congenital stationary night blindness 1D

Summary

congenital stationary night blindness 1D (MONDO:0013450) is a disease caused by SLC24A1 (GenCC Strong), with 1 cohort gene.

At a glance

• Causal gene: SLC24A1 (GenCC Strong)
• Cohort genes: 1
• ClinVar variants: 116

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	congenital stationary night blindness 1D
Mondo ID	MONDO:0013450
OMIM	613830
DOID	DOID:0110868
UMLS	C3151193
MedGen	462543
GARD	0015721
Is cancer (heuristic)	no

Also known as: congenital stationary night blindness 1D · congenital stationary night blindness caused by mutation in SLC24A1 · congenital stationary night blindness type 1D · CSNB1D · night blindness, congenital stationary (complete), 1D, autosomal recessive · night blindness, congenital stationary, type 1D · SLC24A1 congenital stationary night blindness

Data availability: 116 ClinVar variants · 2 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by body system or component › nervous system disorder › congenital nervous system disorder › congenital stationary night blindness 1D

Related subtypes (216): polymicrogyria, congenital myasthenic syndrome with tubular aggregates, prenatal-onset spinal muscular atrophy with congenital bone fractures, anencephaly, cerebral cavernous malformation, meningocele, progressive external ophthalmoplegia, congenital nystagmus, congenital toxoplasmosis, congenital contractural arachnodactyly, congenital trigeminal anesthesia, familial congenital palsy of trochlear nerve, Myhre syndrome, Aase-Smith syndrome, KBG syndrome, autosomal dominant primary microcephaly, Mobius syndrome, MYH7-related skeletal myopathy, congenital stationary night blindness autosomal dominant 2, Prader-Willi syndrome, congenital myopathy 7A, myosin storage, autosomal dominant, Smith-Magenis syndrome, spina bifida, Freeman-Sheldon syndrome, isolated cerebellar hypoplasia/agenesis, Chediak-Higashi syndrome, Cohen syndrome, multiple pterygium-malignant hyperthermia syndrome, corpus callosum, agenesis of, congenital lactic acidosis, Saguenay-Lac-Saint-Jean type, facial dysmorphism-macrocephaly-myopia-Dandy-Walker malformation syndrome, diastematomyelia, EEM syndrome, Mowat-Wilson syndrome, Johanson-Blizzard syndrome, intellectual disability, Buenos-Aires type, myasthenia, congenital, refractory to acetylcholinesterase inhibitors, congenital myasthenic syndrome 6, Bailey-Bloch congenital myopathy, congenital stationary night blindness 1B, radioulnar synostosis-developmental delay-hypotonia syndrome, Schinzel-Giedion syndrome, schizencephaly, intellectual disability, Wolff type, X-linked intellectual disability-plagiocephaly syndrome, X-linked adrenal hypoplasia congenita, syndromic X-linked intellectual disability 7, syndromic X-linked intellectual disability Shashi type, syndromic X-linked intellectual disability Lubs type, syndromic X-linked intellectual disability Abidi type, syndromic X-linked intellectual disability Siderius type, X-linked intellectual disability, Cabezas type, X-linked intellectual disability-cubitus valgus-dysmorphism syndrome, syndromic X-linked intellectual disability Claes-Jensen type, moyamoya angiopathy-short stature-facial dysmorphism-hypergonadotropic hypogonadism syndrome, multiple congenital anomalies-hypotonia-seizures syndrome 2, developmental and epileptic encephalopathy, 36, blepharophimosis - intellectual disability syndrome, MKB type, X-linked intellectual disability-short stature-overweight syndrome, intellectual disability, X-linked, syndromic 33, syndromic X-linked intellectual disability 34, infantile-onset X-linked spinal muscular atrophy, syndromic X-linked intellectual disability 5, holoprosencephaly-hypokinesia-congenital contractures syndrome, X-linked intellectual disability with marfanoid habitus, Wieacker-Wolff syndrome, MERRF syndrome, macrocephaly-spastic paraplegia-dysmorphism syndrome, intellectual disability-sparse hair-brachydactyly syndrome, myofibrillar myopathy 1, isolated hereditary congenital facial paralysis, fibrosis of extraocular muscles, congenital, 2, Pierpont syndrome, congenital cataracts-facial dysmorphism-neuropathy syndrome, Bohring-Opitz syndrome, PHACE syndrome, B4GALT1-congenital disorder of glycosylation, developmental malformations-deafness-dystonia syndrome, sensory ataxic neuropathy, dysarthria, and ophthalmoparesis, AICA-ribosiduria, myofibrillar myopathy 3, fibrosis of extraocular muscles, congenital, 3c, myofibrillar myopathy 4, myofibrillar myopathy 5, cone-rod synaptic disorder, congenital nonprogressive, congenital stationary night blindness autosomal dominant 3, congenital stationary night blindness autosomal dominant 1, intellectual disability, autosomal recessive 12, progressive myoclonic epilepsy type 3, chromosome 15q13.3 microdeletion syndrome, combined pituitary hormone deficiencies, genetic form, DYRK1A-related intellectual disability syndrome, Pitt-Hopkins-like syndrome 2, developmental and epileptic encephalopathy, 15, Schuurs-Hoeijmakers syndrome, severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome, severe intellectual disability-progressive spastic diplegia syndrome, hypotonia, infantile, with psychomotor retardation and characteristic facies, developmental and epileptic encephalopathy, 18, CTCF-related neurodevelopmental disorder, autism spectrum disorder due to AUTS2 deficiency, developmental and epileptic encephalopathy, 23, ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder, Bardet-Biedl syndrome 11, cerebellar-facial-dental syndrome, fibrosis of extraocular muscles, congenital, 5, congenital myasthenic syndrome 15, lethal fetal cerebrorenogenitourinary agenesis/hypoplasia syndrome, autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome, congenital myasthenic syndrome 18, autosomal recessive spinocerebellar ataxia 20, Houge-Janssens syndrome 1, intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome, congenital stationary night blindness 1G, hypomyelinating leukodystrophy 10, developmental and epileptic encephalopathy, 50, congenital insensitivity to pain-hypohidrosis syndrome, macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome, SLC39A8-CDG, spastic paraplegia-severe developmental delay-epilepsy syndrome, cardiac anomalies - developmental delay - facial dysmorphism syndrome, severe intellectual disability-corpus callosum agenesis-facial dysmorphism-cerebellar ataxia syndrome, intellectual disability, autosomal recessive 53, TELO2-related intellectual disability-neurodevelopmental disorder, micrognathia-recurrent infections-behavioral abnormalities-mild intellectual disability syndrome, autosomal recessive limb-girdle muscular dystrophy type 2Y, myofibrillar myopathy 7, short stature-brachydactyly-obesity-global developmental delay syndrome, autosomal recessive limb-girdle muscular dystrophy type 2R1, severe microbrachycephaly-intellectual disability-athetoid cerebral palsy syndrome, congenital laryngeal palsy, congenital or early infantile CACH syndrome, congenital epulis, severe congenital nemaline myopathy, intermediate nemaline myopathy, typical nemaline myopathy, childhood-onset nemaline myopathy, adult-onset nemaline myopathy, qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan, holoprosencephaly, congenital insensitivity to pain with hyperhidrosis, congenital hydrocephalus, familial congenital mirror movements, macrocephaly-short stature-paraplegia syndrome, cephalocele, mitochondrial neurogastrointestinal encephalomyopathy, X-linked intellectual disability-hypogonadism-ichthyosis-obesity-short stature syndrome, 7p22.1 microduplication syndrome, congenital achiasma, congenital retinal arteriovenous communication, 3q27.3 microdeletion syndrome, Prader-Willi-like syndrome, 9q31.1q31.3 microdeletion syndrome, congenital oculomotor nerve palsy, congenital abducens nerve palsy, neurodevelopmental disorder-craniofacial dysmorphism-cardiac defect-hip dysplasia syndrome, congenital insensitivity to pain with severe intellectual disability, X-linked intellectual disability-cerebellar hypoplasia-spondylo-epiphyseal dysplasia syndrome, global developmental delay-visual anomalies-progressive cerebellar atrophy-truncal hypotonia syndrome, lissencephaly spectrum disorders, hyaline body myopathy, 22q11.2 deletion syndrome, craniorachischisis, Leber congenital amaurosis, Ritscher-Schinzel syndrome, Rubinstein-Taybi syndrome, X-linked intellectual disability-hypogammaglobulinemia-progressive neurological deterioration syndrome, X-linked intellectual disability-epilepsy-progressive joint contractures-dysmorphism syndrome, X-linked intellectual disability, Pai type, X-linked intellectual disability, Stevenson type, X-linked intellectual disability, Stoll type, congenital muscular dystrophy, congenital vitreoretinal dysplasia, periventricular nodular heterotopia, postsynaptic congenital myasthenic syndrome, subcortical band heterotopia, congenital fibrosis of extraocular muscles type 1, Al Gazali Khidr Prem Chandran syndrome, distal arthrogryposis Moore weaver type, congenital myotonic dystrophy, myasthenic syndrome, congenital, 7B, presynaptic, autosomal recessive, intellectual disability, autosomal dominant 47, intellectual disability, autosomal dominant 48, spondyloepiphyseal dysplasia, sensorineural hearing loss, impaired intellectual development, and leber congenital amaurosis, myasthenic syndrome, congenital, 23, presynaptic, myasthenic syndrome, congenital, 24, presynaptic, myasthenic syndrome, congenital, 25, presynaptic, developmental and epileptic encephalopathy, 77, night blindness, congenital stationary, type1i, neuropathy, congenital hypomelinating, congenital axonal neuropathy with encephalopathy, developmental and epileptic encephalopathy, 73, PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome, isolated exencephaly, myasthenic syndrome, congenital, 22, intellectual developmental disorder with gastrointestinal difficulties and high pain threshold, intellectual developmental disorder with dysmorphic facies, seizures, and distal limb anomalies, 9q33.3q34.11 microdeletion syndrome, congenital labioscrotal agenesis-cerebellar malformation-corneal dystrophy-facial dysmorphism syndrome, early-onset progressive diffuse brain atrophy-microcephaly-muscle weakness-optic atrophy syndrome, SIN3A-related intellectual disability syndrome, childhood-onset motor and cognitive regression syndrome with extrapyramidal movement disorder, X-linked congenital stationary night blindness, neurodevelopmental disorder with progressive microcephaly, spasticity, and brain anomalies, FOXG1 disorder, alpha-actinopathy, TPM3-related myopathy, X-linked recessive mitochondrial myopathy, RYR1-related myopathy, TTN-related myopathy, TPM2-related myopathy, myopathy caused by variation in POMGNT1, central hypoventilation syndrome, congenital, 1, with or without Hirschsprung disease, segmental spinal dysgenesis, myopathy, myofibrillar, 13, with rimmed vacuoles, congenital neuronal ceroid lipofuscinosis 10

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

116 retrieved; paginated sample, class counts are floors:

59 uncertain significance, 24 conflicting classifications of pathogenicity, 14 benign, 6 likely benign, 5 likely pathogenic, 4 pathogenic, 2 benign/likely benign, 2 pathogenic/likely pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
1068778	NM_004727.3(SLC24A1):c.1963C>T (p.Arg655Ter)	SLC24A1	Pathogenic	criteria provided, multiple submitters, no conflicts
2980958	NM_004727.3(SLC24A1):c.2983C>T (p.Arg995Ter)	SLC24A1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
489397	NM_004727.3(SLC24A1):c.2401G>T (p.Glu801Ter)	SLC24A1	Pathogenic	no assertion criteria provided
489399	NM_004727.3(SLC24A1):c.3291_3294del (p.Val1099fs)	SLC24A1	Pathogenic	criteria provided, single submitter
560508	NM_004727.3(SLC24A1):c.754_755del (p.Met252fs)	SLC24A1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
560509	NM_004727.3(SLC24A1):c.95T>A (p.Leu32Ter)	SLC24A1	Pathogenic	criteria provided, single submitter
1333283	NM_004727.3(SLC24A1):c.2884-1G>C	SLC24A1	Likely pathogenic	criteria provided, multiple submitters, no conflicts
30373	NM_004727.3(SLC24A1):c.1613_1614del (p.Phe538fs)	SLC24A1	Likely pathogenic	criteria provided, single submitter
3764677	NM_004727.3(SLC24A1):c.909_913dup (p.Lys305fs)	SLC24A1	Likely pathogenic	criteria provided, single submitter
4077517	NM_004727.3(SLC24A1):c.1749G>A (p.Trp583Ter)	SLC24A1	Likely pathogenic	criteria provided, single submitter
4293250	NM_004727.3(SLC24A1):c.2015dup (p.Tyr672Ter)	SLC24A1	Likely pathogenic	criteria provided, single submitter
198521	NM_004727.3(SLC24A1):c.2778C>T (p.Pro926=)	SLC24A1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
198522	NM_004727.3(SLC24A1):c.2577C>T (p.Ser859=)	SLC24A1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
286514	NM_004727.3(SLC24A1):c.2764T>C (p.Trp922Arg)	SLC24A1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
287572	NM_004727.3(SLC24A1):c.1859C>T (p.Ala620Val)	SLC24A1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
316788	NM_004727.3(SLC24A1):c.134G>A (p.Arg45Gln)	SLC24A1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
316796	NM_004727.3(SLC24A1):c.1818C>T (p.Ile606=)	SLC24A1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
316798	NM_004727.3(SLC24A1):c.1945-14C>G	SLC24A1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
316801	NM_004727.3(SLC24A1):c.2183C>T (p.Ala728Val)	SLC24A1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
316802	NM_004727.3(SLC24A1):c.2349T>C (p.Gly783=)	SLC24A1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
316805	NM_004727.3(SLC24A1):c.2751C>T (p.Ile917=)	SLC24A1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
316808	NM_004727.3(SLC24A1):c.3021G>A (p.Val1007=)	SLC24A1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
713480	NM_004727.3(SLC24A1):c.1653C>T (p.Leu551=)	SLC24A1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
884500	NM_004727.3(SLC24A1):c.175C>G (p.Pro59Ala)	SLC24A1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
884502	NM_004727.3(SLC24A1):c.309A>G (p.Thr103=)	SLC24A1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
884563	NM_004727.3(SLC24A1):c.2166G>A (p.Ala722=)	SLC24A1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
884564	NM_004727.3(SLC24A1):c.2226C>T (p.Gly742=)	SLC24A1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
886463	NM_004727.3(SLC24A1):c.1542C>T (p.Ile514=)	SLC24A1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
886520	NM_004727.3(SLC24A1):c.2794-11C>A	SLC24A1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
886521	NM_004727.3(SLC24A1):c.2838G>A (p.Met946Ile)	SLC24A1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 3 · 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
SLC24A1	Strong	Autosomal recessive	congenital stationary night blindness 1D	3

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
SLC24A1	HGNC:10975	ENSG00000074621	O60721	Sodium/potassium/calcium exchanger 1	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
SLC24A1	Sodium/potassium/calcium exchanger 1	Calcium, potassium:sodium antiporter that transports 1 Ca(2+) and 1 K(+) in exchange for 4 Na(+).

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)
SLC24A1	Other/Unknown	no		K/Na/Ca-exchanger, SLC24A1, NaCa_Exmemb

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
endothelial cell	1
male germ line stem cell (sensu Vertebrata) in testis	1
sural nerve	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
SLC24A1	220	ubiquitous	marker	endothelial cell, sural nerve, male germ line stem cell (sensu Vertebrata) in testis

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
SLC24A1	1,076

Structural data

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

AlphaFold-only cohort genes (top 30 by pLDDT)

Symbol	UniProt	pLDDT
SLC24A1	O60721	55.56

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 12. 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
Defective SLC24A1 causes congenital stationary night blindness 1D (CSNB1D)	1	11420.0×	0.001	SLC24A1
The phototransduction cascade	1	1268.9×	0.003	SLC24A1
Sodium/Calcium exchangers	1	1038.2×	0.003	SLC24A1
Activation of the phototransduction cascade	1	951.7×	0.003	SLC24A1
Visual phototransduction	1	259.6×	0.009	SLC24A1
SLC transporter disorders	1	203.9×	0.010	SLC24A1
Disorders of transmembrane transporters	1	139.3×	0.012	SLC24A1
R-HSA-425393	1	129.8×	0.012	SLC24A1
Sensory Perception	1	95.2×	0.014	SLC24A1
SLC-mediated transmembrane transport	1	59.2×	0.020	SLC24A1
Transport of small molecules	1	25.1×	0.043	SLC24A1
Disease	1	13.1×	0.076	SLC24A1

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
response to light intensity	1	2106.5×	0.005	SLC24A1
long-term synaptic depression	1	887.0×	0.006	SLC24A1
calcium ion import across plasma membrane	1	543.6×	0.007	SLC24A1
long-term synaptic potentiation	1	280.9×	0.008	SLC24A1
calcium ion transmembrane transport	1	210.7×	0.008	SLC24A1
sodium ion transmembrane transport	1	203.0×	0.008	SLC24A1
calcium ion transport	1	181.2×	0.008	SLC24A1
monoatomic ion transport	1	156.0×	0.008	SLC24A1
intracellular calcium ion homeostasis	1	145.3×	0.008	SLC24A1
potassium ion transmembrane transport	1	135.9×	0.008	SLC24A1
visual perception	1	79.5×	0.013	SLC24A1

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
SLC24A1	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	SLC24A1

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)
SLC24A1	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.