congenital stationary night blindness 1F

Summary

congenital stationary night blindness 1F (MONDO:0014026) is a disease caused by LRIT3 (GenCC Strong), with 1 cohort gene.

At a glance

• Causal gene: LRIT3 (GenCC Strong)
• Cohort genes: 1
• ClinVar variants: 64

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	congenital stationary night blindness 1F
Mondo ID	MONDO:0014026
OMIM	615058
DOID	DOID:0110864
UMLS	C3554399
MedGen	767313
GARD	0015899
Is cancer (heuristic)	no

Also known as: congenital stationary night blindness caused by mutation in LRIT3 · congenital stationary night blindness type 1F · CSNB1F · LRIT3 congenital stationary night blindness · night blindness, congenital stationary (complete), 1F, autosomal recessive · night blindness, congenital stationary, type 1F

Data availability: 64 ClinVar variants · 4 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by body system or component › nervous system disorder › perceptual disorders › vision disorder › blindness (disorder) › night blindness › congenital stationary night blindness › congenital stationary night blindness 1F

Related subtypes (13): congenital stationary night blindness autosomal dominant 2, congenital stationary night blindness 1B, cone-rod synaptic disorder, congenital nonprogressive, congenital stationary night blindness autosomal dominant 3, congenital stationary night blindness autosomal dominant 1, congenital stationary night blindness 1C, congenital stationary night blindness 1D, congenital stationary night blindness 1E, congenital stationary night blindness 1G, congenital stationary night blindness 1H, Oguchi disease, night blindness, congenital stationary, type1i, X-linked congenital stationary night blindness

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

64 retrieved; paginated sample, class counts are floors:

34 uncertain significance, 13 conflicting classifications of pathogenicity, 8 benign, 5 likely benign, 3 pathogenic, 1 benign/likely benign

ClinVar	Variant (HGVS)	Gene	Classification	Review
1323248	NM_198506.5(LRIT3):c.696C>A (p.Cys232Ter)	LRIT3	Pathogenic	criteria provided, single submitter
39440	NM_198506.5(LRIT3):c.1151C>G (p.Ser384Ter)	LRIT3	Pathogenic	no assertion criteria provided
39441	NM_198506.5(LRIT3):c.1538_1539del (p.Ser513fs)	LRIT3	Pathogenic	no assertion criteria provided
195436	NM_198506.5(LRIT3):c.379G>T (p.Asp127Tyr)	LRIT3	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
347180	NM_198506.5(LRIT3):c.30C>A (p.Val10=)	LRIT3	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
347185	NM_198506.5(LRIT3):c.966C>T (p.Asp322=)	LRIT3	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
347186	NM_198506.5(LRIT3):c.1029G>T (p.Val343=)	LRIT3	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
347193	NM_198506.5(LRIT3):c.1445A>C (p.Glu482Ala)	LRIT3	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
347199	NM_198506.5(LRIT3):c.1752_1754del (p.Leu585del)	LRIT3	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
684455	NM_198506.5(LRIT3):c.733C>T (p.Arg245Trp)	LRIT3	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
737160	NM_198506.5(LRIT3):c.222G>A (p.Ala74=)	LRIT3	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
745626	NM_198506.5(LRIT3):c.1644G>A (p.Gly548=)	LRIT3	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
899849	NM_198506.5(LRIT3):c.1677G>A (p.Val559=)	LRIT3	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
900732	NM_198506.5(LRIT3):c.99T>C (p.Asn33=)	LRIT3	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
902556	NM_198506.5(LRIT3):c.327G>A (p.Glu109=)	LRIT3	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
903409	NM_198506.5(LRIT3):c.492A>G (p.Arg164=)	LRIT3	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1046719	NM_198506.5(LRIT3):c.342del (p.Asn115fs)	LRIT3	Uncertain significance	criteria provided, multiple submitters, no conflicts
347183	NM_198506.5(LRIT3):c.660C>T (p.Asp220=)	LRIT3	Uncertain significance	criteria provided, single submitter
347184	NM_198506.5(LRIT3):c.848C>T (p.Pro283Leu)	LRIT3	Uncertain significance	criteria provided, single submitter
347187	NM_198506.5(LRIT3):c.1046C>T (p.Thr349Ile)	LRIT3	Uncertain significance	criteria provided, multiple submitters, no conflicts
347188	NM_198506.5(LRIT3):c.1157T>G (p.Leu386Arg)	LRIT3	Uncertain significance	criteria provided, multiple submitters, no conflicts
347189	NM_198506.5(LRIT3):c.1238C>T (p.Ser413Phe)	LRIT3	Uncertain significance	criteria provided, multiple submitters, no conflicts
347190	NM_198506.5(LRIT3):c.1307T>C (p.Met436Thr)	LRIT3	Uncertain significance	criteria provided, multiple submitters, no conflicts
347191	NM_198506.5(LRIT3):c.1314C>A (p.Asn438Lys)	LRIT3	Uncertain significance	criteria provided, single submitter
347209	NM_198506.5(LRIT3):c.*1108A>G	LRIT3	Uncertain significance	criteria provided, single submitter
347211	NM_198506.5(LRIT3):c.*1157T>C	LRIT3	Uncertain significance	criteria provided, single submitter
347212	NM_198506.5(LRIT3):c.*1191T>C	LRIT3	Uncertain significance	criteria provided, single submitter
347215	NM_198506.5(LRIT3):c.*1322T>C	LRIT3	Uncertain significance	criteria provided, single submitter
347217	NM_198506.5(LRIT3):c.*1516C>A	LRIT3	Uncertain significance	criteria provided, single submitter
39438	NM_198506.5(LRIT3):c.983G>A (p.Cys328Tyr)	LRIT3	Uncertain significance	criteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 5 · 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
LRIT3	Strong	Autosomal recessive	congenital stationary night blindness 1F	5

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
LRIT3	Orphanet:714079	Complete congenital stationary night blindness, Schubert-Bornschein 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
LRIT3	HGNC:24783	ENSG00000183423	Q3SXY7	Leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 3	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
LRIT3	Leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 3	Plays a role in the synapse formation and synaptic transmission between cone photoreceptor cells and retinal bipolar cells.

Protein-family classification

Druggable: 1 · Difficult: 0 · Unknown: 0 · Druggable fraction: 1.0

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
Antibody/Immunoglobulin	1	29.2×	0.034

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
LRIT3	Antibody/Immunoglobulin	yes		Leu-rich_rpt, Leu-rich_rpt_typical-subtyp, Ig_sub2

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
cerebellar hemisphere	1
male germ line stem cell (sensu Vertebrata) in testis	1
superior frontal gyrus	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
LRIT3	114	tissue_specific	marker	male germ line stem cell (sensu Vertebrata) in testis, superior frontal gyrus, cerebellar hemisphere

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
LRIT3	1,992

Structural data

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

AlphaFold-only cohort genes (top 30 by pLDDT)

Symbol	UniProt	pLDDT
LRIT3	Q3SXY7	70.06

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
synapse assembly involved in innervation	1	8426.0×	8e-04	LRIT3
regulation of fibroblast growth factor receptor signaling pathway	1	2407.4×	0.001	LRIT3
synaptic signaling	1	1532.0×	0.002	LRIT3
response to light stimulus	1	887.0×	0.002	LRIT3
intracellular protein localization	1	104.7×	0.013	LRIT3
gene expression	1	79.9×	0.013	LRIT3
visual perception	1	79.5×	0.013	LRIT3

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
LRIT3	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	1	LRIT3
E	Difficult family or no structure, no drug	0

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)
LRIT3	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.