HCG23

Summary

HCG23 (HLA complex group 23, HGNC:19713) is a long non-coding RNA gene on chromosome 6p21.32.

At a glance

• GWAS associations: 31
• Clinical variants (ClinVar): 4 total

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19713
Approved symbol	HCG23
Name	HLA complex group 23
Location	6p21.32
Locus type	RNA, long non-coding
Status	Approved
Aliases	dJ1077I5.3
Entrez	414764
RNAcentral	URS000075B48F — lncRNA, 615 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

4 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): RS1000365591 (6:32388895 C>T), RS1000388513 (6:32391728 G>A), RS1000738756 (6:32391924 C>G,T), RS1000819615 (6:32388690 G>A), RS1002093836 (6:32389856 T>C), RS1002828812 (6:32393095 T>C), RS1003103966 (6:32393384 C>T), RS1004366463 (6:32390930 C>A), RS1004402662 (6:32391252 A>G), RS1006044169 (6:32392723 T>G), RS1006073924 (6:32393047 C>G), RS1006874935 (6:32389199 C>G), RS1007420215 (6:32388955 G>T), RS1007740928 (6:32389293 C>T), RS1008959242 (6:32390540 T>A,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

31 associations (top):

Study	Trait	p-value
GCST001942_21	Prostate cancer	5.000000e-09
GCST003773_15	Loneliness (multivariate analysis)	2.000000e-06
GCST004122_3	Fibrinogen levels	9.000000e-09
GCST004521_1	Autism spectrum disorder or schizophrenia	2.000000e-16
GCST004521_10	Autism spectrum disorder or schizophrenia	2.000000e-13
GCST004521_118	Autism spectrum disorder or schizophrenia	3.000000e-15
GCST004521_126	Autism spectrum disorder or schizophrenia	2.000000e-10
GCST004521_13	Autism spectrum disorder or schizophrenia	2.000000e-12
GCST004521_130	Autism spectrum disorder or schizophrenia	2.000000e-10
GCST004521_143	Autism spectrum disorder or schizophrenia	2.000000e-09
GCST004521_17	Autism spectrum disorder or schizophrenia	2.000000e-12
GCST004521_170	Autism spectrum disorder or schizophrenia	4.000000e-14
GCST004521_173	Autism spectrum disorder or schizophrenia	4.000000e-14
GCST004521_179	Autism spectrum disorder or schizophrenia	3.000000e-11
GCST004521_211	Autism spectrum disorder or schizophrenia	5.000000e-15
GCST004521_226	Autism spectrum disorder or schizophrenia	4.000000e-12
GCST004521_228	Autism spectrum disorder or schizophrenia	4.000000e-11
GCST004521_296	Autism spectrum disorder or schizophrenia	6.000000e-18
GCST004521_81	Autism spectrum disorder or schizophrenia	1.000000e-14
GCST004521_85	Autism spectrum disorder or schizophrenia	1.000000e-12
GCST004750_61	Squamous cell lung carcinoma	6.000000e-15
GCST004923_2	Tuberculosis	8.000000e-11
GCST006252_5	Childhood steroid-sensitive nephrotic syndrome	9.000000e-07
GCST007876_87	Estimated glomerular filtration rate	7.000000e-09
GCST008916_16	Asthma	3.000000e-17
GCST008916_27	Asthma	5.000000e-31
GCST008916_90	Asthma	4.000000e-15
GCST011359_1	Venous thromboembolism	4.000000e-38
GCST012230_428	Waist-to-hip ratio adjusted for BMI	2.000000e-08
GCST90020025_766	Waist-to-hip ratio adjusted for BMI	6.000000e-10

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007865	loneliness measurement
EFO:0007788	BMI-adjusted waist-hip ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

2 total (human), top 2 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Tobacco Smoke Pollution	decreases expression	1
Cadmium Chloride	decreases expression	1

Clinical trials (associated diseases)

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