LINC00673

Summary

LINC00673 (long intergenic non-protein coding RNA 673, HGNC:44354) is a long non-coding RNA gene on chromosome 17q24.3.

This gene produces a long non-protein coding RNA that is involved in the regulation of gene expression during tumor progression. This transcript can promote cell proliferation in gastric cancer through interaction with enhancer of zeste 2 and other epigenetic suppressors of gene expression, thereby downregulating target genes including Kruppel like factors 2 and 4. This transcript may also act as a tumor suppressor by promoting interaction between protein tyrosine phosphatase, non-receptor type 11 (Ptpn11) and ubiquitin ligase, resulting in degradation of Ptpn11 and lowered oncogenic signalling. Naturally-occurring variation at this locus results in the formation of a binding site for miR-1231, which negatively regulates activity of this transcript. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 100499467 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 5 total

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:44354
Approved symbol	LINC00673
Name	long intergenic non-protein coding RNA 673
Location	17q24.3
Locus type	RNA, long non-coding
Status	Approved
Aliases	HI-LNC75, SLNCR1, ERRLR01, LUCAIR1, RASON, SLNCR
OMIM	617079
Entrez	100499467
RNAcentral	URS000075D66E — lncRNA, 2275 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 0

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

None — 0 exons

Expression profiles

Top tissues by expression

0 total, by Bgee expression score (0-100, higher = more expressed):

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 26)

• findings suggested that linc00673 could play crucial role in non-small cell lung cancer progression (PMID:27027352)
• Increased expression of this lncRNA, SLNCR1, mediates melanoma invasion through a highly conserved sequence similar to that of the lncRNA SRA1. (PMID:27210747)
• Loss of LINC00673 is associated with Pancreatic cancer. (PMID:27213290)
• Results indicate that linc00673 could silence HOXA5 expression by recruiting epigenetic repressor, EZH2, at its promoter regions, and identified the role of lin00673 in promoting invasion and migration of non-small-cell lung cancer cells. (PMID:28423732)
• miR-150-5p inhibition abrogated linc00673 silence mediated proliferation, migration, invasion and epithelial mesenchymal transition suppressing effect. (PMID:28697764)
• data suggest ERRLR01 operates as an oncogene in triple-negative breast cancer, as well as a biomarker in breast cancer patients (PMID:28795861)
• lncRNA 00312 may serve an important role in the tumorigenesis and deterioration of human NSCLC. Moreover, linc00673 is upregulated in LAD but not in LSCC tissues, implying that it can be a potential candidate tissue specific lncRNA for NSCLC. (PMID:28849087)
• we verified that the LINC00673 rs11655237 C>T polymorphism might be associated with neuroblastoma susceptibility. Prospective studies with a large sample size and different ethnicities are needed to validate our findings. (PMID:29339420)
• The expression level of lncRNA00673 is up-regulated in colorectal cancer tissues and cells, which is related to the degree of malignancy and poor prognosis (PMID:29461596)
• LINC00673 promotes the proliferation and metastasis of thyroid carcinoma.Upregulation of LINC00673 in thyroid carcinoma.LINC00673 regulates the metastasis of thyroid carcinoma cell lines by modulating epithelial-mesenchymal transition.KLF-2 is a downstream target of LINC00673 in the thyroid carcinoma. (PMID:30106140)
• Case-control study results indicate that LINC00673 rs11655237 significantly increased susceptibility of cervical cancer in a Chinese population, possibly by down-regulating LINC00673 expression in cervical tissues. (PMID:30286619)
• These findings add new evidence of the importance of LINC00673 rs11655237 C>T to the risk of developing neuroblastoma. (PMID:31005956)
• SLNCR recruits AR to EGR1-bound genomic loci and switches EGR1-mediated transcriptional activation to repression of the tumor suppressor p21(Waf1/Cip1). (PMID:31116991)
• any association between the LINC00673 rs11655237 C>T polymorphism and Wilm’s tumor risk, was not found. (PMID:31257678)
• lncRNA SLNCR1 and secretory sPLA2 were both upregulated in NSCLC. lncRNA SLNCR1 may regulate cancer cell migration, invasion and stemness in NSCLC through interactions with secretory sPLA2. (PMID:31524254)
• Increased LINC00673 expression in breast cancer associated with poor prognosis. (PMID:31623640)
• we failed to provide any evidence in favor of the significant susceptibility of rs11655237 C>T polymorphism in LINC00673 to Wilms tumor. These data could be useful for reinforcing our understanding of the potential contribution of LINC00673 rs11655237 C>T to Wilms tumor susceptibility. (PMID:31657076)
• Long non-coding RNA LINC00673 silencing inhibits proliferation and drug resistance of prostate cancer cells via decreasing KLF4 promoter methylation. (PMID:31881124)
• Targeting the Oncogenic Long Non-coding RNA SLNCR1 by Blocking Its Sequence-Specific Binding to the Androgen Receptor. (PMID:31940495)
• Association of LINC00673 rs11655237 polymorphism with cancer susceptibility: A meta-analysis based on 23,478 subjects. (PMID:32650095)
• A review of linc00673 as a novel lncRNA for tumor regulation. (PMID:33390809)
• [Effects of long-chain noncoding RNA Linc00673 overexpression on proliferation and apoptosis of gastric cancer cell line MGC-803]. (PMID:35634670)
• Association between the LINC00673 rs11655237 C> T polymorphisms with cancer risk in the Chinese population: A meta-analysis. (PMID:36123911)
• A novel protein RASON encoded by a lncRNA controls oncogenic RAS signaling in KRAS mutant cancers. (PMID:36241718)
• Genetic Polymorphisms of lncRNA LINC00673 as Predictors of Hepatocellular Carcinoma Progression in an Elderly Population. (PMID:36361527)
• Linc00673-V3 positively regulates autophagy by promoting Smad3-mediated LC3B transcription in NSCLC. (PMID:38527804)

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Canonical reviewed UniProt: None (reviewed: )

All UniProt accessions (0):

RefSeq proteins (0): (*=MANE)

Domains & families (InterPro)

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 0 (showing top):

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

0 interactions, top by confidence:

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

5 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000040740 (17:72474299 A>C), RS1000050458 (17:72473233 G>A), RS1000065465 (17:72495687 C>G,T), RS1000092477 (17:72449446 G>A,T), RS1000099338 (17:72540982 T>A,C), RS1000110133 (17:72482029 A>G), RS1000111871 (17:72569238 C>T), RS1000115766 (17:72561447 C>T), RS1000117325 (17:72486564 A>G,T), RS1000140858 (17:72517864 C>T), RS1000165465 (17:72470270 C>A,T), RS1000196248 (17:72508441 C>G), RS1000215772 (17:72441395 G>A), RS1000229622 (17:72471596 CTCTTTTTTTT>C), RS1000232097 (17:72565850 G>T)

Disease associations

OMIM: gene MIM:617079 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

7 associations (top):

Study	Trait	p-value
GCST002991_13	Pancreatic cancer	1.000000e-14
GCST004029_9	Angiotensin-converting enzyme inhibitor intolerance	9.000000e-06
GCST004640_19	Western dietary pattern	8.000000e-06
GCST004744_6	Lung adenocarcinoma	3.000000e-06
GCST004748_6	Lung cancer	2.000000e-07
GCST005434_13	Pancreatic cancer	9.000000e-15
GCST010653_94	Thyroid stimulating hormone levels	6.000000e-21

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0005325	response to angiotensin-converting enzyme inhibitor
EFO:0008111	diet measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 0 entries

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases methylation, increases expression	2
Valproic Acid	affects expression, increases expression	2
bisphenol A	affects cotreatment, decreases methylation	1
trichostatin A	affects cotreatment, increases expression	1
aflatoxin B2	decreases methylation	1
1-hydroxypyrene	decreases methylation, affects cotreatment	1
fipronil	affects cotreatment, increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Benzo(a)pyrene	decreases expression, affects reaction, increases expression	1
DEET	affects cotreatment, increases expression	1
Estradiol	increases expression	1
Methotrexate	increases expression	1
Smoke	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Triclosan	increases expression	1
Aflatoxin B1	affects methylation	1
Metals, Heavy	affects cotreatment, decreases methylation	1
Particulate Matter	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.