LRIT3 (leucine rich repeat, Ig-like and transmembrane domains 3)

Gene Gene information from NCBI Gene database.
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID 345193
Gene name Leucine rich repeat, Ig-like and transmembrane domains 3
Gene symbol LRIT3
Synonyms (NCBI Gene)
CSNB1FFIGLER4
Chromosome 4
Chromosome location 4q25
Summary 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
SNPs SNP information provided by dbSNP.
4
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Show/Hide all (4)
SNP ID Visualize variation Clinical significance Consequence
rs376610215 G>A Pathogenic Coding sequence variant, missense variant, genic downstream transcript variant
rs397509378 C>A,T Pathogenic Coding sequence variant, stop gained, synonymous variant, genic downstream transcript variant
rs397509379 C>G Pathogenic Coding sequence variant, stop gained, genic downstream transcript variant
rs397509380 CT>- Pathogenic Coding sequence variant, frameshift variant, genic downstream transcript variant
miRNA miRNA information provided by mirtarbase database.
65
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Show/Hide all (65)
miRTarBase ID miRNA Experiments Reference
MIRT443953 hsa-miR-4677-3p PAR-CLIP 22100165
MIRT443952 hsa-miR-143-3p PAR-CLIP 22100165
MIRT443950 hsa-miR-4770 PAR-CLIP 22100165
MIRT443951 hsa-miR-6088 PAR-CLIP 22100165
MIRT443949 hsa-miR-4708-5p PAR-CLIP 22100165
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
17
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Show/Hide all (17)
GO ID Ontology Definition Evidence Reference
GO:0005783 Component Endoplasmic reticulum IEA
GO:0005789 Component Endoplasmic reticulum membrane IEA
GO:0007601 Process Visual perception IEA
GO:0007601 Process Visual perception IEA
GO:0008104 Process Intracellular protein localization IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
MIM HGNC e!Ensembl
615004 24783 ENSG00000183423
Protein Protein information from UniProt database.
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q3SXY7
Protein name Leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 3
Protein function Plays a role in the synapse formation and synaptic transmission between cone photoreceptor cells and retinal bipolar cells (By similarity). Required for normal transmission of a light-evoked stimulus from the cone photoreceptor cells to the ON-b
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF13855 LRR_8 59 → 117 Leucine rich repeat Repeat
PF13855 LRR_8 129 → 181 Leucine rich repeat Repeat
PF13927 Ig_3 253 → 332 Domain
Tissue specificity TISSUE SPECIFICITY: Detected in the outer plexiform layer (OPL) of the retina where it localizes to ON-bipolar cells (at protein level). {ECO:0000269|PubMed:23246293}.
Sequence 
MHLFACLCIVLSFLEGVGCLCPSQCTCDYHGRNDGSGSRLVLCNDMDMNELPTNLPVDTV
KLRIEKTVIRRISAEAFYYLVELQYLWVTYNSVASIDPSSFYNLKQLHELRLDGNSLAAF
PWASLLDMPLLRTLDLHNNKITSVPNEALRYLKNLAYLDLSSNRLTTLPPDFLESWTHLV
STPSGVLDLSPSRIILGLQDNPWFCDCHISKMIELSKVVDPAIVLLDPLMTCSEPERLTG
ILFQRAELEHCLKPSVMTSATKIMSALGSNVLLRCDATGFPTPQITWTRSDSSPVNYTVI
QESPEEGVRWSIMSLTGISSKDAGDYKCKAKNLAGMSEAVVTVTVLGITTTPIPPDTSER
TGDHPEWDVQPGSGRSTSVSSASSYLWSSSFSPTSSFSASTLSPPSTASFSLSPFSSSTV
SSTTTLSTSISASTTMANKRSFQLHQGGKRNLKVAKNGSKLPPASTSKKEELALLDQTML
TETNAAIENLRVVSETKESVTLTWNMINTTHNSAVTVLYSKYGGKDLLLLNADSSKNQVT
IDGLEPGGQYMACVCPKGVPPQKDQCITFSTERVEGDDSQWSLLLVVTSTACVVILPLIC
FLLYKVCKLQCKSEPFWEDDLAKETYIQFETLFPRSQSVGELWTRSHRDDSEKLLLCSRS
SVESQVTFKSEGSRPEYYC
Sequence length 679
Interactions View interactions
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
12
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Show/Hide Causal Diseases (2)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Congenital stationary night blindness 1F Pathogenic rs2125900955, rs397509379, rs397509380 RCV001783612
RCV000032635
RCV000032636
★★★★★
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Stargardt disease Pathogenic rs2545576663 RCV002466764
★★★★★
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Show/Hide Unknown Diseases (10)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
CONGENITAL STATIONARY NIGHT BLINDNESS — GWAS catalog
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Congenital Stationary Night Blindness, Recessive Benign; Likely benign; Conflicting classifications of pathogenicity ClinVar
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
LRIT3-related disorder Conflicting classifications of pathogenicity; Likely benign; Benign ClinVar
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
NIGHT BLINDNESS, CONGENITAL STATIONARY — CTD, Disgenet
CTD, Disgenet
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Show/Hide Text Mining Associations (24)
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Cone-rod synaptic disorder, congenital nonprogressive Congenital stationary night blindness CTD_human_DG
★★★★★
★☆☆☆☆
Found in Text Mining only
Congenital stationary night blindness Congenital stationary night blindness Orphanet
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Disorder of eye Disorder Of Eye GENOMICS_ENGLAND_DG
★★★★★
★☆☆☆☆
Found in Text Mining only
Hypoplasia of optic disc Hypoplasia Of Optic Disc HPO_DG
★★★★★
★☆☆☆☆
Found in Text Mining only
Myopia Myopia HPO_DG
★★★★★
★☆☆☆☆
Found in Text Mining only
Night blindness congenital stationary Night blindness, congenital stationary Pubtator 23246293, 24715752 Associate
★★★★★
★☆☆☆☆
Found in Text Mining only
Night blindness, congenital stationary Night blindness BEFREE 23246293, 31578364
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Night blindness, congenital stationary Night blindness GENOMICS_ENGLAND_DG 23246293
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Night blindness, congenital stationary Night blindness ORPHANET_DG 23246293
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Night blindness, congenital stationary Night blindness HPO_DG
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations