PCDH9-AS4

Summary

PCDH9-AS4 (PCDH9 antisense RNA 4, HGNC:40428) is a long non-coding RNA gene on chromosome 13q21.32.

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:40428
Approved symbol	PCDH9-AS4
Name	PCDH9 antisense RNA 4
Location	13q21.32
Locus type	RNA, long non-coding
Status	Approved
Ensembl gene	ENSG00000233840
Entrez	100874087
RNAcentral	URS000075BBAD — lncRNA, 429 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, 73 present calls, max score 98.87.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
corpus callosum	UBERON:0002336	98.87	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.41	gold quality
sural nerve	UBERON:0015488	78.17	gold quality
calcaneal tendon	UBERON:0003701	74.46	gold quality
colonic epithelium	UBERON:0000397	73.95	gold quality
bone marrow cell	CL:0002092	71.90	silver quality
skeletal muscle tissue	UBERON:0001134	68.19	silver quality
kidney	UBERON:0002113	65.09	gold quality
adrenal tissue	UBERON:0018303	58.88	gold quality
primary visual cortex	UBERON:0002436	56.73	gold quality
monocyte	CL:0000576	56.47	gold quality
superior frontal gyrus	UBERON:0002661	55.89	gold quality
prefrontal cortex	UBERON:0000451	55.60	gold quality
adrenal gland	UBERON:0002369	55.35	gold quality
intestine	UBERON:0000160	54.84	gold quality
testis	UBERON:0000473	54.63	gold quality
left testis	UBERON:0004533	54.63	gold quality
pancreas	UBERON:0001264	54.58	gold quality
right testis	UBERON:0004534	53.89	gold quality
gastrocnemius	UBERON:0001388	53.55	gold quality
lung	UBERON:0002048	52.69	gold quality
stomach	UBERON:0000945	52.32	gold quality
heart	UBERON:0000948	51.42	gold quality
blood	UBERON:0000178	49.91	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	49.68	gold quality
body of pancreas	UBERON:0001150	49.66	gold quality
multicellular organism	UBERON:0000468	49.54	gold quality
Ammon’s horn	UBERON:0001954	47.35	gold quality
liver	UBERON:0002107	47.10	silver quality
Brodmann (1909) area 9	UBERON:0013540	47.10	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.96

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): RS1000421942 (13:66990101 A>T), RS1000858136 (13:66992653 C>G,T), RS1000889337 (13:66992381 T>C), RS1000935805 (13:66999925 G>A,T), RS1001078999 (13:66999428 A>G), RS1001144757 (13:66996681 T>C), RS1001290654 (13:66991852 T>C,G), RS1001486454 (13:66998208 A>G), RS1001537355 (13:66998525 A>G), RS1001702899 (13:66991512 A>C,G), RS1001984400 (13:66992949 A>C,G), RS1002048989 (13:66991295 T>C), RS1002297912 (13:66993402 A>T), RS1002410915 (13:66993158 C>G,T), RS1002438022 (13:66993265 A>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

0 associations (top):

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.