYX gene were found in four families with high myopia with or without CSNB1. (PMID:25802485)
• Two Novel NYX Gene Mutations in the Chinese Families with X-linked Congenital Stationary Night Blindness were described. (PMID:26234941)
• Frameshift mutation in NYX gene is associated with congenital stationary night blindness. (PMID:31826698)
• Complete congenital stationary night blindness associated with a novel NYX variant (p.Asn216Lys) in middle-aged and older adult patients. (PMID:33769208)
• NYX-related Congenital Stationary Night Blindness in Two Siblings due to Probable Maternal Germline Mosaicism. (PMID:34165036)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	nyx	ENSDARG00000061791
mus_musculus	Nyx	ENSMUSG00000051228
rattus_norvegicus	Nyx	ENSRNOG00000009646

Paralogs (22): DCN (ENSG00000011465), RTN4R (ENSG00000040608), ASPN (ENSG00000106819), FLRT3 (ENSG00000125848), FLRT1 (ENSG00000126500), LRRC4 (ENSG00000128594), LRRC4B (ENSG00000131409), PODNL1 (ENSG00000132000), LRTM1 (ENSG00000144771), LRRC4C (ENSG00000148948), LRRTM1 (ENSG00000162951), LRRC15 (ENSG00000172061), PODN (ENSG00000174348), LRRTM4 (ENSG00000176204), BGN (ENSG00000182492), LRRC19 (ENSG00000184434), FLRT2 (ENSG00000185070), GP1BA (ENSG00000185245), RTN4RL1 (ENSG00000185924), RTN4RL2 (ENSG00000186907), LRRC66 (ENSG00000188993), LRRTM3 (ENSG00000198739)

Protein

Protein identifiers

Nyctalopin — Q9GZU5 (reviewed: Q9GZU5)

All UniProt accessions (1): Q9GZU5

UniProt curated annotations — full annotation on UniProt →

Function. Required for normal vision. Is a critical factor for light-induced depolarization of retinal ON-bipolar cells, likely acting as a scaffold for TRPM1 and GRM6. Required for TRPM1 trafficking to dendritic tips of ON-bipolar cells.

Subunit / interactions. Interacts with TRPM1 and GRM6.

Subcellular location. Secreted. Extracellular space. Extracellular matrix. Cell projection. Dendrite. Postsynapse.

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.

Disease relevance. 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. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the small leucine-rich proteoglycan (SLRP) family. SLRP class IV subfamily.

RefSeq proteins (2): NP_001365406, NP_072089 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000483	Cys-rich_flank_reg_C	Domain
IPR001611	Leu-rich_rpt	Repeat
IPR003591	Leu-rich_rpt_typical-subtyp	Repeat
IPR032675	LRR_dom_sf	Homologous_superfamily
IPR050541	LRR_TM_domain-containing	Family

Pfam: PF13855

UniProt features (44 total): sequence variant 24, repeat 11, glycosylation site 6, signal peptide 1, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9GZU5-F1	82.68	0.70

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Glycosylation sites (6): 92, 178, 295, 388, 427, 434

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 78 (showing top): LFA1_Q6, BLALOCK_ALZHEIMERS_DISEASE_UP, GOBP_SENSORY_PERCEPTION_OF_LIGHT_STIMULUS, MARTIN_VIRAL_GPCR_SIGNALING_UP, GOBP_SENSORY_PERCEPTION, GOCC_NEURON_PROJECTION, HAND1E47_01, LIU_BREAST_CANCER, GOCC_POSTSYNAPSE, GOCC_SYNAPSE, GOCC_SOMATODENDRITIC_COMPARTMENT, E4BP4_01, chrXp11, GOCC_DENDRITIC_TREE, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY

GO Biological Process (1): visual perception (GO:0007601)

GO Molecular Function (2): signaling receptor activity (GO:0038023), protein binding (GO:0005515)

GO Cellular Component (3): dendrite (GO:0030425), postsynapse (GO:0098794), extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
sensory perception of light stimulus	1
molecular transducer activity	1
binding	1
neuron projection	1
dendritic tree	1
synapse	1

Protein interactions and networks

STRING

1184 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NYX	TRPM1	Q7Z4N2	975
NYX	CACNA1F	O60840	962
NYX	GRM6	O15303	959
NYX	CABP4	P57796	837
NYX	GPR179	Q6PRD1	819
NYX	OPN1LW	P04000	804
NYX	FRMD7	Q6ZUT3	790
NYX	RPGR	Q92834	705
NYX	GPR143	P51810	654
NYX	PDE6B	P35913	647
NYX	SLC25A14	O95258	636
NYX	OPTC	Q9UBM4	633
NYX	LRIT3	Q3SXY7	594
NYX	CACNA2D4	Q7Z3S7	586
NYX	GNAT1	P11488	571

IntAct

11 interactions, top by confidence:

A	B	Type	Score
RBMX	NYX	psi-mi:“MI:0915”(physical association)	0.560
NYX	JPH3	psi-mi:“MI:0915”(physical association)	0.560
NYX	LYPLA2	psi-mi:“MI:0914”(association)	0.530
STPG2	TF	psi-mi:“MI:0914”(association)	0.530
NYX	POTEF	psi-mi:“MI:0914”(association)	0.350
NYX	RBMX	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (32): COX16 (Affinity Capture-MS), HSPA5 (Affinity Capture-MS), AMD1 (Affinity Capture-MS), CNPY3 (Affinity Capture-MS), GALNT1 (Affinity Capture-MS), TUBA4A (Affinity Capture-MS), MCU (Affinity Capture-MS), EMB (Affinity Capture-MS), LYPLA2 (Affinity Capture-MS), SPRYD7 (Affinity Capture-MS), SHROOM1 (Affinity Capture-MS), CTU1 (Affinity Capture-MS), NYX (Affinity Capture-MS), LYPLA2 (Affinity Capture-MS), SHROOM1 (Affinity Capture-MS)

ESM2 similar proteins: A0A8P0N4K0, A5YM72, A6NIK2, A6NIX2, D3KCC4, D3Z7H8, D3ZU57, O08742, O43822, O75427, O95382, P40197, Q02779, Q13470, Q14160, Q149C3, Q15653, Q16584, Q24K06, Q32P44, Q3UGP9, Q505F5, Q5BKY1, Q5I2M8, Q5RKR3, Q5U651, Q66HA1, Q6EMK4, Q6NSJ5, Q6UXK2, Q6UY18, Q76KP1, Q80U72, Q80XI6, Q80ZD5, Q86WK7, Q8C013, Q8K3W2, Q8N1G4, Q8WUA8

Diamond homologs: A3KNN3, A4IIW9, A6H789, A6H793, A6NJW4, A8WHP9, E9Q7T7, O46379, O75093, O75094, O88280, O94769, P21793, P24014, P51884, P51885, P51886, P59034, P59035, P83503, Q05443, Q3MHH9, Q5FW85, Q5M7S9, Q65YW8, Q6EMK4, Q6NUI6, Q6R5N8, Q8R5M3, Q8VCH9, Q96PB8, Q9BY71, Q9GKQ6, Q9GZU5, Q9TTE2, Q9WVB4, Q9WVC1, Q9Z0L0, A8WGA3, B1H134

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

484 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	35
Likely pathogenic	17
Uncertain significance	284
Likely benign	100
Benign	12

Top pathogenic / likely-pathogenic (30)

Variant ID	HGVS	Classification
1025245	NC_000023.10:g.(?41332744)(41334152_?)del	Pathogenic
11422	NM_001378477.3(NYX):c.90C>A (p.Cys30Ter)	Pathogenic
11423	NC_000023.11:g.41474012_41474013delinsAA	Pathogenic
11424	NM_001378477.3(NYX):c.266G>C (p.Arg89Pro)	Pathogenic
11425	NM_001378477.3(NYX):c.287T>C (p.Ile96Thr)	Pathogenic
1213862	NM_001378477.3(NYX):c.689dup (p.Leu231fs)	Pathogenic
1347562	NM_001378477.3(NYX):c.776del (p.Asn259fs)	Pathogenic
1387183	NM_001378477.3(NYX):c.770del (p.Gly257fs)	Pathogenic
1403748	NM_001378477.3(NYX):c.950_977del (p.Phe317fs)	Pathogenic
1462042	NM_001378477.3(NYX):c.587C>A (p.Ser196Ter)	Pathogenic
1467177	NM_001378477.3(NYX):c.820G>T (p.Glu274Ter)	Pathogenic
1502310	NM_001378477.3(NYX):c.518_528del (p.Leu173fs)	Pathogenic
1695293	NM_001378477.3(NYX):c.506dup (p.Pro170fs)	Pathogenic
1975933	NM_001378477.3(NYX):c.-6C>T	Pathogenic
2000574	NM_001378477.3(NYX):c.558_574dup (p.Val192fs)	Pathogenic
2030892	NM_001378477.3(NYX):c.516del (p.Leu173fs)	Pathogenic
2040255	NM_001378477.3(NYX):c.119C>A (p.Ser40Ter)	Pathogenic
2133670	NM_001378477.3(NYX):c.100_101insTAGCA (p.Thr34fs)	Pathogenic
2138553	NM_001378477.3(NYX):c.804G>A (p.Trp268Ter)	Pathogenic
2750697	NM_001378477.3(NYX):c.807_819dup (p.Glu274delinsArgTer)	Pathogenic
2834595	NM_001378477.3(NYX):c.1023G>A (p.Trp341Ter)	Pathogenic
3248955	NM_001378477.3(NYX):c.944_971del (p.Val315fs)	Pathogenic
3249790	NM_001378477.3(NYX):c.880C>T (p.Gln294Ter)	Pathogenic
3249933	NM_001378477.3(NYX):c.285_286insG (p.Ile96fs)	Pathogenic
3249935	NM_001378477.3(NYX):c.81del (p.Ala28fs)	Pathogenic
3381812	NM_001378477.3(NYX):c.22+5G>T	Pathogenic
3643766	NM_001378477.3(NYX):c.42del (p.Ser15fs)	Pathogenic
3656981	NM_001378477.3(NYX):c.1071del (p.Cys357fs)	Pathogenic
3727679	NM_001378477.3(NYX):c.946del (p.Ala316fs)	Pathogenic
4683112	NM_001378477.3(NYX):c.1108dup (p.Gln370fs)	Pathogenic

SpliceAI

369 predictions. Top by Δscore:

Variant	Effect	Δscore
X:41473476:ACCCT:A	acceptor_gain	0.9900
X:41447515:CGG:C	donor_loss	0.9800
X:41447517:G:A	donor_loss	0.9800
X:41447518:T:G	donor_loss	0.9800
X:41473464:C:A	acceptor_gain	0.9800
X:41473476:A:AG	acceptor_gain	0.9800
X:41473477:C:G	acceptor_gain	0.9800
X:41473489:AGC:A	acceptor_gain	0.9800
X:41473490:GCG:G	acceptor_gain	0.9800
X:41447512:GGACG:G	donor_gain	0.9700
X:41447513:GACGG:G	donor_gain	0.9700
X:41447517:G:GG	donor_gain	0.9700
X:41473474:C:G	acceptor_gain	0.9700
X:41473480:T:A	acceptor_gain	0.9700
X:41473489:A:AG	acceptor_gain	0.9700
X:41473490:G:GA	acceptor_gain	0.9700
X:41473490:GCGGT:G	acceptor_gain	0.9700
X:41447513:GACG:G	donor_gain	0.9600
X:41473489:AGCG:A	acceptor_gain	0.9600
X:41473490:GCGG:G	acceptor_gain	0.9600
X:41473473:A:AG	acceptor_gain	0.9500
X:41473490:GC:G	acceptor_gain	0.9500
X:41473486:CGCA:C	acceptor_loss	0.9400
X:41473487:GCAG:G	acceptor_loss	0.9400
X:41473488:CAGC:C	acceptor_loss	0.9400
X:41473489:A:T	acceptor_loss	0.9400
X:41473490:G:GT	acceptor_loss	0.9400
X:41447848:GGTA:G	acceptor_gain	0.9200
X:41447925:TGG:T	donor_loss	0.9200
X:41447927:GT:G	donor_loss	0.9200

AlphaMissense

3051 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:41473755:T:A	I101N	0.995
X:41473740:A:T	N96I	0.993
X:41473741:C:A	N96K	0.992
X:41473741:C:G	N96K	0.992
X:41473770:T:C	F106S	0.992
X:41473739:A:T	N96Y	0.989
X:41473751:T:C	F100L	0.988
X:41473753:C:A	F100L	0.988
X:41473753:C:G	F100L	0.988
X:41473755:T:C	I101T	0.988
X:41473813:C:A	N120K	0.988
X:41473813:C:G	N120K	0.988
X:41473960:C:A	N169K	0.988
X:41473960:C:G	N169K	0.988
X:41474173:C:A	N240K	0.988
X:41474173:C:G	N240K	0.988
X:41473698:T:G	F82C	0.986
X:41474171:A:T	N240Y	0.986
X:41473755:T:G	I101S	0.985
X:41473770:T:G	F106C	0.985
X:41474229:T:A	L259H	0.985
X:41474317:C:A	N288K	0.985
X:41474317:C:G	N288K	0.985
X:41474172:A:T	N240I	0.983
X:41474389:C:A	N312K	0.983
X:41474389:C:G	N312K	0.983
X:41474085:T:A	L211H	0.981
X:41474387:A:T	N312Y	0.980
X:41474465:T:A	W338R	0.980
X:41474465:T:C	W338R	0.980

dbSNP variants (sampled 300 via entrez): RS1000041197 (X:41456425 G>A,T), RS1000189454 (X:41468000 T>C), RS1000448645 (X:41463568 G>A), RS1000458555 (X:41463911 G>A), RS1000708191 (X:41471955 G>A,T), RS1000785300 (X:41465968 T>A,G), RS1000940587 (X:41456389 T>C), RS1000950885 (X:41446698 T>C), RS1000982433 (X:41473389 C>T), RS1001003254 (X:41447111 C>T), RS1001195575 (X:41455482 G>T), RS1001311359 (X:41470277 G>A), RS1001401566 (X:41470878 G>A,C), RS1001452487 (X:41461437 A>G), RS1001611291 (X:41452017 A>G)

Disease associations

OMIM: gene MIM:300278 | disease phenotypes: MIM:310500, MIM:268000, MIM:300423, MIM:613216

GenCC curated gene-disease

Disease	Classification	Inheritance
congenital stationary night blindness 1A	Definitive	X-linked
congenital stationary night blindness	Supportive	Autosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
NYX-related retinopathy	Definitive	XL

Mondo (6): congenital stationary night blindness 1A (MONDO:0010690), inherited retinal dystrophy (MONDO:0019118), retinitis pigmentosa (MONDO:0019200), syndromic X-linked intellectual disability Hedera type (MONDO:0010319), congenital stationary night blindness 1C (MONDO:0013183), congenital stationary night blindness (MONDO:0016293)

Orphanet (4): Congenital stationary night blindness (Orphanet:215), OBSOLETE: Inherited retinal disorder (Orphanet:71862), Retinitis pigmentosa (Orphanet:791), X-linked intellectual disability, Hedera type (Orphanet:93952)

HPO phenotypes

5 total (6 of 5 shown, HPO-id order):

HPO	Term
HP:0001419	X-linked recessive inheritance
HP:0007642	Early-onset non-progressive night blindness
HP:0011003	High myopia
HP:0011463	Childhood onset
HP:0012047	Hemeralopia
HP:0000556	Retinal dystrophy

GWAS associations

0 associations (top):

MeSH disease descriptors (5)

Descriptor	Name	Tree numbers
D058499	Retinal Dystrophies	C11.768.585.658
D012174	Retinitis Pigmentosa	C11.270.684; C11.768.585.658.500; C16.320.290.684
C567704	CSNB1C (supp.)
C564516	Mental Retardation, X-Linked, with Epilepsy (supp.)
C536122	Night blindness, congenital stationary (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
bisphenol A	decreases methylation	1
benzo(e)pyrene	increases methylation	1
CGP 52608	increases reaction, affects binding	1
Resveratrol	affects cotreatment, decreases expression	1
Methapyrilene	increases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

260 trials via MONDO — disease-level, not drug-specific.

Trial	Phase	Status	Title
NCT00717080	PHASE4	COMPLETED	The Role of Capsular Tension Ring (CTR) in Anterior Capsular Contraction
NCT04224207	PHASE3	COMPLETED	Management of Retinitis Pigmentosa by Mesenchymal Stem Cells by Wharton’s Jelly Derived Mesenchymal Stem Cells
NCT07082855	PHASE3	NOT_YET_RECRUITING	A Multicenter, Randomized, Double-Blind, Controlled Clinical Study of Minocycline for the Treatment of Retinitis Pigmentosa
NCT00000114	PHASE3	COMPLETED	Randomized Trial of Vitamin A and Vitamin E Supplementation for Retinitis Pigmentosa
NCT00000116	PHASE3	COMPLETED	Randomized Trial of DHA for Retinitis Pigmentosa Patients Receiving Vitamin A
NCT00346333	PHASE3	COMPLETED	Clinical Trial of Lutein for Patients With Retinitis Pigmentosa Receiving Vitamin A
NCT01786395	PHASE3	TERMINATED	Phase III Efficacy and Safety Clinical Study of UF-021 for Treatment of Retinitis Pigmentosa
NCT04636853	PHASE3	COMPLETED	CB-PRP in Retinitis Pigmentosa and Dry Age-related Macular Degeneration
NCT05537220	PHASE3	ACTIVE_NOT_RECRUITING	Oral N-acetylcysteine for Retinitis Pigmentosa
NCT05800301	PHASE3	COMPLETED	Management of Retinitis Pigmentosa Via Combination of Wharton’s Jelly-derived Mesenchymal Stem Cells and Magnovision
NCT05926583	PHASE3	ACTIVE_NOT_RECRUITING	A Study of AAV5-hRKp.RPGR for the Treatment of Japanese Participants With X-linked Retinitis Pigmentosa
NCT06388200	PHASE3	ACTIVE_NOT_RECRUITING	A Phase 3 Study Of OCU400 Gene Therapy for the Treatment Of Retinitis Pigmentosa
NCT07290530	PHASE3	NOT_YET_RECRUITING	24-Month Trial of NPI-001 for the Preservation of Photoreceptors in Retinitis Pigmentosa Associated With Usher Syndrome
NCT03763227	PHASE2	COMPLETED	Intravitreal Ranibizumab (Lucentis®) in the Treatment of Non-leaking Macular Cysts in Retinal Dystrophy
NCT04068207	PHASE2	COMPLETED	Minocycline Treatment in Retinitis Pigmentosa
NCT04945772	PHASE2	COMPLETED	Efficacy and Safety of MCO-010 Optogenetic Therapy in Adults With Retinitis Pigmentosa [RESTORE]
NCT00100230	PHASE2	COMPLETED	DHA and X-Linked Retinitis Pigmentosa
NCT00447980	PHASE2	COMPLETED	A Study of Encapsulated Cell Technology (ECT) Implant for Participants With Early Stage Retinitis Pigmentosa
NCT00447993	PHASE2	COMPLETED	A Study of Encapsulated Cell Technology (ECT) Implant for Patients With Late Stage Retinitis Pigmentosa
NCT01233609	PHASE2	COMPLETED	Trial of Oral Valproic Acid for Retinitis Pigmentosa
NCT01399515	PHASE2	COMPLETED	Efficacy and Safety of Oral Valproic Acid for Retinitis Pigmentosa
NCT01530659	PHASE2	COMPLETED	Retinal Imaging in CNTF -Releasing Encapsulated Cell Implant Treated Patients for Early-stage Retinitis Pigmentosa
NCT01560715	PHASE2	COMPLETED	Autologous Bone Marrow-Derived Stem Cells Transplantation For Retinitis Pigmentosa
NCT02609165	PHASE2	COMPLETED	Nerve Growth Factor Eye Drops Treatment in Patients With Retinitis Pigmentosa and Cystoid Macular Edema
NCT02661711	PHASE2	COMPLETED	Aflibercept for Macular Oedema With Underlying Retinitis Pigmentosa (AMOUR) Study
NCT02804360	PHASE2	UNKNOWN	Intravitreal Dexamethasone Implant in Retinitis Pigmentosa-related Macular Edema- a Retrospective Study
NCT02837640	PHASE2	UNKNOWN	Studying a Potential Protective Effect of L-Dopa on Retinitis Pigmentosa
NCT03073733	PHASE2	COMPLETED	Safety and Efficacy of Intravitreal Injection of Human Retinal Progenitor Cells in Adults With Retinitis Pigmentosa
NCT04356716	PHASE2	COMPLETED	Sildenafil for Treatment of Choroidal Ischemia
NCT04604899	PHASE2	COMPLETED	Safety of Repeat Intravitreal Injection of Human Retinal Progenitor Cells (jCell) in Adult Subjects With Retinitis Pigmentosa
NCT04763369	PHASE2	UNKNOWN	Investigation of Therapeutic Efficacy and Safety of UMSCs for the Management of Retinitis Pigmentosa (RP)
NCT04864496	PHASE2	UNKNOWN	Effects of Treatment With N- Acetylcysteine on Visual Outcomes in Patients With Retinitis Pigmentosa
NCT05085964	PHASE2	TERMINATED	An Open-Label Extension Study to Evaluate Safety & Tolerability of QR-421a in Subjects With Retinitis Pigmentosa
NCT05392179	PHASE2	COMPLETED	A Study in Subjects With Retinitis Pigmentosa
NCT06627179	PHASE2	RECRUITING	Study to Evaluate Ultevursen in Subjects With Retinitis Pigmentosa (RP) Due to Mutations in Exon 13 of the USH2A Gene
NCT06628947	PHASE2	RECRUITING	A Phase II Study of Intravitreal KIO-301 in Patients With Late-stage Retinitis Pigmentosa
NCT06912633	PHASE2	RECRUITING	Safety of a Single, Intravitreal Injection of 6.0M jCell (Famzeretcel) in Retinitis Pigmentosa (RP)
NCT05902962	PHASE1	COMPLETED	SAD of IVT VP-001 in PRPF31 Mutation-Associated Retinal Dystrophy Subjects
NCT06319872	PHASE1	RECRUITING	The Effects of Disulfiram (Antabuse®) on Visual Acuity in Patients With Retinal Degeneration
NCT06455826	PHASE1	COMPLETED	MAD of IVT VP-001 in PRPF31 Mutation-Associated Retinal Dystrophy Subjects (Wallaby)