LRIT3
geneOn this page
Also known as FLJ44691FIGLER4CSNB1F
Summary
LRIT3 (leucine rich repeat, Ig-like and transmembrane domains 3, HGNC:24783) is a protein-coding gene on chromosome 4q25, encoding Leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 3 (Q3SXY7). Plays a role in the synapse formation and synaptic transmission between cone photoreceptor cells and retinal bipolar cells.
This gene encodes a protein that has a fibronectin type III domain and a C-terminal transmembrane domain, as well as a leucine-rich repeat domain and immunoglobulin-like domain near the N-terminus. The encoded protein may regulate fibroblast growth factor receptors and affect the modification of these receptors, which are glycosylated differently in the Golgi and endoplasmic reticulum. Mutations in this gene are associated with congenital stationary night blindness, type 1F.
Source: NCBI Gene 345193 — RefSeq curated summary.
At a glance
- Gene–disease (curated): congenital stationary night blindness 1F (Strong, GenCC) — +1 more curated relationship
- Clinical variants (ClinVar): 463 total — 4 pathogenic, 1 likely-pathogenic
- Phenotypes (HPO): 9
- MANE Select transcript:
NM_198506
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:24783 |
| Approved symbol | LRIT3 |
| Name | leucine rich repeat, Ig-like and transmembrane domains 3 |
| Location | 4q25 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | FLJ44691, FIGLER4, CSNB1F |
| Ensembl gene | ENSG00000183423 |
| Ensembl biotype | protein_coding |
| OMIM | 615004 |
| Entrez | 345193 |
Gene structure
Transcript identifiers
Ensembl transcripts: 3 — 3 protein_coding
ENST00000327908, ENST00000594814, ENST00000876618
RefSeq mRNA: 1 — MANE Select: NM_198506
NM_198506
CCDS: CCDS3688
Canonical transcript exons
ENST00000594814 — 4 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001310990 | 109867641 | 109867946 |
| ENSE00001576743 | 109869645 | 109872315 |
| ENSE00003166914 | 109848107 | 109848317 |
| ENSE00003180982 | 109851504 | 109851976 |
Expression profiles
Bgee: expression breadth ubiquitous, 114 present calls, max score 78.85.
FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0188 / max 18.5591, expressed in 4 samples.
FANTOM5 promoters (1 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 49250 | 0.0188 | 4 |
Top tissues by expression
128 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 78.85 | gold quality |
| superior frontal gyrus | UBERON:0002661 | 55.92 | gold quality |
| cerebellar hemisphere | UBERON:0002245 | 55.91 | gold quality |
| cerebellar cortex | UBERON:0002129 | 55.89 | gold quality |
| cerebellum | UBERON:0002037 | 55.76 | gold quality |
| right hemisphere of cerebellum | UBERON:0014890 | 55.58 | gold quality |
| primary visual cortex | UBERON:0002436 | 54.30 | gold quality |
| Brodmann (1909) area 9 | UBERON:0013540 | 54.29 | gold quality |
| cortex of kidney | UBERON:0001225 | 54.28 | gold quality |
| metanephros cortex | UBERON:0010533 | 54.23 | gold quality |
| tibial nerve | UBERON:0001323 | 53.13 | gold quality |
| granulocyte | CL:0000094 | 53.04 | gold quality |
| right frontal lobe | UBERON:0002810 | 52.73 | gold quality |
| skeletal muscle tissue | UBERON:0001134 | 52.64 | gold quality |
| dorsolateral prefrontal cortex | UBERON:0009834 | 52.11 | gold quality |
| skin of leg | UBERON:0001511 | 51.32 | gold quality |
| right coronary artery | UBERON:0001625 | 51.25 | gold quality |
| zone of skin | UBERON:0000014 | 51.07 | gold quality |
| skin of abdomen | UBERON:0001416 | 50.64 | gold quality |
| right lobe of liver | UBERON:0001114 | 50.48 | silver quality |
| adult mammalian kidney | UBERON:0000082 | 50.47 | gold quality |
| endometrium | UBERON:0001295 | 50.42 | silver quality |
| right uterine tube | UBERON:0001302 | 50.38 | gold quality |
| nucleus accumbens | UBERON:0001882 | 50.30 | gold quality |
| cerebral cortex | UBERON:0000956 | 50.09 | gold quality |
| kidney | UBERON:0002113 | 50.05 | gold quality |
| muscle tissue | UBERON:0002385 | 49.85 | silver quality |
| frontal cortex | UBERON:0001870 | 49.77 | gold quality |
| popliteal artery | UBERON:0002250 | 49.77 | gold quality |
| tibial artery | UBERON:0007610 | 49.77 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | yes | 4.43 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
71 targeting LRIT3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):
| miRNA | Max score | Avg score | miRNA target_count |
|---|---|---|---|
| HSA-MIR-4476 | 100.00 | 68.18 | 2030 |
| HSA-MIR-6876-5P | 100.00 | 67.68 | 2126 |
| HSA-MIR-4533 | 100.00 | 69.48 | 2758 |
| HSA-MIR-1252-5P | 100.00 | 69.80 | 2774 |
| HSA-MIR-3613-3P | 100.00 | 76.36 | 7965 |
| HSA-MIR-4282 | 99.99 | 75.36 | 6408 |
| HSA-MIR-186-5P | 99.99 | 70.83 | 3707 |
| HSA-MIR-12136 | 99.98 | 72.81 | 5713 |
| HSA-MIR-3692-3P | 99.98 | 70.27 | 2139 |
| HSA-MIR-548P | 99.98 | 72.25 | 3784 |
| HSA-MIR-548AT-5P | 99.96 | 70.83 | 2666 |
| HSA-MIR-548AJ-3P | 99.96 | 73.38 | 5345 |
| HSA-MIR-548X-3P | 99.96 | 73.38 | 5345 |
| HSA-MIR-3658 | 99.96 | 73.87 | 4379 |
| HSA-MIR-1468-3P | 99.96 | 72.74 | 3797 |
| HSA-MIR-545-3P | 99.95 | 70.74 | 2783 |
| HSA-MIR-548J-3P | 99.94 | 72.61 | 4881 |
| HSA-MIR-552-5P | 99.93 | 68.56 | 1583 |
| HSA-MIR-548AE-3P | 99.93 | 72.66 | 4867 |
| HSA-MIR-548AH-3P | 99.93 | 72.54 | 4872 |
| HSA-MIR-548AM-3P | 99.93 | 72.54 | 4872 |
| HSA-MIR-548AQ-3P | 99.93 | 72.66 | 4867 |
| HSA-MIR-6809-3P | 99.91 | 71.45 | 3814 |
| HSA-MIR-498-3P | 99.91 | 71.27 | 1114 |
| HSA-MIR-4753-3P | 99.90 | 71.03 | 3786 |
| HSA-MIR-548E-5P | 99.89 | 72.73 | 4486 |
| HSA-MIR-130B-5P | 99.83 | 68.50 | 1888 |
| HSA-MIR-4799-5P | 99.82 | 70.60 | 2663 |
| HSA-MIR-204-5P | 99.79 | 71.62 | 2439 |
| HSA-MIR-211-5P | 99.79 | 71.65 | 2440 |
Literature-anchored findings (GeneRIF, showing 3)
- The exact role of this LRR protein in cCSNB remains to be elucidated. (PMID:23246293)
- In this study, a novel compound heterozygous mutation, c.[1A>G]; [608G>T] (p.[0?]; p.[W203L]), was identified in the LRIT3 gene of a proband. No mutations were identified in the CABP4 or GPR179 gene. (PMID:27428514)
- LRIT3 is likely involved in coordination of the transsynaptic communication between cones and ON-BCs during synapse formation and (PMID:28334377)
Cross-species orthologs
8 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | lrit3a | ENSDARG00000055463 |
| danio_rerio | lrit3b | ENSDARG00000057054 |
| mus_musculus | Lrit3 | ENSMUSG00000093865 |
| rattus_norvegicus | Lrit3 | ENSRNOG00000061097 |
| drosophila_melanogaster | Con | FBGN0005775 |
| drosophila_melanogaster | kek3 | FBGN0028370 |
| caenorhabditis_elegans | lron-9 | WBGENE00011971 |
| caenorhabditis_elegans | WBGENE00020649 |
Paralogs (22): CHADL (ENSG00000100399), LGI1 (ENSG00000108231), LGR6 (ENSG00000133067), CHAD (ENSG00000136457), LRIG3 (ENSG00000139263), LGR5 (ENSG00000139292), LRIG1 (ENSG00000144749), LRRTM2 (ENSG00000146006), LRIT1 (ENSG00000148602), LGI2 (ENSG00000153012), LGI4 (ENSG00000153902), LRRC52 (ENSG00000162763), ELFN2 (ENSG00000166897), LGI3 (ENSG00000168481), LRG1 (ENSG00000171236), CPN2 (ENSG00000178772), LRRC26 (ENSG00000184709), LRIG2 (ENSG00000198799), LGR4 (ENSG00000205213), ELFN1 (ENSG00000225968), LRRC24 (ENSG00000254402), TRIL (ENSG00000255690)
Protein
Protein identifiers
Leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 3 — Q3SXY7 (reviewed: Q3SXY7)
All UniProt accessions (2): A0A0A0MR64, Q3SXY7
UniProt curated annotations — full annotation on UniProt →
Function. Plays a role in the synapse formation and synaptic transmission between cone photoreceptor cells and retinal bipolar cells. Required for normal transmission of a light-evoked stimulus from the cone photoreceptor cells to the ON-bipolar cells and ON-ganglion cells in the inner retina. Required in retinal ON-bipolar cells for normal localization of the cation channel TRPM1 at dendrite tips. Seems to play a specific role in synaptic contacts made by ON-bipolar cells with cone photoreceptor pedicles. May also have a role in cone synapse formation. Might facilitate FGFR1 exit from the endoplasmic reticulum to the Golgi. Could be a regulator of the FGFRs.
Subcellular location. Cell projection. Dendrite. Perikaryon. Endoplasmic reticulum membrane.
Tissue specificity. Detected in the outer plexiform layer (OPL) of the retina where it localizes to ON-bipolar cells (at protein level).
Post-translational modifications. Glycosylated.
Disease relevance. Night blindness, congenital stationary, 1F (CSNB1F) [MIM:615058] An autosomal recessive form of congenital stationary night blindness, a non-progressive retinal disorder characterized by impaired night vision, often associated with nystagmus and myopia. The disease is caused by variants affecting the gene represented in this entry.
Isoforms (2)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q3SXY7-1 | 1 | yes |
| Q3SXY7-2 | 2 |
RefSeq proteins (1): NP_940908* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR001611 | Leu-rich_rpt | Repeat |
| IPR003591 | Leu-rich_rpt_typical-subtyp | Repeat |
| IPR003598 | Ig_sub2 | Domain |
| IPR003599 | Ig_sub | Domain |
| IPR003961 | FN3_dom | Domain |
| IPR007110 | Ig-like_dom | Domain |
| IPR013783 | Ig-like_fold | Homologous_superfamily |
| IPR032675 | LRR_dom_sf | Homologous_superfamily |
| IPR036116 | FN3_sf | Homologous_superfamily |
| IPR036179 | Ig-like_dom_sf | Homologous_superfamily |
| IPR050467 | LRFN | Family |
Pfam: PF13855, PF13927
UniProt features (29 total): sequence variant 8, repeat 5, domain 3, splice variant 2, topological domain 2, signal peptide 1, chain 1, region of interest 1, compositionally biased region 1, glycosylation site 1, disulfide bond 1, mutagenesis site 1, sequence conflict 1, transmembrane region 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q3SXY7-F1 | 70.06 | 0.35 |
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Disulfide bonds (1): 275–328
Glycosylation sites (1): 296
Mutagenesis-validated functional residues (1):
| Position | Phenotype |
|---|---|
| 53 | no effect on lrit3 function. |
Function
Pathways and Gene Ontology
Reactome pathways
0 pathways
MSigDB gene sets: 79 (showing top):
chr4q25, GOBP_REGULATION_OF_CELLULAR_RESPONSE_TO_GROWTH_FACTOR_STIMULUS, GOBP_SYNAPSE_ASSEMBLY, GOBP_CELL_CELL_SIGNALING, GOBP_CELL_JUNCTION_ORGANIZATION, GOBP_SENSORY_PERCEPTION_OF_LIGHT_STIMULUS, GOBP_RESPONSE_TO_FIBROBLAST_GROWTH_FACTOR, GOBP_REGULATION_OF_FIBROBLAST_GROWTH_FACTOR_RECEPTOR_SIGNALING_PATHWAY, GOBP_NERVE_DEVELOPMENT, GOBP_RESPONSE_TO_RADIATION, GOBP_SYNAPTIC_SIGNALING, GOBP_RESPONSE_TO_ABIOTIC_STIMULUS, GOBP_RESPONSE_TO_GROWTH_FACTOR, GOBP_SENSORY_PERCEPTION, GOBP_FIBROBLAST_GROWTH_FACTOR_RECEPTOR_SIGNALING_PATHWAY
GO Biological Process (7): visual perception (GO:0007601), intracellular protein localization (GO:0008104), response to light stimulus (GO:0009416), gene expression (GO:0010467), regulation of fibroblast growth factor receptor signaling pathway (GO:0040036), synapse assembly involved in innervation (GO:0060386), synaptic signaling (GO:0099536)
GO Molecular Function (1): protein binding (GO:0005515)
GO Cellular Component (8): endoplasmic reticulum membrane (GO:0005789), dendrite (GO:0030425), perikaryon (GO:0043204), synapse (GO:0045202), cell tip (GO:0051286), endoplasmic reticulum (GO:0005783), membrane (GO:0016020), cell projection (GO:0042995)
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| cellular anatomical structure | 3 |
| sensory perception of light stimulus | 1 |
| macromolecule localization | 1 |
| response to radiation | 1 |
| macromolecule biosynthetic process | 1 |
| fibroblast growth factor receptor signaling pathway | 1 |
| regulation of signal transduction | 1 |
| regulation of cellular response to growth factor stimulus | 1 |
| synapse assembly | 1 |
| innervation | 1 |
| cell-cell signaling | 1 |
| synapse | 1 |
| binding | 1 |
| organelle membrane | 1 |
| nuclear outer membrane-endoplasmic reticulum membrane network | 1 |
| endoplasmic reticulum subcompartment | 1 |
| neuron projection | 1 |
| dendritic tree | 1 |
| neuronal cell body | 1 |
| cell junction | 1 |
| cell pole | 1 |
| cytoplasm | 1 |
| endomembrane system | 1 |
| intracellular membrane-bounded organelle | 1 |
Protein interactions and networks
STRING
1984 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| LRIT3 | TRPM1 | Q7Z4N2 | 853 |
| LRIT3 | GPR179 | Q6PRD1 | 774 |
| LRIT3 | CACNA1F | O60840 | 772 |
| LRIT3 | CABP4 | P57796 | 756 |
| LRIT3 | GRM6 | O15303 | 723 |
| LRIT3 | SLC24A1 | O60721 | 641 |
| LRIT3 | GNAT1 | P11488 | 604 |
| LRIT3 | NYX | Q9GZU5 | 594 |
| LRIT3 | CACNA2D4 | Q7Z3S7 | 593 |
| LRIT3 | RGS11 | O94810 | 582 |
| LRIT3 | RGS7 | P49802 | 576 |
| LRIT3 | CACNA1S | Q13698 | 562 |
| LRIT3 | PDE6B | P35913 | 527 |
| LRIT3 | GNB5 | O14775 | 523 |
| LRIT3 | EGFLAM | Q63HQ2 | 517 |
IntAct
3 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| LRIT3 | TRAF2 | psi-mi:“MI:0914”(association) | 0.350 |
| rep | DHFR | psi-mi:“MI:2364”(proximity) | 0.270 |
BioGRID (5): LRIT3 (Proximity Label-MS), BIRC2 (Affinity Capture-MS), TRAF2 (Affinity Capture-MS), NCDN (Affinity Capture-MS), GPR107 (Affinity Capture-MS)
ESM2 similar proteins: A0N0X6, A4IIW9, B0BLW3, B1H134, B1H234, B4F7C5, D3ZAL8, D3ZTV3, D4A7P2, E5DHB5, F1NUK7, F7D3V9, O43155, O43300, O94898, P58681, Q32Q07, Q3SXY7, Q3URE9, Q504C1, Q50L44, Q52KR2, Q5R482, Q5R6T0, Q5RDJ4, Q61809, Q66HV9, Q6RKD8, Q6UXK5, Q70AK3, Q7L985, Q80XG9, Q80ZD7, Q80ZD8, Q80ZD9, Q86VH4, Q86VH5, Q8BGA3, Q8BGT1, Q8BLU0
Diamond homologs: A3KNN3, A6H789, A6H793, A6NJW4, A8WHP9, E7FE13, F1MLX5, G5EFX6, O02678, O02833, O35367, O46378, O46379, O46542, O60938, O62702, O75093, O75094, O88279, O88280, O94813, P07359, P07585, P21793, P24014, P28654, P28675, P35858, P35859, P51884, P51885, P51886, P51888, P51890, P58874, P59034, P59035, P70186, P70389, P83286
SIGNOR signaling
0 interactions.
Disease & clinical
Clinical variants and AI predictions
ClinVar
463 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 4 |
| Likely pathogenic | 1 |
| Uncertain significance | 270 |
| Likely benign | 136 |
| Benign | 26 |
Top pathogenic / likely-pathogenic (5)
| Variant ID | HGVS | Classification |
|---|---|---|
| 1323248 | NM_198506.5(LRIT3):c.696C>A (p.Cys232Ter) | Pathogenic |
| 1803094 | NM_198506.5(LRIT3):c.59_61del (p.Leu20del) | Pathogenic |
| 39440 | NM_198506.5(LRIT3):c.1151C>G (p.Ser384Ter) | Pathogenic |
| 39441 | NM_198506.5(LRIT3):c.1538_1539del (p.Ser513fs) | Pathogenic |
| 3381802 | NM_198506.5(LRIT3):c.269dup (p.Tyr90Ter) | Likely pathogenic |
SpliceAI
631 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 4:109848314:CAAG:C | donor_loss | 1.0000 |
| 4:109848316:AGGTA:A | donor_loss | 1.0000 |
| 4:109848317:GGTA:G | donor_loss | 1.0000 |
| 4:109848318:G:T | donor_loss | 1.0000 |
| 4:109848319:T:A | donor_loss | 1.0000 |
| 4:109851502:AGGTT:A | acceptor_gain | 1.0000 |
| 4:109851503:GGTTG:G | acceptor_gain | 1.0000 |
| 4:109869643:A:AG | acceptor_gain | 1.0000 |
| 4:109869644:G:GG | acceptor_gain | 1.0000 |
| 4:109869644:GTA:G | acceptor_gain | 1.0000 |
| 4:109851498:CACTA:C | acceptor_loss | 0.9900 |
| 4:109851499:ACTAG:A | acceptor_gain | 0.9900 |
| 4:109851500:CTAGG:C | acceptor_loss | 0.9900 |
| 4:109851501:TA:T | acceptor_loss | 0.9900 |
| 4:109851502:A:AC | acceptor_loss | 0.9900 |
| 4:109851503:G:GT | acceptor_loss | 0.9900 |
| 4:109851503:GGTT:G | acceptor_gain | 0.9900 |
| 4:109851974:TTGG:T | donor_loss | 0.9900 |
| 4:109851975:TGGTA:T | donor_loss | 0.9900 |
| 4:109851976:GGT:G | donor_loss | 0.9900 |
| 4:109851977:GT:G | donor_loss | 0.9900 |
| 4:109851978:T:TT | donor_loss | 0.9900 |
| 4:109867935:T:G | donor_gain | 0.9900 |
| 4:109867942:TACAG:T | donor_loss | 0.9900 |
| 4:109867945:AG:A | donor_loss | 0.9900 |
| 4:109867946:GG:G | donor_loss | 0.9900 |
| 4:109867948:T:G | donor_loss | 0.9900 |
| 4:109869639:TTCCA:T | acceptor_loss | 0.9900 |
| 4:109869641:CCAGT:C | acceptor_loss | 0.9900 |
| 4:109869643:A:AC | acceptor_loss | 0.9900 |
AlphaMissense
4414 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 4:109867910:T:A | W287R | 0.999 |
| 4:109867910:T:C | W287R | 0.999 |
| 4:109867912:G:C | W287C | 0.999 |
| 4:109867912:G:T | W287C | 0.999 |
| 4:109869731:T:A | C328S | 0.999 |
| 4:109869732:G:C | C328S | 0.999 |
| 4:109867874:T:A | C275S | 0.998 |
| 4:109867874:T:C | C275R | 0.998 |
| 4:109867875:G:C | C275S | 0.998 |
| 4:109869680:T:C | S311P | 0.998 |
| 4:109869731:T:C | C328R | 0.998 |
| 4:109869745:T:A | N332K | 0.998 |
| 4:109869745:T:G | N332K | 0.998 |
| 4:109867658:T:A | W203R | 0.997 |
| 4:109867658:T:C | W203R | 0.997 |
| 4:109867869:T:C | L273P | 0.997 |
| 4:109867875:G:A | C275Y | 0.996 |
| 4:109867876:T:G | C275W | 0.996 |
| 4:109869679:G:C | W310C | 0.996 |
| 4:109869679:G:T | W310C | 0.996 |
| 4:109869725:T:G | Y326D | 0.996 |
| 4:109869733:T:G | C328W | 0.996 |
| 4:109869737:G:C | A330P | 0.996 |
| 4:109869764:G:C | A339P | 0.995 |
| 4:109851716:T:C | L110S | 0.994 |
| 4:109867660:G:C | W203C | 0.994 |
| 4:109867660:G:T | W203C | 0.994 |
| 4:109867880:G:C | A277P | 0.994 |
| 4:109867911:G:C | W287S | 0.994 |
| 4:109851751:T:A | W122R | 0.993 |
dbSNP variants (sampled 300 via entrez): RS10000621 (4:109847511 T>A,C), RS1000120547 (4:109846552 C>G), RS1000313073 (4:109865298 C>A), RS1000367001 (4:109865700 T>C), RS1000380582 (4:109850579 C>A,T), RS1000442588 (4:109858591 T>A), RS1000551533 (4:109871014 A>G), RS1000616683 (4:109872300 A>G,T), RS1000622020 (4:109862824 A>G), RS10006613 (4:109849109 T>C), RS10007135 (4:109858653 G>A,C), RS1000911362 (4:109863253 A>G,T), RS10011256 (4:109871751 A>G), RS1001173448 (4:109853957 G>A,C,T), RS1001189464 (4:109857428 A>G)
Disease associations
OMIM: gene MIM:615004 | disease phenotypes: MIM:615058, MIM:248200
GenCC curated gene-disease
| Disease | Classification | Inheritance |
|---|---|---|
| congenital stationary night blindness 1F | Strong | Autosomal recessive |
| congenital stationary night blindness | Supportive | Autosomal dominant |
Mondo (5): congenital stationary night blindness 1F (MONDO:0014026), optic atrophy (MONDO:0003608), Stargardt disease (MONDO:0019353), inherited retinal dystrophy (MONDO:0019118), congenital stationary night blindness (MONDO:0016293)
Orphanet (3): Congenital stationary night blindness (Orphanet:215), Stargardt disease (Orphanet:827), OBSOLETE: Inherited retinal disorder (Orphanet:71862)
HPO phenotypes
9 total (10 of 9 shown, HPO-id order):
| HPO | Term |
|---|---|
| HP:0000007 | Autosomal recessive inheritance |
| HP:0000486 | Strabismus |
| HP:0000662 | Nyctalopia |
| HP:0007642 | Early-onset non-progressive night blindness |
| HP:0007663 | Reduced visual acuity |
| HP:0007984 | ERG: Reduced dark-adapted b-wave amplitude |
| HP:0011003 | High myopia |
| HP:0011463 | Childhood onset |
| HP:0011958 | Retinal perforation |
| HP:0000556 | Retinal dystrophy |
GWAS associations
0 associations (top):
MeSH disease descriptors (4)
| Descriptor | Name | Tree numbers |
|---|---|---|
| D009896 | Optic Atrophy | C10.292.700.225; C11.640.451 |
| D058499 | Retinal Dystrophies | C11.768.585.658 |
| D000080362 | Stargardt Disease | C11.270.872; C11.768.585.439.339; C16.320.290.724 |
| C536122 | Night blindness, congenital stationary (supp.) |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
6 total (human), top 6 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| aristolochic acid I | increases expression | 1 |
| bisphenol S | decreases methylation | 1 |
| Resveratrol | affects cotreatment, decreases expression | 1 |
| Benzo(a)pyrene | increases methylation | 1 |
| Copper | affects cotreatment, decreases expression | 1 |
| Tobacco Smoke Pollution | increases expression | 1 |
Clinical trials (associated diseases)
94 trials via MONDO — disease-level, not drug-specific.
| Trial | Phase | Status | Title |
|---|---|---|---|
| NCT03772665 | PHASE3 | COMPLETED | Safety and Efficacy of Emixustat in Stargardt Disease |
| NCT05244304 | PHASE3 | COMPLETED | Phase 3, Randomized, Placebo-Controlled Study of Tinlarebant to Explore Safety and Efficacy in Adolescent Stargardt Disease |
| NCT07419334 | PHASE3 | RECRUITING | Study of ALK-001 on the Progression of Stargardt Disease |
| NCT04224207 | PHASE3 | COMPLETED | Management of Retinitis Pigmentosa by Mesenchymal Stem Cells by Wharton’s Jelly Derived Mesenchymal Stem Cells |
| NCT07082855 | PHASE3 | NOT_YET_RECRUITING | A Multicenter, Randomized, Double-Blind, Controlled Clinical Study of Minocycline for the Treatment of Retinitis Pigmentosa |
| NCT02402660 | PHASE2 | ENROLLING_BY_INVITATION | Phase 2 Tolerability and Effects of ALK-001 on Stargardt Disease |
| NCT03033108 | PHASE2 | COMPLETED | Pharmacodynamic Study of Emixustat Hydrochloride in Subjects With Macular Atrophy Secondary to Stargardt Disease |
| NCT04239625 | PHASE2 | ACTIVE_NOT_RECRUITING | Open-Label Extension: Tolerability and Effects of ALK-001 on Stargardt Disease (TEASE) |
| NCT04489511 | PHASE2 | COMPLETED | Study of STG-001 in Subjects With Stargardt Disease |
| NCT05417126 | PHASE2 | COMPLETED | Safety and Effects of a Single Intravitreal Injection of vMCO-010 Optogenetic Therapy in Subjects With Stargardt Disease |
| NCT03763227 | PHASE2 | COMPLETED | Intravitreal Ranibizumab (Lucentis®) in the Treatment of Non-leaking Macular Cysts in Retinal Dystrophy |
| NCT04068207 | PHASE2 | COMPLETED | Minocycline Treatment in Retinitis Pigmentosa |
| NCT04945772 | PHASE2 | COMPLETED | Efficacy and Safety of MCO-010 Optogenetic Therapy in Adults With Retinitis Pigmentosa [RESTORE] |
| NCT01064505 | PHASE1 | COMPLETED | Safety Study of a Single IVT Injection of QPI-1007 in Chronic Optic Nerve Atrophy and Recent Onset NAION Patients |
| NCT05147701 | PHASE1 | RECRUITING | Safety of Cultured Allogeneic Adult Umbilical Cord Derived Mesenchymal Stem Cells for NAION |
| NCT02230228 | PHASE1 | COMPLETED | Phase 1 Safety Study of ALK-001 in Healthy Volunteers |
| NCT03772938 | PHASE1 | UNKNOWN | Stem Cells Therapy in Degenerative Diseases of the Retina |
| NCT06319872 | PHASE1 | RECRUITING | The Effects of Disulfiram (Antabuse®) on Visual Acuity in Patients With Retinal Degeneration |
| NCT07417566 | PHASE1 | RECRUITING | A Study of DC6001 Tablet in Healthy Chinese Adult Subjects |
| NCT07594236 | PHASE1 | RECRUITING | Phase 1 Study of C.001 in Retinal Degeneration |
| NCT05902962 | PHASE1 | COMPLETED | SAD of IVT VP-001 in PRPF31 Mutation-Associated Retinal Dystrophy Subjects |
| NCT06455826 | PHASE1 | COMPLETED | MAD of IVT VP-001 in PRPF31 Mutation-Associated Retinal Dystrophy Subjects (Wallaby) |
| NCT02435940 | Not specified | RECRUITING | Inherited Retinal Degenerative Disease Registry |
| NCT02909985 | Not specified | COMPLETED | Visual Activity Evoked by Infrared in Humans After Dark Adaptation |
| NCT02882477 | PHASE2/PHASE3 | UNKNOWN | Treatment of Wolfram Syndrome Type 2 With the Chelator Deferiprone and Incretin Based Therapy |
| NCT01834079 | PHASE1/PHASE2 | UNKNOWN | Study the Safety and Efficacy of Bone Marrow Derived Autologous Cells for the Treatment of Optic Nerve Disease |
| NCT04680143 | PHASE1/PHASE2 | COMPLETED | Systemic Erythropoietin Injection in Patients Having Optic Atrophy |
| NCT03011541 | Not specified | RECRUITING | Stem Cell Ophthalmology Treatment Study II |
| NCT04580979 | Not specified | COMPLETED | Natural History Study of FDXR Mutation-related Mitochondriopathy |
| NCT04594590 | Not specified | COMPLETED | Natural History Study of SLC25A46 Mutation-related Mitochondriopathy |
| NCT04723160 | Not specified | COMPLETED | Computer Aided Diagnosis of Multiple Eye Fundus Diseases From Color Fundus Photograph |
| NCT06390579 | Not specified | COMPLETED | Building Research With Artificial Intelligence in Neuro-Ophthalmology |
| NCT05956626 | PHASE2/PHASE3 | ACTIVE_NOT_RECRUITING | A Phase 2/3 Trial to Assess the Efficacy and Safety of OCU410ST for Stargardt Disease |
| NCT06388083 | PHASE2/PHASE3 | ACTIVE_NOT_RECRUITING | A Phase 2/3 Study to Evaluate the Efficacy and Safety of Tinlarebant in Subjects With Stargardt Disease |
| NCT04545736 | PHASE1/PHASE2 | RECRUITING | Oral Metformin for Treatment of ABCA4 Retinopathy |
| NCT05266014 | PHASE1/PHASE2 | COMPLETED | This is a Dose-finding Study Followed by 2-year Extension Study to Evaluate Safety and Tolerability of Tinlarebant in Adolescent Subjects With Stargardt Disease |
| NCT06300476 | PHASE1/PHASE2 | ACTIVE_NOT_RECRUITING | Safety and Efficacy of a Single Subretinal Injection of JWK006 Gene Therapy in Subjects With Stargardt Disease(STGD1) |
| NCT06467344 | PHASE1/PHASE2 | RECRUITING | Study to Evaluate ACDN-01 in ABCA4-related Stargardt Retinopathy (STELLAR) |
| NCT06942572 | PHASE1/PHASE2 | RECRUITING | A Phase 1/2, First-in-Human Dose Escalation/Expansion Study to Evaluate the Safety, Tolerability and Preliminary Efficacy of a Subretinal Injection of SB-007 in Subjects With Stargardt Disease (STGD1) |
| NCT07002398 | PHASE1/PHASE2 | RECRUITING | Safety and Preliminary Efficacy of VG801 in Patients With ABCA4 Mutation-associated Retinal Dystrophy (Stargardt Disease) |
Related Atlas pages
- Associated diseases: congenital stationary night blindness 1F, congenital stationary night blindness
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): congenital stationary night blindness, congenital stationary night blindness 1F, Stargardt disease