LINC02398

Summary

LINC02398 (long intergenic non-protein coding RNA 2398, HGNC:53325) is a long non-coding RNA gene on chromosome 12p12.2.

At a glance

• GWAS associations: 5

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:53325
Approved symbol	LINC02398
Name	long intergenic non-protein coding RNA 2398
Location	12p12.2
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000256287
Entrez	100506393
RNAcentral	URS000075DC09 — lncRNA, 526 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

Bgee: expression breadth ubiquitous, 113 present calls, max score 86.76.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ascending aorta	UBERON:0001496	86.76	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.74	gold quality
thoracic aorta	UBERON:0001515	86.66	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.91	silver quality
descending thoracic aorta	UBERON:0002345	85.56	gold quality
tibial artery	UBERON:0007610	83.34	gold quality
popliteal artery	UBERON:0002250	83.33	gold quality
left coronary artery	UBERON:0001626	75.11	gold quality
right coronary artery	UBERON:0001625	74.12	gold quality
placenta	UBERON:0001987	69.62	gold quality
stromal cell of endometrium	CL:0002255	66.21	gold quality
calcaneal tendon	UBERON:0003701	62.42	gold quality
mucosa of stomach	UBERON:0001199	61.29	gold quality
body of pancreas	UBERON:0001150	59.97	gold quality
pancreas	UBERON:0001264	59.82	gold quality
lymph node	UBERON:0000029	59.49	gold quality
gall bladder	UBERON:0002110	57.80	gold quality
prefrontal cortex	UBERON:0000451	57.17	gold quality
heart	UBERON:0000948	57.10	gold quality
hindlimb stylopod muscle	UBERON:0004252	56.39	gold quality
apex of heart	UBERON:0002098	56.31	gold quality
vermiform appendix	UBERON:0001154	56.01	gold quality
islet of Langerhans	UBERON:0000006	55.77	gold quality
liver	UBERON:0002107	55.74	gold quality
endometrium	UBERON:0001295	55.52	gold quality
right uterine tube	UBERON:0001302	55.42	gold quality
cortex of kidney	UBERON:0001225	55.03	gold quality
smooth muscle tissue	UBERON:0001135	54.67	gold quality
superior frontal gyrus	UBERON:0002661	54.67	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	54.56	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.63

Regulation

Is transcription factor: no

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

0 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): RS1000024587 (12:20056149 G>A), RS1000028677 (12:20093571 C>A,T), RS1000060069 (12:20080138 A>G), RS1000062602 (12:20020706 T>A), RS1000068015 (12:20099145 A>G), RS1000089858 (12:20025268 G>A,T), RS1000125831 (12:20070135 C>G,T), RS1000142326 (12:20061836 G>A), RS1000195419 (12:20062500 A>G,T), RS1000257430 (12:20062188 G>A), RS1000257722 (12:20083104 TA>T,TAA,TAAA), RS1000270397 (12:20042315 G>A), RS1000285413 (12:20089006 C>G,T), RS1000292279 (12:20022220 G>A), RS1000337206 (12:20088810 G>A,T)

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

5 associations (top):

Study	Trait	p-value
GCST010479_24	Coronary artery disease	1.000000e-08
GCST010767_3	Coronary atherosclerosis (time to event)	6.000000e-08
GCST010866_92	Coronary artery disease	7.000000e-17
GCST011364_19	Myocardial infarction	2.000000e-08
GCST012297_5	Schizophrenia, bipolar disorder or major depressive disorder	6.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004918	age at diagnosis
EFO:0007938	coronary atherosclerosis measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 0 entries

Clinical trials (associated diseases)

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