LINC01580

Summary

LINC01580 (long intergenic non-protein coding RNA 1580, HGNC:51414) is a long non-coding RNA gene on chromosome 15q26.2.

At a glance

• Clinical variants (ClinVar): 1 total — 1 pathogenic

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:51414
Approved symbol	LINC01580
Name	long intergenic non-protein coding RNA 1580
Location	15q26.2
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000258785
Entrez	101927129
RNAcentral	URS000075B22B — lncRNA, 771 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 broad, 97 present calls, max score 89.93.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0177 / max 4.1439, expressed in 10 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
148671	0.0177	10

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.93	gold quality
sural nerve	UBERON:0015488	72.88	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	71.46	gold quality
left testis	UBERON:0004533	67.84	gold quality
right testis	UBERON:0004534	67.78	gold quality
testis	UBERON:0000473	65.87	gold quality
secondary oocyte	CL:0000655	62.32	gold quality
sperm	CL:0000019	59.15	gold quality
mucosa of stomach	UBERON:0001199	58.54	gold quality
monocyte	CL:0000576	55.99	gold quality
ganglionic eminence	UBERON:0004023	55.90	silver quality
hindlimb stylopod muscle	UBERON:0004252	55.63	silver quality
blood	UBERON:0000178	55.04	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	54.93	gold quality
bone marrow	UBERON:0002371	53.07	gold quality
parotid gland	UBERON:0001831	52.41	gold quality
muscle of leg	UBERON:0001383	49.83	gold quality
oocyte	CL:0000023	49.38	gold quality
gastrocnemius	UBERON:0001388	49.20	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	48.89	gold quality
prefrontal cortex	UBERON:0000451	48.75	gold quality
islet of Langerhans	UBERON:0000006	48.65	silver quality
right lobe of liver	UBERON:0001114	48.25	silver quality
adult organism	UBERON:0007023	47.98	gold quality
tibial artery	UBERON:0007610	47.33	gold quality
popliteal artery	UBERON:0002250	47.29	gold quality
gall bladder	UBERON:0002110	47.10	gold quality
lower esophagus muscularis layer	UBERON:0035833	46.73	gold quality
right ovary	UBERON:0002118	46.18	gold quality
cortex of kidney	UBERON:0001225	46.12	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.45

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

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	0
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
144251	GRCh38/hg38 15q26.1-26.3(chr15:93198717-101843270)x1	Pathogenic

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000007694 (15:93923520 A>G,T), RS1000019109 (15:93905666 C>G,T), RS1000042792 (15:93923252 G>A,T), RS1000088005 (15:93904310 C>T), RS1000114816 (15:93982620 A>T), RS1000165527 (15:93982929 C>A), RS1000209398 (15:93930149 G>A), RS1000399263 (15:93941401 T>C), RS1000430246 (15:93941717 G>A,C), RS1000433685 (15:93935644 G>A), RS1000485217 (15:93976534 G>A), RS1000550473 (15:93942908 G>T), RS1000585900 (15:93900799 G>C,T), RS1000597845 (15:93907059 A>C), RS1000614746 (15:93942022 C>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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 0 entries

CTD chemical–gene interactions

1 total (human), top 1 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
methyleugenol	decreases expression	1

Clinical trials (associated diseases)

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