Congenital stationary night blindness autosomal dominant 3

Summary

Congenital stationary night blindness autosomal dominant 3 (MONDO:0012497) is a disease caused by GNAT1 (GenCC Definitive), with 1 cohort gene.

At a glance

• Causal gene: GNAT1 (GenCC Definitive)
• Cohort genes: 1
• ClinVar variants: 56

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	congenital stationary night blindness autosomal dominant 3
Mondo ID	MONDO:0012497
MeSH	C566475
OMIM	610444
DOID	DOID:0110715
UMLS	C1864870
MedGen	355313
GARD	0015487
Is cancer (heuristic)	no

Also known as: congenital stationary night blindness autosomal dominant type 3 · CSNBAD3 · night blindness, congenital stationary, autosomal dominant 3 · night blindness, congenital stationary, autosomal dominant type 3

Data availability: 56 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 › autosomal genetic disease › autosomal dominant disease › congenital stationary night blindness autosomal dominant 3

Related subtypes (191): autosomal dominant polycystic liver disease, cerebral arteriopathy, autosomal dominant, with subcortical infarcts and leukoencephalopathy, type 1, tuberous sclerosis, Treacher-Collins syndrome, hereditary breast ovarian cancer syndrome, autosomal dominant polycystic kidney disease, Lynch syndrome, branchio-oto-renal syndrome, autosomal dominant Aarskog syndrome, acroosteolysis dominant type, ADULT syndrome, autosomal dominant Alport syndrome, amelogenesis imperfecta type 1B, Townes-Brocks syndrome, nevoid basal cell carcinoma syndrome, blepharophimosis, ptosis, and epicanthus inversus syndrome, autosomal dominant brachyolmia, branchiooculofacial syndrome, pheochromocytoma/paraganglioma syndrome 4, cataract-aberrant oral frenula-growth delay syndrome, cherubism, autosomal dominant chondrodysplasia punctata, autosomal dominant popliteal pterygium syndrome, blepharocheilodontic syndrome, cochleosaccular degeneration-cataract syndrome, renal coloboma syndrome, Beare-Stevenson cutis gyrata syndrome, autosomal dominant vibratory urticaria, neurohypophyseal diabetes insipidus, autosomal dominant Kenny-Caffey syndrome, Rapp-Hodgkin syndrome, Ehlers-Danlos syndrome, classic type, autosomal dominant Ehlers-Danlos syndrome, vascular type, multiple endocrine neoplasia type 1, Coffin-Siris syndrome 1, isolated congenital adermatoglyphia, Flynn-Aird syndrome, Frasier syndrome, hand-foot-genital syndrome, Holt-Oram syndrome, hyperkeratosis-hyperpigmentation syndrome, autosomal dominant ichthyosis vulgaris, hyper-IgE recurrent infection syndrome 1, autosomal dominant, autosomal dominant keratitis, autosomal dominant keratitis-ichthyosis-hearing loss syndrome, LADD syndrome, trichorhinophalangeal syndrome type II, Noonan syndrome with multiple lentigines, microcephaly with or without chorioretinopathy, lymphedema, or intellectual disability, Marfan syndrome, melanoma, cutaneous malignant, susceptibility to, 2, autosomal dominant primary microcephaly, autosomal dominant progressive external ophthalmoplegia, monilethrix, Muir-Torre syndrome, autosomal dominant myoglobinuria, autosomal dominant centronuclear myopathy, nail-patella syndrome, multiple endocrine neoplasia type 2B, autosomal dominant omodysplasia, pheochromocytoma/paraganglioma syndrome 1, Pelger-Huet anomaly, multiple endocrine neoplasia type 2A, piebaldism, autosomal dominant medullary cystic kidney disease with or without hyperuricemia, generalized juvenile polyposis/juvenile polyposis coli, juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome, Peutz-Jeghers syndrome, contractures, pterygia, and spondylocarpotarsal fusion syndrome 1A, autosomal dominant distal renal tubular acidosis, retinoschisis, autosomal dominant, autosomal dominant Robinow syndrome, scapuloperoneal spinal muscular atrophy, autosomal dominant, autosomal dominant sideroblastic anemia, spondyloepiphyseal dysplasia tarda, autosomal dominant, proximal symphalangism, calcaneonavicular coalition, thanatophoric dysplasia type 1, trichorhinophalangeal syndrome type I, Muckle-Wells syndrome, autosomal dominant hypophosphatemic rickets, von Hippel-Lindau disease, Denys-Drash syndrome, autosomal dominant severe congenital neutropenia, Costello syndrome, EEC syndrome, multiple cutaneous and mucosal venous malformations, diffuse nonepidermolytic palmoplantar keratoderma, Timothy syndrome, pheochromocytoma/paraganglioma syndrome 2, spondyloepimetaphyseal dysplasia with multiple dislocations, Brooke-Spiegler syndrome, macrocephaly-autism syndrome, pheochromocytoma/paraganglioma syndrome 3, Duane-radial ray syndrome, PCWH syndrome, heart-hand syndrome, Slovenian type, mandibulofacial dysostosis-microcephaly syndrome, multiple endocrine neoplasia type 4, juvenile cataract-microcornea-renal glucosuria syndrome, Crouzon syndrome-acanthosis nigricans syndrome, Birk-Barel syndrome, thrombophilia due to protein S deficiency, autosomal dominant, dyskeratosis congenita, autosomal dominant 2, dyskeratosis congenita, autosomal dominant 3, colorectal cancer, hereditary nonpolyposis, type 6, colorectal cancer, hereditary nonpolyposis, type 7, brain small vessel disease 2A, autosomal dominant, intellectual disability, autosomal dominant 14, intellectual disability, autosomal dominant 15, intellectual disability, autosomal dominant 16, hypopigmentation-punctate palmoplantar keratoderma syndrome, intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency, postaxial polydactyly-anterior pituitary anomalies-facial dysmorphism syndrome, intellectual developmental disorder with microcephaly and with or without ocular malformations or hypogonadotropic hypogonadism, intellectual disability, autosomal dominant 29, intellectual disability, autosomal dominant 30, Houge-Janssens syndrome 2, severe achondroplasia-developmental delay-acanthosis nigricans syndrome, dyskeratosis congenita, autosomal dominant 6, epidermolysis bullosa simplex 6, generalized, with scarring and hair loss, autosomal dominant complex spastic paraplegia, early-onset autosomal dominant Alzheimer disease, muscular dystrophy, limb-girdle, autosomal dominant, Feingold syndrome, Carney complex, neuronopathy, distal hereditary motor, autosomal dominant, autosomal dominant coarctation of aorta, autosomal dominant spondylocostal dysostosis, autosomal dominant hypohidrotic ectodermal dysplasia, Cowden disease, autosomal dominant distal myopathy, autosomal dominant rhegmatogenous retinal detachment, palmoplantar keratoderma-spastic paralysis syndrome, Alagille syndrome due to a JAG1 point mutation, PTEN hamartoma tumor syndrome, gastric adenocarcinoma and proximal polyposis of the stomach, autosomal dominant proximal renal tubular acidosis, autosomal dominant spastic ataxia, Waardenburg syndrome, hereditary retinoblastoma, autosomal dominant hypocalcemia, Li-Fraumeni syndrome, Loeys-Dietz syndrome, hereditary hemorrhagic telangiectasia, hereditary inclusion body myopathy-joint contractures-ophthalmoplegia syndrome, microcephalic osteodysplastic dysplasia, Saul-Wilson type, autosomal dominant intermediate Charcot-Marie-Tooth disease, autosomal dominant cutis laxa, autosomal dominant nonsyndromic hearing loss, autosomal dominant optic atrophy, autosomal dominant Emery-Dreifuss muscular dystrophy, autosomal dominant cerebellar ataxia, autosomal dominant osteopetrosis, autosomal dominant epidermolytic ichthyosis, ventricular arrhythmias due to cardiac ryanodine receptor calcium release deficiency syndrome, distal arthrogryposis type 2B1, neurofibromatosis, autosomal dominant cataract, arthrogryposis, distal, type 2B2, arthrogryposis, distal, type 2B3, Charcot-Marie-Tooth disease, demyelinating, type 1G, Delpire-McNeill syndrome, LAMA5-related multisystemic syndrome, autosomal dominant oculocutaneous albinism, Charcot-Marie-tooth disease, axonal, type 2DD, Pilarowski-Bjornsson syndrome, intellectual disability, autosomal dominant, fatty acyl-CoA reductase 1 upregulation, GUCY2D-related dominant retinopathy, RPE65-related dominant retinopathy, autosomal dominant titinopathy, NOG-related symphalangism spectrum disorder, ALPL-related autosomal dominant hypophosphatasia, MYH10-related neurodevelopmental disorder with congenital anomalies, spastic paraplegia 30A, autosomal dominant, TMEM127-related tumor predisposition, MAX-related tumor predisposition, BMPR1A-related juvenile polyposis syndrome, RP1-related dominant retinopathy, Birt-Hogg-Dube syndrome, inclusion body myopathy and brain white matter abnormalities, KINSSHIP syndrome, autosomal dominant nebulin-related myopathy, IMPG1-related dominant retinopathy, PROM1-related dominant retinopathy, PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome, ALG8-related autosomal dominant polycystic kidney and/or liver disease, NOTCH1-related AOS spectrum disorder, FLNB-associated autosomal dominant filamin related bone disorder, familial antiphospholipid syndrome

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

56 retrieved; paginated sample, class counts are floors:

27 uncertain significance, 12 benign, 7 benign/likely benign, 6 conflicting classifications of pathogenicity, 2 pathogenic, 1 pathogenic/likely pathogenic, 1 likely benign

ClinVar	Variant (HGVS)	Gene	Classification	Review
1075132	NM_144499.3(GNAT1):c.273C>A (p.Tyr91Ter)	GNAT1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
15926	NM_144499.3(GNAT1):c.113G>A (p.Gly38Asp)	GNAT1	Pathogenic	no assertion criteria provided
190967	NM_144499.3(GNAT1):c.598C>G (p.Gln200Glu)	GNAT1	Pathogenic	no assertion criteria provided
346046	NM_144499.3(GNAT1):c.83G>A (p.Arg28Gln)	GNAT1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
346048	NM_144499.3(GNAT1):c.241G>A (p.Val81Ile)	GNAT1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
346053	NM_144499.3(GNAT1):c.882C>T (p.Asp294=)	GNAT1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
855140	NM_144499.3(GNAT1):c.359C>A (p.Ser120Ter)	GNAT1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
902548	NM_144499.3(GNAT1):c.149+8C>A	GNAT1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
902549	NM_144499.3(GNAT1):c.165C>T (p.Asp55=)	GNAT1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1301808	NM_144499.3(GNAT1):c.450-11G>T	GNAT1	Uncertain significance	criteria provided, single submitter
346051	NM_144499.3(GNAT1):c.830C>T (p.Ala277Val)	GNAT1	Uncertain significance	criteria provided, single submitter
346054	NM_144499.3(GNAT1):c.926G>C (p.Arg309Pro)	GNAT1	Uncertain significance	criteria provided, multiple submitters, no conflicts
346056	NM_144499.3(GNAT1):c.*5C>T	GNAT1	Uncertain significance	criteria provided, multiple submitters, no conflicts
346057	NM_144499.3(GNAT1):c.*128T>A	GNAT1	Uncertain significance	criteria provided, single submitter
346061	NM_144499.3(GNAT1):c.*551C>T	GNAT1	Uncertain significance	criteria provided, single submitter
346063	NM_144499.3(GNAT1):c.*1101C>T	GNAT1	Uncertain significance	criteria provided, single submitter
346066	NM_144499.3(GNAT1):c.*1205C>T	GNAT1	Uncertain significance	criteria provided, single submitter
346067	NM_144499.3(GNAT1):c.*1369G>T	GNAT1	Uncertain significance	criteria provided, single submitter
346068	NM_144499.3(GNAT1):c.*1379G>A	GNAT1	Uncertain significance	criteria provided, single submitter
346071	NM_144499.3(GNAT1):c.*1789A>G	GNAT1	Uncertain significance	criteria provided, single submitter
346072	NM_144499.3(GNAT1):c.*1954C>T	GNAT1	Uncertain significance	criteria provided, single submitter
346073	NM_144499.3(GNAT1):c.*1991G>A	GNAT1	Uncertain significance	criteria provided, single submitter
346074	NM_144499.3(GNAT1):c.*2074T>C	GNAT1	Uncertain significance	criteria provided, single submitter
346075	NM_144499.3(GNAT1):c.*2129G>A	GNAT1	Uncertain significance	criteria provided, single submitter
346076	NM_144499.3(GNAT1):c.*2267C>T	GNAT1	Uncertain significance	criteria provided, single submitter
3893141	NM_144499.3(GNAT1):c.883G>A (p.Ala295Thr)	GNAT1	Uncertain significance	criteria provided, single submitter
634632	NM_144499.3(GNAT1):c.488A>C (p.Tyr163Ser)	GNAT1	Uncertain significance	criteria provided, single submitter
900948	NM_144499.3(GNAT1):c.*678C>T	GNAT1	Uncertain significance	criteria provided, single submitter
900949	NM_144499.3(GNAT1):c.*728C>T	GNAT1	Uncertain significance	criteria provided, single submitter
900950	NM_144499.3(GNAT1):c.*806G>A	GNAT1	Uncertain significance	criteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 7 · Orphanet: 1 · 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
GNAT1	Definitive	Autosomal dominant	congenital stationary night blindness autosomal dominant 3	7

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
GNAT1	Orphanet:714096	Congenital stationary night blindness, Riggs type

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
GNAT1	HGNC:4393	ENSG00000114349	P11488	Guanine nucleotide-binding protein G(t) subunit alpha-1	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
GNAT1	Guanine nucleotide-binding protein G(t) subunit alpha-1	Functions as a signal transducer for the rod photoreceptor RHO.

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)
GNAT1	Other/Unknown	no		Gprotein_alpha_su, Gprotein_alpha_I, GproteinA_insert

Expression context

Cohort genes with no expression data: 0.

1 cohort gene are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

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

Top tissues across cohort

Tissue	Cohort genes
endometrium epithelium	1
frontal pole	1
neuron projection bundle connecting eye with brain	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
GNAT1	97	tissue_specific	marker	neuron projection bundle connecting eye with brain, endometrium epithelium, frontal pole

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
GNAT1	1,865

Structural data

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

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
GNAT1	P11488	1

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 3. Enrichment computed across 1 evidence-associated genes (1 with Reactome annotation).

Pathways 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.

Pathway	Cohort genes	Fold	FDR	Sample cohort genes
Activation of the phototransduction cascade	1	951.7×	0.003	GNAT1
Inactivation, recovery and regulation of the phototransduction cascade	1	317.2×	0.005	GNAT1
G alpha (i) signalling events	1	39.0×	0.026	GNAT1

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
negative regulation of cyclic-nucleotide phosphodiesterase activity	1	16852.0×	9e-04	GNAT1
background adaptation	1	8426.0×	9e-04	GNAT1
dopamine secretion	1	5617.3×	9e-04	GNAT1
retinal cone cell differentiation	1	5617.3×	9e-04	GNAT1
neural tissue regeneration	1	4213.0×	9e-04	GNAT1
G protein-coupled opsin signaling pathway	1	3370.4×	1e-03	GNAT1
visual behavior	1	2808.7×	0.001	GNAT1
sensory perception of umami taste	1	2407.4×	0.001	GNAT1
retinal rod cell differentiation	1	1872.4×	0.001	GNAT1
regulation of opsin-mediated signaling pathway	1	1685.2×	0.001	GNAT1
phototransduction, visible light	1	1296.3×	0.001	GNAT1
cellular response to electrical stimulus	1	1296.3×	0.001	GNAT1
response to light stimulus	1	887.0×	0.002	GNAT1
eye photoreceptor cell development	1	842.6×	0.002	GNAT1
detection of light stimulus involved in visual perception	1	648.1×	0.002	GNAT1
detection of chemical stimulus involved in sensory perception of bitter taste	1	481.5×	0.003	GNAT1
adenylate cyclase-modulating G protein-coupled receptor signaling pathway	1	337.0×	0.003	GNAT1
cell population proliferation	1	102.8×	0.011	GNAT1
visual perception	1	79.5×	0.013	GNAT1
signal transduction	1	16.1×	0.062	GNAT1

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
GNAT1	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	GNAT1

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)
GNAT1	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.