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 (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 (361 variants)
• Inborn_genetic_diseases (55 variants)
• Congenital_stationary_night_blindness_1A (36 variants)
• Retinal_dystrophy (21 variants)
• NYX-related_disorder (14 variants)
• Congenital_stationary_night_blindness (7 variants)
• not_specified (6 variants)
• Congenital_stationary_night_blindness_1C (2 variants)
• inherited_retinal_disease (1 variants)
• Retinitis_pigmentosa (1 variants)
• Abnormality_of_the_eye (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. These statistics are base on transcript: NM_001378477.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	87	3	91
missense	5	11	250	5	5	276
nonsense	8	6				14
start loss						0
frameshift	18	4	2			24
splice donor/acceptor (+/-2bp)		1				1
Total	31	22	253	92	8

Highest pathogenic variant AF is 0.000030793224

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