LHX4-AS1

Summary

LHX4-AS1 (LHX4 antisense RNA 1, HGNC:40982) is a long non-coding RNA gene on chromosome 1q25.2.

At a glance

• Clinical variants (ClinVar): 16 total — 3 pathogenic, 1 likely-pathogenic

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:40982
Approved symbol	LHX4-AS1
Name	LHX4 antisense RNA 1
Location	1q25.2
Locus type	RNA, long non-coding
Status	Approved
Entrez	100527964
RNAcentral	URS000075C729 — lncRNA, 2673 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

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

Classification	Count (floor)
Pathogenic	3
Likely pathogenic	1
Uncertain significance	10
Likely benign	0
Benign	1

Top pathogenic / likely-pathogenic (4)

Variant ID	HGVS	Classification
7506	NM_033343.4(LHX4):c.607-1G>C	Pathogenic
7509	NM_033343.4(LHX4):c.569T>G (p.Leu190Arg)	Pathogenic
7510	NM_033343.4(LHX4):c.1162C>A (p.Pro388Thr)	Pathogenic
452128	NM_033343.4(LHX4):c.784C>T (p.Gln262Ter)	Likely pathogenic

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000163051 (1:180270915 G>A), RS1000203220 (1:180269403 G>A), RS1000254261 (1:180269657 T>A,G), RS1000765875 (1:180269852 G>A), RS1001064814 (1:180275722 C>G), RS1001194044 (1:180276375 G>A), RS1001473967 (1:180269892 C>T), RS1001819837 (1:180269694 T>C), RS1002278732 (1:180274632 A>G), RS1003024062 (1:180273277 C>A,G,T), RS1003063481 (1:180272967 G>A,T), RS1003089742 (1:180271100 G>A), RS1003475655 (1:180273080 G>A,C,T), RS1004329466 (1:180275308 C>T), RS1004549341 (1:180269923 C>T)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:262700

GenCC curated gene-disease

Mondo (1): short stature-pituitary and cerebellar defects-small sella turcica syndrome (MONDO:0009880)

Orphanet (1): Short stature-pituitary and cerebellar defects-small sella turcica syndrome (Orphanet:85442)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C567492	Pituitary Hormone Deficiency, Combined, 4 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 0 entries

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases expression	2
fipronil	affects cotreatment, decreases expression	1
DEET	affects cotreatment, decreases expression	1
Rotenone	decreases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1

Clinical trials (associated diseases)

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