LRIG2 leucine rich repeats and immunoglobulin like domains 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: LRIG2provided by HGNC
Official Full Name: leucine rich repeats and immunoglobulin like domains 2provided by HGNC
Primary source: HGNC:HGNC:20889
See related: Ensembl:ENSG00000198799 MIM:608869; AllianceGenome:HGNC:20889
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: LIG2; UFS2; LIG-2
Summary: This gene encodes a transmembrane protein containing leucine-rich repeats and immunoglobulin-like domains. The encoded protein promotes epidermal growth factor signalling, resulting in increased proliferation. Its expression in the cytoplasm of glioma cells is correlated with poor survival. Mutations in this gene can cause urofacial syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2015]
Expression: Ubiquitous expression in thyroid (RPKM 2.7), ovary (RPKM 2.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p13.2

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (113073198..113132260)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (113085129..113144193)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (113615820..113674882)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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?

A SINE-VNTR-Alu at the LRIG2 locus is associated with proximal and distal gene expression in CRISPR and population models.
Title: A SINE-VNTR-Alu at the LRIG2 locus is associated with proximal and distal gene expression in CRISPR and population models.
LRIG2 regulates cell proliferation, migration and apoptosis of osteosarcoma.
Title: LRIG2 regulates cell proliferation, migration and apoptosis of osteosarcoma.
Prognostic significance of LRIG2 and LRIG3 proteins in urothelial bladder carcinoma.
Title: Prognostic significance of LRIG2 and LRIG3 proteins in urothelial bladder carcinoma.
Targeting LRIG2 overcomes resistance to EGFR inhibitor in glioblastoma by modulating GAS6/AXL/SRC signaling.
Title: Targeting LRIG2 overcomes resistance to EGFR inhibitor in glioblastoma by modulating GAS6/AXL/SRC signaling.
LRIG proteins regulate lipid metabolism via BMP signaling and affect the risk of type 2 diabetes.
Title: LRIG proteins regulate lipid metabolism via BMP signaling and affect the risk of type 2 diabetes.
A SINE-VNTR-Alu in the LRIG2 Promoter Is Associated with Gene Expression at the Locus.
Title: A SINE-VNTR-Alu in the LRIG2 Promoter Is Associated with Gene Expression at the Locus.
epidermal LRIG2 excess is associated with activated EGFR/ERBB4-MAPK signaling and accelerated tumor progression.
Title: The transmembrane protein LRIG2 increases tumor progression in skin carcinogenesis.
Study discovered novel homozygous missense LRIG2 variants that were predicted to be pathogenic in 2 individuals with non-syndromic bladder outlet obstruction. These observations provide evidence that a peripheral neuropathy is central to the pathobiology of functional bladder outlet obstruction in urofacial syndrome and emphasize the importance of LRIG2 and heparanase 2 for nerve patterning in the urinary tract.
Title: Lrig2 and Hpse2, mutated in urofacial syndrome, pattern nerves in the urinary bladder.
LRIG2 was identified as the downstream target of miR-149-5p and its expression was regulated by LINC00461/miR-149-5p axis.
Title: Long non-coding RNA LINC00461/miR-149-5p/LRIG2 axis regulates hepatocellular carcinoma progression.
Study demonstrated that LRIG2 promoted the PDGFRBinduced proliferation of glioblastoma multiforme cells in vitro and in vivo through regulating the PDGFRB signalingmediated cell cycle progression.
Title: LRIG2 promotes the proliferation and cell cycle progression of glioblastoma cells in vitro and in vivo through enhancing PDGFRβ signaling.

Submit: New GeneRIF Correction See all GeneRIFs (19)

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
Urofacial syndrome 2 MedGen: C3554520 OMIM: 615112 GeneReviews: Urofacial Syndrome	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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Markers

SHGC-106802 (e-PCR)
- UniSTS:170018

A008L45 (e-PCR)
- UniSTS:19779

SHGC-75336 (e-PCR)
- UniSTS:6006

LRIG2__6423 (e-PCR)
- UniSTS:464046

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables signaling receptor binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in innervation	IEA Inferred from Electronic Annotation more info
involved_in membrane protein ectodomain proteolysis	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of axon regeneration	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of membrane protein ectodomain proteolysis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of protein localization to cell surface	IEA Inferred from Electronic Annotation more info
involved_in protein localization to cell surface	IEA Inferred from Electronic Annotation more info
involved_in regulation of neuron migration	IEA Inferred from Electronic Annotation more info
involved_in regulation of platelet-derived growth factor receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in sensory perception of sound	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
is_active_in extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in growth cone	IEA Inferred from Electronic Annotation more info
located_in intracellular vesicle	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: leucine-rich repeats and immunoglobulin-like domains protein 2

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_042819.2 RefSeqGene

Range

5002..64064

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001312686.2 → NP_001299615.1 leucine-rich repeats and immunoglobulin-like domains protein 2 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) contains an alternate exon in the 5' region and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus than isoform 1.

Source sequence(s)

AB018349, AL357055, CR936669, DA506094

UniProtKB/Swiss-Prot

O94898

Conserved Domains (7) summary

cd05763
Location:516 → 590

Ig_1; Subgroup of the immunoglobulin (Ig) superfamily

TIGR00864
Location:313 → 390

PCC; polycystin cation channel protein

COG4886
Location:46 → 342

LRR; Leucine-rich repeat (LRR) protein [Transcription]

pfam07679
Location:593 → 680

I-set; Immunoglobulin I-set domain

sd00031
Location:19 → 42

LRR_1; leucine-rich repeat [structural motif]

sd00033
Location:43 → 65

LRR_RI; leucine-rich repeat [structural motif]

pfam13927
Location:394 → 481

Ig_3; Immunoglobulin domain
NM_014813.3 → NP_055628.1 leucine-rich repeats and immunoglobulin-like domains protein 2 isoform 1 precursor

See identical proteins and their annotated locations for NP_055628.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the shorter transcript and encodes the longer isoform (1).

Source sequence(s)

AK291031, AL357055, CR936669

Consensus CDS

CCDS30808.1

UniProtKB/Swiss-Prot

O94898, Q9NSN2

Related

ENSP00000355396.4, ENST00000361127.6

Conserved Domains (9) summary

cd05763
Location:619 → 693

Ig_1; Subgroup of the immunoglobulin (Ig) superfamily

smart00082
Location:445 → 493

LRRCT; Leucine rich repeat C-terminal domain

smart00409
Location:504 → 598

IG; Immunoglobulin

cd00116
Location:46 → 205

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

pfam07679
Location:602 → 692

I-set; Immunoglobulin I-set domain

sd00031
Location:122 → 145

LRR_1; leucine-rich repeat [structural motif]

sd00033
Location:146 → 168

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:312 → 371

LRR_8; Leucine rich repeat

cl11960
Location:714 → 783

Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

113073198..113132260

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005271369.3 → XP_005271426.1 leucine-rich repeats and immunoglobulin-like domains protein 2 isoform X3

Conserved Domains (8) summary

cd05763
Location:512 → 586

Ig_1; Subgroup of the immunoglobulin (Ig) superfamily

smart00082
Location:445 → 492

LRRCT; Leucine rich repeat C-terminal domain

cd00116
Location:46 → 205

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

pfam07679
Location:495 → 585

I-set; Immunoglobulin I-set domain

sd00031
Location:122 → 145

LRR_1; leucine-rich repeat [structural motif]

sd00033
Location:146 → 168

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:312 → 371

LRR_8; Leucine rich repeat

cl11960
Location:607 → 676

Ig; Immunoglobulin domain
XM_024451227.2 → XP_024306995.1 leucine-rich repeats and immunoglobulin-like domains protein 2 isoform X2

Conserved Domains (7) summary

cd05763
Location:516 → 590

Ig_1; Subgroup of the immunoglobulin (Ig) superfamily

TIGR00864
Location:313 → 390

PCC; polycystin cation channel protein

COG4886
Location:46 → 342

LRR; Leucine-rich repeat (LRR) protein [Transcription]

pfam07679
Location:593 → 680

I-set; Immunoglobulin I-set domain

sd00031
Location:19 → 42

LRR_1; leucine-rich repeat [structural motif]

sd00033
Location:43 → 65

LRR_RI; leucine-rich repeat [structural motif]

pfam13927
Location:394 → 481

Ig_3; Immunoglobulin domain
XM_047435521.1 → XP_047291477.1 leucine-rich repeats and immunoglobulin-like domains protein 2 isoform X1

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

113085129..113144193

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054339874.1 → XP_054195849.1 leucine-rich repeats and immunoglobulin-like domains protein 2 isoform X3
XM_054339873.1 → XP_054195848.1 leucine-rich repeats and immunoglobulin-like domains protein 2 isoform X2
XM_054339872.1 → XP_054195847.1 leucine-rich repeats and immunoglobulin-like domains protein 2 isoform X1