LINC01317

Summary

LINC01317 (long intergenic non-protein coding RNA 1317, HGNC:50523) is a long non-coding RNA gene on chromosome 2p22.3.

At a glance

• GWAS associations: 5

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:50523
Approved symbol	LINC01317
Name	long intergenic non-protein coding RNA 1317
Location	2p22.3
Locus type	RNA, long non-coding
Status	Approved
Entrez	104355287
RNAcentral	URS00007E39B5 — lncRNA, 772 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): RS1000000730 (2:33923185 C>A,T), RS1000019399 (2:33968168 C>T), RS1000033111 (2:33923392 G>A), RS1000033296 (2:34122034 C>G), RS1000039464 (2:33751070 C>G), RS1000044877 (2:34289927 A>C,G), RS1000048442 (2:33919772 A>C), RS1000048605 (2:34138014 G>T), RS1000049240 (2:33956811 A>G,T), RS1000051506 (2:34055512 T>A,G), RS1000053187 (2:34182960 T>C), RS1000058917 (2:33888752 A>C), RS1000068744 (2:34254681 G>C), RS1000068850 (2:33829542 T>C), RS1000072557 (2:33817433 G>A)

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
GCST008748_3	Epigenetic age acceleration in alcohol use disorder	1.000000e-06
GCST009613_1	HDL cholesterol levels x loop diuretics use interaction	7.000000e-07
GCST009897_1	Reading disability	1.000000e-06
GCST010725_50	Malaria	3.000000e-07
GCST012484_16	Cerebral amyloid angiopathy x APOEe4 status interaction in Alzheimer’s disease	5.000000e-06

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0000473	epigenetic status
EFO:0022597	aging
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0007659	APOE carrier status

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 0 entries

CTD chemical–gene interactions

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
benzo(e)pyrene	affects methylation	1
aflatoxin B2	increases methylation	1
Benzo(a)pyrene	affects methylation	1
Methapyrilene	affects methylation	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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