NYX

nyctalopin

Basic information

Region (hg38): X:41447343-41475710

Previous symbols: [ "CSNB1", "CSNB4" ]

Links

ENSG00000188937 ∙ NCBI:60506 ∙ OMIM:300278 ∙ HGNC:8082 ∙ Uniprot:Q9GZU5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• congenital stationary night blindness 1A (Definitive), mode of inheritance: XLR
• congenital stationary night blindness (Supportive), mode of inheritance: AD
• congenital stationary night blindness 1A (Strong), mode of inheritance: XL
• congenital stationary night blindness 1A (Definitive), mode of inheritance: XL
• NYX-related retinopathy (Definitive), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Night blindness, congenital stationary, type 1A	XL	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	8434607; 9662400; 11062471; 11062472; 16670814; 18617546; 20301423; 20850105; 22183355

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NYX gene.

• not provided (17 variants)
• Retinal dystrophy (2 variants)
• Congenital stationary night blindness 1A (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NYX gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	75	3	79
missense		1	201	3	5	210
nonsense	6	2				8
start loss						0
frameshift	9	1	2			12
inframe indel	2	1	4	1		8
splice donor/acceptor (+/-2bp)		1				1
splice region						0
non coding	1		13	6	4	24
Total	18	6	221	85	12

Highest pathogenic variant AF is 0.0000180

Variants in NYX

This is a list of pathogenic ClinVar variants found in the NYX region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-41447562-T-C		Congenital stationary night blindness 1A	Uncertain significance (Jan 13, 2018)
X-41447576-A-G		Congenital stationary night blindness 1A	Benign (Nov 12, 2018)
X-41447611-T-C		Congenital stationary night blindness 1A	Benign (Nov 12, 2018)
X-41447615-T-C		Congenital stationary night blindness 1A	Uncertain significance (Jan 13, 2018)
X-41447804-T-G		Congenital stationary night blindness 1A	Uncertain significance (Jan 13, 2018)
X-41447882-C-G		NYX-related disorder	Likely benign (Sep 05, 2024)
X-41447899-C-T			Pathogenic (Sep 29, 2023)
X-41447900-G-A			Uncertain significance (Jul 09, 2022)
X-41447904-G-T			Uncertain significance (Nov 06, 2021)
X-41447931-G-A		Congenital stationary night blindness 1A	Uncertain significance (Sep 01, 2022)
X-41447931-G-T		Retinal dystrophy	Pathogenic (May 27, 2024)
X-41447942-G-A			Benign (Jan 31, 2024)
X-41447942-G-T			Likely benign (Sep 09, 2022)
X-41473475-C-G			Likely benign (Aug 23, 2022)
X-41473479-C-G			Likely benign (Oct 16, 2023)
X-41473490-GC-TT		Congenital stationary night blindness 1A • NYX-related disorder	Pathogenic/Likely pathogenic (Jun 08, 2022)
X-41473500-T-A			Uncertain significance (Jul 29, 2022)
X-41473502-G-A			Uncertain significance (May 12, 2023)
X-41473502-G-C			Uncertain significance (May 29, 2022)
X-41473506-T-G		Inborn genetic diseases	Uncertain significance (Jul 14, 2023)
X-41473525-G-C			Likely benign (Feb 24, 2022)
X-41473526-G-A		Inborn genetic diseases	Uncertain significance (May 16, 2023)
X-41473528-GGCCTGCGCCCGCGCTTGTCCCGCC-G		Retinal dystrophy • Congenital stationary night blindness 1A	Pathogenic (May 08, 2024)
X-41473545-G-C			not provided (-)
X-41473546-T-G			Uncertain significance (Aug 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NYX	protein_coding	protein_coding	ENST00000342595	2	28277

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.130	0.788	117392	0	2	117394	0.00000852

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.11	126	213	0.592	0.0000225	2946
Missense in Polyphen		33	71.804	0.45958		1229
Synonymous	2.77	68	104	0.654	0.0000114	1105
Loss of Function	1.39	2	5.54	0.361	4.75e-7	78

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000739	0.0000739
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.238

Haploinsufficiency Scores

• pHI: 0.218
• hipred: N
• hipred_score: 0.429
• ghis: 0.426

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Nyx
• Phenotype: vision/eye phenotype

Zebrafish Information Network

• Gene name: nyx
• Affected structure: detection of light stimulus involved in visual perception
• Phenotype tag: abnormal
• Phenotype quality: disrupted

Gene ontology

• Biological process: visual perception;biological_process;response to stimulus
• Cellular component: extracellular space;extracellular matrix
• Molecular function: molecular_function