LRIT3 leucine rich repeat, Ig-like and transmembrane domains 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: LRIT3provided by HGNC
Official Full Name: leucine rich repeat, Ig-like and transmembrane domains 3provided by HGNC
Primary source: HGNC:HGNC:24783
See related: Ensembl:ENSG00000183423 MIM:615004; AllianceGenome:HGNC:24783
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: CSNB1F; FIGLER4
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 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. [provided by RefSeq, May 2013]
Expression: Low expression observed in reference dataset See more
Orthologs: mouse all
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Genomic context

Location:: 4q25

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (109848107..109872315)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (113150166..113174389)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (110769263..110793471)

Chromosome 4 - NC_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
Title: Mutation screening of the LRIT3, CABP4, and GPR179 genes in Chinese patients with Schubert-Bornschein congenital stationary night blindness.
LRIT3 is likely involved in coordination of the transsynaptic communication between cones and ON-BCs during synapse formation and
Title: LRIT3 Differentially Affects Connectivity and Synaptic Transmission of Cones to ON- and OFF-Bipolar Cells.
The exact role of this LRR protein in cCSNB remains to be elucidated.
Title: Whole-exome sequencing identifies LRIT3 mutations as a cause of autosomal-recessive complete congenital stationary night blindness.
Observational study of gene-disease association. (HuGE Navigator)
Title: A systematic gene-based screen of chr4q22-q32 identifies association of a novel susceptibility gene, DKK2, with the quantitative trait of alcohol dependence symptom counts.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Congenital stationary night blindness 1F MedGen: C3554399 OMIM: 615058 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Process	Evidence Code	Pubs
involved_in gene expression	IEA Inferred from Electronic Annotation more info
involved_in protein localization	IEA Inferred from Electronic Annotation more info
involved_in regulation of fibroblast growth factor receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in response to light stimulus	IEA Inferred from Electronic Annotation more info
involved_in synapse assembly involved in innervation	IEA Inferred from Electronic Annotation more info
involved_in synaptic signaling	IEA Inferred from Electronic Annotation more info
involved_in visual perception	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cell tip	IEA Inferred from Electronic Annotation more info
located_in dendrite	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
located_in perikaryon	IEA Inferred from Electronic Annotation more info
located_in synapse	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 3

Names: fibronectin type III, immunoglobulin and leucine rich repeat domains 4; leucine-rich repeat, immunoglobulin-like and transmembrane domains 3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_033249.1 RefSeqGene

Range

4924..29132

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_198506.5 → NP_940908.3 leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 3 precursor

See identical proteins and their annotated locations for NP_940908.3

Status: REVIEWED

Source sequence(s)

AC005509, AC126283, BC104037, BM665581, DT932743, JQ354981

Consensus CDS

CCDS3688.3

UniProtKB/Swiss-Prot

C9J1C2, Q3SXY7, Q6ZTG1

Related

ENSP00000469759.1, ENST00000594814.6

Conserved Domains (6) summary

smart00060
Location:486 → 550

FN3; Fibronectin type 3 domain

smart00410
Location:267 → 345

IG_like; Immunoglobulin like

sd00031
Location:59 → 82

LRR_1; leucine-rich repeat [structural motif]

pfam12799
Location:131 → 170

LRR_4; Leucine Rich repeats (2 copies)

pfam13855
Location:105 → 165

LRR_8; Leucine rich repeat

cl11960
Location:267 → 345

Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000004.12 Reference GRCh38.p14 Primary Assembly

Range

109848107..109872315

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017008168.2 → XP_016863657.1 leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 3 isoform X2
XM_017008167.2 → XP_016863656.1 leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 3 isoform X1

UniProtKB/TrEMBL

A0A0A0MR64

Related

ENSP00000328222.3, ENST00000327908.3

Conserved Domains (3) summary

smart00060
Location:303 → 367

FN3; Fibronectin type 3 domain

smart00410
Location:84 → 162

IG_like; Immunoglobulin like

cl11960
Location:84 → 162

Ig; Immunoglobulin domain

Alternate T2T-CHM13v2.0

Genomic

NC_060928.1 Alternate T2T-CHM13v2.0

Range

113150166..113174389

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054349949.1 → XP_054205924.1 leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 3 isoform X2
XM_054349948.1 → XP_054205923.1 leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 3 isoform X1