LINC00548

Summary

LINC00548 (long intergenic non-protein coding RNA 548, HGNC:43683) is a long non-coding RNA gene on chromosome 13q14.11.

At a glance

• GWAS associations: 4

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:43683
Approved symbol	LINC00548
Name	long intergenic non-protein coding RNA 548
Location	13q14.11
Locus type	RNA, long non-coding
Status	Approved
Aliases	FLJ42392
Entrez	400123
RNAcentral	URS000075AA30 — lncRNA, 2551 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

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): RS1000083748 (13:40196615 G>A,C), RS1000266669 (13:40206039 C>T), RS1000320888 (13:40219784 G>C), RS1000378931 (13:40199848 G>A), RS1000496518 (13:40213254 G>C), RS1000573284 (13:40207382 G>C,T), RS1000604327 (13:40207696 T>C), RS1000643163 (13:40213462 G>A,C), RS1000783847 (13:40207992 C>A), RS1000793683 (13:40207759 C>G), RS1000838780 (13:40195375 A>G), RS1000861314 (13:40194568 C>G,T), RS1001086667 (13:40194848 A>C), RS1001115903 (13:40201346 C>T), RS1001170200 (13:40196891 T>G)

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

4 associations (top):

Study	Trait	p-value
GCST001872_13	Presence of antiphospholipid antibodies	7.000000e-06
GCST004030_29	Primary sclerosing cholangitis	2.000000e-06
GCST008526_22	Coffee consumption	2.000000e-06
GCST009798_42	Asthma	4.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0006781	coffee consumption 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.