congenital stationary night blindness 1A

Summary

congenital stationary night blindness 1A (MONDO:0010690) is a disease caused by NYX (GenCC Definitive), with 1 cohort gene and 1 clinical trial.

At a glance

• Causal gene: NYX (GenCC Definitive)
• Cohort genes: 1
• ClinVar variants: 52
• Clinical trials: 1

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	congenital stationary night blindness 1A
Mondo ID	MONDO:0010690
OMIM	310500
DOID	DOID:0110870
UMLS	C3495587
MedGen	501208
GARD	0015306
Is cancer (heuristic)	no

Also known as: congenital stationary night blindness caused by mutation in NYX · congenital stationary night blindness type 1A · CSNB1A · hemeralopia-myopia · myopia-night blindness · night blindness, congenital stationary (complete), 1A, X-linked, X-linked recessive · night blindness, congenital stationary, type 1A · NYX congenital stationary night blindness · NYX-related congenital stationary night blindness

Data availability: 52 ClinVar variants · 3 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › hereditary disease › X-linked disease › X-linked congenital stationary night blindness › congenital stationary night blindness 1A

Related subtypes (1): congenital stationary night blindness 2A

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

ClinVar germline variants

52 retrieved; paginated sample, class counts are floors:

23 uncertain significance, 6 pathogenic, 5 conflicting classifications of pathogenicity, 5 benign, 5 benign/likely benign, 3 likely pathogenic, 3 likely benign, 2 pathogenic/likely pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
11422	NM_001378477.3(NYX):c.90C>A (p.Cys30Ter)	NYX	Pathogenic	no assertion criteria provided
11423	NC_000023.11:g.41474012_41474013delinsAA	NYX	Pathogenic	no assertion criteria provided
11424	NM_001378477.3(NYX):c.266G>C (p.Arg89Pro)	NYX	Pathogenic	no assertion criteria provided
11425	NM_001378477.3(NYX):c.287T>C (p.Ile96Thr)	NYX	Pathogenic	no assertion criteria provided
4683112	NM_001378477.3(NYX):c.1108dup (p.Gln370fs)	NYX	Pathogenic	criteria provided, single submitter
496942	NM_001378477.3(NYX):c.23-1_23delinsTT	NYX	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
812361	NM_001378477.3(NYX):c.1054_1055del (p.Val352fs)	NYX	Pathogenic	criteria provided, single submitter
99841	NM_001378477.3(NYX):c.70_93del (p.Arg24_Ala31del)	NYX	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
1184477	NM_001378477.3(NYX):c.1293dup (p.Leu432fs)	NYX	Likely pathogenic	no assertion criteria provided
1710009	NM_001378477.3(NYX):c.419_420delinsAA (p.Cys140Ter)	NYX	Likely pathogenic	criteria provided, single submitter
1710113	NM_001378477.3(NYX):c.944_971dup (p.Phe327fs)	NYX	Likely pathogenic	no assertion criteria provided
11421	NM_001378477.3(NYX):c.1034G>A (p.Trp345Ter)	NYX	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
596320	NM_001378477.3(NYX):c.567C>A (p.Ile189=)	NYX	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
756676	NM_001378477.3(NYX):c.1379G>T (p.Cys460Phe)	NYX	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
914664	NM_001378477.3(NYX):c.645C>G (p.Ala215=)	NYX	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
931985	NM_001378477.3(NYX):c.604_612dup (p.Arg202_Arg204dup)	NYX	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1024916	NM_001378477.3(NYX):c.699C>G (p.Asn233Lys)	NYX	Uncertain significance	criteria provided, multiple submitters, no conflicts
1025763	NM_001378477.3(NYX):c.58G>A (p.Gly20Arg)	NYX	Uncertain significance	criteria provided, multiple submitters, no conflicts
1213864	NM_001378477.3(NYX):c.371_372dup (p.Thr125fs)	NYX	Uncertain significance	criteria provided, single submitter
1333398	NM_001378477.3(NYX):c.467T>C (p.Leu156Pro)	NYX	Uncertain significance	criteria provided, single submitter
1710112	NM_001378477.3(NYX):c.22+5G>A	NYX	Uncertain significance	no assertion criteria provided
2104505	NM_001378477.3(NYX):c.1396_1405dup (p.Val469fs)	NYX	Uncertain significance	criteria provided, multiple submitters, no conflicts
3367202	NM_001378477.3(NYX):c.544G>C (p.Ala182Pro)	NYX	Uncertain significance	criteria provided, single submitter
3598286	NM_001378477.3(NYX):c.94T>C (p.Cys32Arg)	NYX	Uncertain significance	criteria provided, single submitter
368264	NM_001378477.3(NYX):c.-57+46T>C	NYX	Uncertain significance	criteria provided, single submitter
368267	NM_001378477.3(NYX):c.-56-45T>G	NYX	Uncertain significance	criteria provided, single submitter
368274	NM_001378477.3(NYX):c.*72T>C	NYX	Uncertain significance	criteria provided, single submitter
368275	NM_001378477.3(NYX):c.*103G>A	NYX	Uncertain significance	criteria provided, single submitter
368276	NM_001378477.3(NYX):c.*157C>G	NYX	Uncertain significance	criteria provided, single submitter
4293315	NM_001378477.3(NYX):c.832C>T (p.Leu278Phe)	NYX	Uncertain significance	criteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 4 · Orphanet: 0 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

Gene	Classification	Inheritance	Disease	Records
NYX	Definitive	X-linked	congenital stationary night blindness 1A	4

Cohort genes → proteins

1 cohort genes, 1 distinct canonical proteins.

Evidence partition

Subset	Genes
multi_evidence	1

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
NYX	HGNC:8082	ENSG00000188937	Q9GZU5	Nyctalopin	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
NYX	Nyctalopin	Required for normal vision.

Protein-family classification

Druggable: 0 · Difficult: 0 · Unknown: 1 · Druggable fraction: 0.0

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

Family	Genes	Fold	FDR
Other/Unknown	1	1.8×	0.558

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
NYX	Other/Unknown	no		Cys-rich_flank_reg_C, Leu-rich_rpt, Leu-rich_rpt_typical-subtyp

Expression context

Cohort genes with no expression data: 0.

Breadth distribution (Bgee present_calls)

Bucket	Genes
narrow (1-5 tissues)	0
moderate (6-20)	1
broad (>20)	0
unknown	0

Top tissues across cohort

Tissue	Cohort genes
pancreatic ductal cell	1
primordial germ cell in gonad	1
tendon of biceps brachii	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
NYX	20	tissue_specific	yes	tendon of biceps brachii, primordial germ cell in gonad, pancreatic ductal cell

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
NYX	1,227

Structural data

PDB: 0 · AlphaFold-only: 1 · No structure: 0

AlphaFold-only cohort genes (top 30 by pLDDT)

Symbol	UniProt	pLDDT
NYX	Q9GZU5	82.68

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 0. Enrichment computed across 1 evidence-associated genes (0 with Reactome annotation).

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO term	Cohort genes	Fold	FDR	Sample cohort genes
visual perception	1	79.5×	0.013	NYX

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 1

Druggability breadth: 0 of 1 evidence-associated genes (0%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

Symbol	Molecules	Max phase
NYX	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

Pharmacogenomics

Cohort genes with a PharmGKB record: 1; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

0 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

Tier	Definition	Genes	Symbols
A	Approved (phase 4 drug)	0
B	Phased (≥1) drug, not yet approved	0
C	Druggable family + PDB, no drug	0
D	Druggable family + AlphaFold only, no drug	0
E	Difficult family or no structure, no drug	1	NYX

Undrugged target profiles

1 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

Symbol	ChEMBL assays	Drugged partners (top 3)
NYX	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 1.

Phase distribution (across all retrieved trials)

Phase	Trials
Not specified	1

Top trials by phase / activity

NCT	Phase	Status	Title
NCT02965534	Not specified	COMPLETED	Evaluation of a Night Spectacle Correction Concerning an Improvement of Mesopic Vision Quality