RUNX1-IT1

Summary

RUNX1-IT1 (RUNX1 intronic transcript 1, HGNC:16623) is a long non-coding RNA gene on chromosome 21q22.12.

At a glance

• GWAS associations: 2

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16623
Approved symbol	RUNX1-IT1
Name	RUNX1 intronic transcript 1
Location	21q22.12
Locus type	RNA, long non-coding
Status	Approved
Aliases	FLJ20856
Entrez	80215
RNAcentral	URS000075E3D1 — lncRNA, 1502 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 6)

• LncRNA RUNX1-IT1 inhibits proliferation and promotes apoptosis of hepatocellular carcinoma by regulating MAPK pathways. (PMID:31646558)
• The lncRNA RUNX1-IT1 regulates C-FOS transcription by interacting with RUNX1 in the process of pancreatic cancer proliferation, migration and invasion. (PMID:32487998)
• MiR-195 connects lncRNA RUNX1-IT1 and cyclin D1 to regulate the proliferation of glioblastoma cells. (PMID:33507136)
• LncRNA RUNX1-IT1 affects the differentiation of Th1 cells by regulating NrCAM transcription in Graves’ disease. (PMID:35220890)
• LncRNA RUNX1-IT1 is downregulated in gastric cancer and suppresses the maturation of miR-20a by binding to its precursor. (PMID:36722424)
• [LncRNA RUNX1-IT1 regulating malignant pleomorphic adenoma via mir-195/CyclinD1]. (PMID:36973850)

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): RS1000029636 (21:35041408 T>C), RS1003156859 (21:35040331 C>G), RS1003515575 (21:35039985 T>C), RS1003645542 (21:35039264 C>T), RS1003881885 (21:35038877 T>C), RS1003937615 (21:35039540 A>C,G), RS1004097628 (21:35038914 C>T), RS1004782098 (21:35041064 C>G), RS1006333357 (21:35037645 C>T), RS1006340089 (21:35039877 C>T), RS1006449538 (21:35037460 G>A,C), RS1007988165 (21:35037796 C>T), RS1008331049 (21:35040693 C>G,T), RS1009344182 (21:35039997 G>C), RS1009622091 (21:35039629 T>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

2 associations (top):

Study	Trait	p-value
GCST009798_46	Asthma	5.000000e-11
GCST009798_85	Asthma	1.000000e-08

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Nickel	increases expression	2
polyhexamethyleneguanidine	decreases expression	1
Acetaminophen	increases expression	1
Benzo(a)pyrene	increases methylation	1
Calcitriol	decreases expression	1
Tetrachlorodibenzodioxin	increases expression	1

Clinical trials (associated diseases)

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