LINC00473

Summary

LINC00473 (long intergenic non-protein coding RNA 473, HGNC:21160) is a long non-coding RNA gene on chromosome 6q27. May play a role in cAMP-mediated gene transcription.

Involved in DNA-templated transcription.

Source: NCBI Gene 90632 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 3 total

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21160
Approved symbol	LINC00473
Name	long intergenic non-protein coding RNA 473
Location	6q27
Locus type	RNA, long non-coding
Status	Approved
Aliases	bA142J11.1, LNC473
Entrez	90632
RNAcentral	URS000075D5B0 — lncRNA, 1832 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)

• C6orf176 as a potential biomarker and/or therapeutic target in context with diseases linked to deregulated cAMP signaling. (PMID:22108211)
• The authors found that cAMP-PKA pathway regulates the expression of LINC00473 through IL-11-mediated STAT3 phosphorylation. (PMID:26947914)
• LINC00473 transcription is suppressed by binding to ZBTB7A in chemoresistant osteosarcoma cells. (PMID:28942243)
• Loss-of-function of LINC00473 in vivo effectively promoted the regression of Wilms tumour via miR-195/IKKalpha-mediated growth inhibition. (PMID:29159834)
• LINC00473 acts as a promising biomarker and therapeutic target for human CRTC1-MAML2-positive mucoepidermoid carcinomas. (PMID:29353885)
• LNC473 could recruit deubiquitinase USP9X to inhibit the ubiquitination level of survivin and then increase survivin expression. (PMID:29605299)
• LINC00473 is associated with the malignant status and prognosis in gastric cancer cases. (PMID:30071345)
• BCL-2-related anti-apoptosis pathway was activated and the multidrug-resistant (MDR) genes LRP, MDR1 were up-regulated by LINC00473. Furthermore, inhibition of LINC00473 in vivo could overcome the Taxol resistance of CRC cells, could recover the expression of tumor suppressor miR-15a and chemotherapy-induced tumor regression, indicating that LINC00473 functioned as oncogene in CRC via miR-15a (PMID:30126852)
• we found that LINC00473 is also required for maintaining the expression levels of the noncoding RNACCND1 s and recruiting corepressor FUS to the CCND1 promoter. Altogether, the activation effect of LINC00473 on CCND1 is a net effect of two antagonistic regulatory pathways (PMID:30848493)
• LINC00473/miR-374a-5p regulates esophageal squamous cell carcinoma via targeting SPIN1 to weaken the effect of radiotherapy. (PMID:31017716)
• Long noncoding RNA LINC00473 indicates a poor prognosis of breast cancer and accelerates tumor carcinogenesis by competing endogenous sponging miR-497. (PMID:31081095)
• LINC00473 silencing blocked the pancreatic cancer progression through enhancing miR-195-5p-targeted downregulation of PD-L1 (PMID:31206665)
• LINC00473 could act as a ceRNA of miR-637 to promote glioma progression through regulating CDK6 expression (PMID:31561732)
• LINC00473 promotes hepatocellular carcinoma progression by functioning as a ceRNA for microRNA-195 and increasing HMGA2 expression. (PMID:31562977)
• PRKAA1 was confirmed as a downstream target gene for miR-497-5p. PRKAA1 could combine with miR-497-5p, and LINC00473 knockdown or miR-497-5p overexpression downregulated the mRNA and protein expression of PRKAA1. (PMID:31584290)
• Long noncoding RNA LINC00473/miR1955p promotes glioma progression via YAP1TEAD1Hippo signaling. (PMID:31894297)
• Sex-Specific Role for the Long Non-coding RNA LINC00473 in Depression. (PMID:32304628)
• The long non-coding RNA LINC00473 contributes to cell proliferation via JAK-STAT3 signaling pathway by regulating miR-195-5p/SEPT2 axis in prostate cancer. (PMID:32440687)
• LINC00473 functions as an oncogene and predicts poor prognosis in pancreatic cancer via the cAMP/beta-catenin axis. (PMID:32495868)
• LINC00473 regulated apoptosis, proliferation and migration but could not reverse cell cycle arrest of human bone marrow mesenchymal stem cells induced by a high-dosage of dexamethasone. (PMID:32829248)
• Long intergenic noncoding RNA 00473 promoting migration and invasion of trophoblastic cell line HTR-8/SVneo via regulating miR-424-5p-mediated wnt3a/beta-catenin signaling pathway. (PMID:34109708)
• DNAJB1-PRKACA in HEK293T cells induces LINC00473 overexpression that depends on PKA signaling. (PMID:35167623)
• Long Non-coding RNA LINC00473 Promotes Breast Cancer Progression via miR-424-5p/CCNE1 Pathway. (PMID:36305147)
• Expression of the primate-specific LINC00473 RNA in mouse neurons promotes excitability and CREB-regulated transcription. (PMID:37019214)
• DNAJB1-PRKACA fusion protein-regulated LINC00473 promotes tumor growth and alters mitochondrial fitness in fibrolamellar carcinoma. (PMID:38512964)
• The placental blood perfusion and LINC00473-mediated promotion of trophoblast apoptosis in fetal growth restriction. (PMID:38942180)

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Putative transcriptional regulator encoded by LINC00473 — A8K010 (reviewed: A8K010)

All UniProt accessions (0):

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in cAMP-mediated gene transcription.

Induction. Up-regulated upon activation of cAMP signaling.

RefSeq proteins (0): (*=MANE)

Domains & families (InterPro)

UniProt features (4 total): chain 1, region of interest 1, compositionally biased region 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A8K010-F1	43.39	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 0 (showing top):

GO Biological Process (1): DNA-templated transcription (GO:0006351)

GO Molecular Function (0):

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
gene expression	1
RNA biosynthetic process	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A2RU37, A2RUQ5, A6NH13, A6NM66, A8K010, A8MU10, A8MUN3, B7Z368, E5RJ46, O71302, O83993, O93195, P0C687, P0C854, P0CG42, P0CG43, P0DJI6, P0DRI5, P12936, P24026, P37125, P40205, P49671, P87743, Q05499, Q06235, Q5T0J3, Q5T742, Q6UXP9, Q6ZP68, Q6ZS52, Q6ZTR6, Q6ZUL3, Q6ZV60, Q6ZVN7, Q80IU8, Q8IYB0, Q8JMY5, Q8N326, Q8N6C7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	3
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): RS1000080891 (6:165948132 G>T), RS1000097565 (6:165983242 C>T), RS1000114542 (6:165957676 A>C), RS1000125583 (6:165950454 C>A), RS1000225355 (6:165965157 T>C), RS1000236350 (6:165957669 C>T), RS1000253841 (6:165952601 A>G), RS1000270243 (6:165988596 C>G,T), RS1000284190 (6:165947888 G>A,T), RS1000331134 (6:165927928 C>T), RS1000341433 (6:165962587 C>T), RS1000360376 (6:165952976 T>C), RS1000383505 (6:165927586 C>G,T), RS1000395105 (6:165933037 A>G), RS1000397550 (6:165957410 G>A,C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST007094_129	Diastolic blood pressure	5.000000e-12
GCST007099_49	Systolic blood pressure	2.000000e-07
GCST007576_203	Chronotype	7.000000e-11

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0006336	diastolic blood pressure
EFO:0006335	systolic blood pressure
EFO:0008328	chronotype measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases expression, decreases expression, decreases methylation	4
securinine	increases expression	1
hydroxyhydroquinone	decreases expression	1
torcetrapib	increases expression	1
jinfukang	affects cotreatment, decreases expression	1
Arsenic	affects methylation	1
Cisplatin	affects cotreatment, decreases expression	1
Dexamethasone	decreases expression	1
Rotenone	increases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
Propofol	decreases expression	1
Aflatoxin B1	decreases methylation	1
Permethrin	increases expression	1

Clinical trials (associated diseases)

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