CT83

Summary

CT83 (cancer/testis antigen 83, HGNC:33494) is a protein-coding gene on chromosome Xq23, encoding Kita-kyushu lung cancer antigen 1 (Q5H943).

Located in nucleus.

Source: NCBI Gene 203413 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 12 total — 1 pathogenic
• Druggable target: yes
• MANE Select transcript: NM_001017978

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33494
Approved symbol	CT83
Name	cancer/testis antigen 83
Location	Xq23
Locus type	gene with protein product
Status	Approved
Aliases	KK-LC-1, FLJ20611, FLJ22913
Ensembl gene	ENSG00000204019
Ensembl biotype	protein_coding
OMIM	300625
Entrez	203413

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000371894

RefSeq mRNA: 1 — MANE Select: NM_001017978 NM_001017978

CCDS: CCDS35372

Canonical transcript exons

ENST00000371894 — 2 exons

Exon	Start	End
ENSE00001456400	116461686	116462007
ENSE00001456402	116462782	116462976

Expression profiles

Bgee: expression breadth broad, 80 present calls, max score 97.64.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.8736 / max 88.4127, expressed in 129 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
200245	0.6882	117
200246	0.1229	46
200248	0.0388	21
200247	0.0237	17

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	97.64	gold quality
right testis	UBERON:0004534	94.73	gold quality
left testis	UBERON:0004533	94.06	gold quality
testis	UBERON:0000473	91.32	gold quality
adult organism	UBERON:0007023	81.40	gold quality
mucosa of stomach	UBERON:0001199	69.34	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	68.30	gold quality
buccal mucosa cell	CL:0002336	56.49	gold quality
minor salivary gland	UBERON:0001830	53.33	gold quality
saliva-secreting gland	UBERON:0001044	51.81	gold quality
mouth mucosa	UBERON:0003729	51.61	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
cauda epididymis	UBERON:0004360	42.82	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
upper leg skin	UBERON:0004262	41.50	silver quality
vastus lateralis	UBERON:0001379	41.41	gold quality
quadriceps femoris	UBERON:0001377	41.37	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality
mucosa of paranasal sinus	UBERON:0005030	40.98	gold quality
amniotic fluid	UBERON:0000173	40.69	gold quality
jejunal mucosa	UBERON:0000399	40.59	gold quality
biceps brachii	UBERON:0001507	40.57	gold quality
epithelium of nasopharynx	UBERON:0001951	40.45	gold quality
myocardium	UBERON:0002349	40.45	gold quality
gingival epithelium	UBERON:0001949	40.43	gold quality
germinal epithelium of ovary	UBERON:0001304	40.33	gold quality
esophagus squamous epithelium	UBERON:0006920	40.29	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	40.27	gold quality
jejunum	UBERON:0002115	40.18	gold quality
cartilage tissue	UBERON:0002418	40.06	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.13

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 11)

• The frequency of KK-LC-1 expression was higher than that of the other CTAs. KK-LC-1 might be a useful target for immunotherapy and in diagnosis of gastric cancer. (PMID:26026129)
• CXorf61 is a target for T cell based immunotherapy of triple-negative breast cancer. (PMID:26327325)
• KK-LC-1 was frequently expressed in gastric cancer caused by H. pylori infection. (PMID:28438869)
• The KK-LC-1 expression rate was high even in patients with stage I cancer, suggesting that KK-LC-1 is a useful biomarker for early diagnosis of gastric cancer. (PMID:29290656)
• Consequently, KK-LC-1 would be detected at the pre-cancerous condition of the stomach, and may be a useful marker to predict gastric cancer. (PMID:29666402)
• High KK-LC-1 expression was detected in breast cancer, especially in oestrogen receptor-negative subtypes. (PMID:30275220)
• We defined the KK-LC-1/presenilin-1/Notch1/Hes1 as a novel signalling pathway that was involved in the growth and metastasis of hepatocellular carcinoma. (PMID:30895661)
• KK-LC-1 may be an effective prognostic biomarker for gastric cancer. (PMID:33711953)
• Multiomics analysis reveals CT83 is the most specific gene for triple negative breast cancer and its hypomethylation is oncogenic in breast cancer. (PMID:34108519)
• Six CT83-related Genes-based Prognostic Signature for Lung Adenocarcinoma. (PMID:34259140)
• Cancer-testis antigen KK-LC-1 is a potential biomarker associated with immune cell infiltration in lung adenocarcinoma. (PMID:35907786)

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Kita-kyushu lung cancer antigen 1 — Q5H943 (reviewed: Q5H943)

Alternative names: Cancer/testis antigen 83

All UniProt accessions (1): Q5H943

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cell membrane.

Tissue specificity. Specifically expressed in testis. Expressed by cancer cell lines.

RefSeq proteins (1): NP_001017978* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027940	KKLCAg1	Family

Pfam: PF15204

UniProt features (5 total): topological domain 2, chain 1, transmembrane region 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5H943-F1	71.69	0.20

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Glycosylation sites (1): 83

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 13 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_DN, chrXq23, UBN1_TARGET_GENES, GSE18791_CTRL_VS_NEWCASTLE_VIRUS_DC_1H_DN, GSE18791_CTRL_VS_NEWCASTLE_VIRUS_DC_2H_DN, GSE2706_R848_VS_R848_AND_LPS_2H_STIM_DC_UP, GSE29615_CTRL_VS_DAY7_LAIV_FLU_VACCINE_PBMC_DN, GSE2770_IL12_AND_TGFB_VS_IL4_TREATED_ACT_CD4_TCELL_48H_DN, GSE1112_OT1_CD8AB_VS_HY_CD8AA_THYMOCYTE_RTOC_CULTURE_DN, GSE34156_UNTREATED_VS_6H_NOD2_AND_TLR1_TLR2_LIGAND_TREATED_MONOCYTE_UP, GSE34156_NOD2_LIGAND_VS_NOD2_AND_TLR1_TLR2_LIGAND_24H_TREATED_MONOCYTE_UP, GSE45365_WT_VS_IFNAR_KO_CD11B_DC_MCMV_INFECTION_DN, GSE45365_WT_VS_IFNAR_KO_BCELL_DN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (3): nucleus (GO:0005634), plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membrane-bounded organelle	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

428 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CT83	HLA-B	P01889	691
CT83	CTAG1A	P78358	571
CT83	MAGEA1	P43355	571
CT83	ACTL8	Q9H568	542
CT83	MAGEA3	P43357	507
CT83	MAGEA4	P43358	480
CT83	PSEN1	P49768	458
CT83	TMCO2	Q7Z6W1	437
CT83	HORMAD1	Q86X24	435
CT83	C4orf51	C9J302	432
CT83	ZNF165	P49910	432
CT83	CCDC187	A0A096LP49	430
CT83	CCDC54	Q8NEL0	428
CT83	BACE1	P56817	424
CT83	NCSTN	Q92542	418

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A6ZS79, B0BCM0, B3LPN5, B7VIS1, C0H3W7, C7GLQ0, C8ZFN1, C9J3I9, G2TRL3, O31894, O32026, P03636, P05397, P05720, P09521, P0CE23, P20194, P20563, P24439, P25097, P35517, P39983, P40342, P41472, P51366, P52365, Q01024, Q06423, Q3V4T4, Q46262, Q46440, Q49Z23, Q54BH8, Q5H943, Q5I123, Q5UQV4, Q5Y9A9, Q68XW8, Q6FQJ5, Q81DD0

Diamond homologs: Q4R717, Q5H943

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
684964	GRCh37/hg19 Xq21.32-28(chrX:92814516-155233731)x1	Pathogenic

SpliceAI

73 predictions. Top by Δscore:

Variant	Effect	Δscore
X:116462004:TTCTC:T	acceptor_loss	0.9900
X:116462006:CT:C	acceptor_gain	0.9900
X:116462006:CTCT:C	acceptor_loss	0.9900
X:116462007:TC:T	acceptor_loss	0.9900
X:116462008:C:T	acceptor_loss	0.9900
X:116462009:T:A	acceptor_loss	0.9900
X:116462776:CATTA:C	donor_loss	0.9900
X:116462778:TTAC:T	donor_loss	0.9900
X:116462781:C:CT	donor_loss	0.9900
X:116462003:TTTCT:T	acceptor_gain	0.9800
X:116462004:TTCT:T	acceptor_gain	0.9800
X:116462005:TCT:T	acceptor_gain	0.9800
X:116462006:CTC:C	acceptor_gain	0.9800
X:116462007:TCT:T	acceptor_gain	0.9800
X:116462008:C:CC	acceptor_gain	0.9800
X:116462008:C:G	acceptor_gain	0.9500
X:116462769:CAT:C	donor_gain	0.9500
X:116462799:T:TA	donor_gain	0.9400
X:116462770:A:C	donor_gain	0.9200
X:116462771:T:C	donor_gain	0.9000
X:116462780:A:AC	donor_gain	0.8600
X:116462781:C:CC	donor_gain	0.8600
X:116462781:C:CG	donor_gain	0.8600
X:116462778:TTA:T	donor_gain	0.8500
X:116462780:A:AT	donor_gain	0.8500
X:116462549:TAGGG:T	donor_gain	0.8100
X:116462550:AGGGA:A	donor_gain	0.8100
X:116462779:TA:T	donor_gain	0.8100
X:116462777:ATTAC:A	donor_gain	0.7900
X:116462780:ACCTG:A	donor_gain	0.7600

AlphaMissense

729 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:116462827:G:C	S10R	0.938
X:116462827:G:T	S10R	0.938
X:116462829:T:G	S10R	0.938
X:116462830:G:C	S9R	0.919
X:116462830:G:T	S9R	0.919
X:116462832:T:G	S9R	0.919
X:116462820:A:G	C13R	0.910
X:116461832:A:G	L84P	0.859
X:116461802:A:G	L94P	0.816
X:116461811:A:G	L91P	0.815
X:116462816:G:T	A14D	0.801
X:116462803:G:C	F18L	0.719
X:116462803:G:T	F18L	0.719
X:116462805:A:G	F18L	0.719
X:116461799:T:A	E95V	0.716
X:116462807:A:T	V17D	0.697
X:116462785:A:C	F24L	0.695
X:116462785:A:T	F24L	0.695
X:116462787:A:G	F24L	0.695
X:116462834:G:T	A8E	0.680
X:116462800:C:A	W19C	0.643
X:116462800:C:G	W19C	0.643
X:116461820:T:A	E88V	0.642
X:116462822:A:C	L12R	0.632
X:116461849:C:A	K78N	0.621
X:116461849:C:G	K78N	0.621
X:116461847:C:G	R79P	0.618
X:116461852:C:A	Q77H	0.617
X:116461852:C:G	Q77H	0.617
X:116462802:A:G	W19R	0.615

dbSNP variants (sampled 300 via entrez): RS1002063927 (X:116464693 A>G), RS1003601097 (X:116462998 C>T), RS1006735587 (X:116461563 G>A), RS1009327141 (X:116464634 T>C), RS1011416035 (X:116462614 C>A,T), RS1017864106 (X:116463158 A>C), RS1017896735 (X:116463600 A>C), RS1019594715 (X:116461604 A>G), RS1022089779 (X:116464657 G>A), RS1022131642 (X:116464188 G>A,C), RS1023759609 (X:116462635 T>A), RS1031541429 (X:116461652 T>A,C), RS1033501834 (X:116464697 C>A), RS1035175264 (X:116462665 A>G,T), RS1039160267 (X:116464485 A>G)

Disease associations

OMIM: gene MIM:300625 | 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: yes

ChEMBL targets (1): CHEMBL5169155 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases methylation	1
Cadmium	decreases expression, increases abundance	1
Cadmium Chloride	increases abundance, decreases expression	1
Permethrin	increases expression	1

ChEMBL screening assays

4 unique, capped per target: 4 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5109749	Binding	Binding affinity to recombinant KK-LC-1 (unknown origin) using FITC-labeled compound at 0.1 to 1000 uM incubated for 2 hrs and measured by FLISA assay	An auristatin-based peptide-drug conjugate targeting Kita-Kyushu lung cancer antigen 1 for precision chemoradiotherapy in gastric cancer. — Eur J Med Chem

Cellosaurus cell lines

4 cell lines: 4 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_E1M3	HyCyte MDA-MB-231 KO-hCT83	Cancer cell line	Female
CVCL_E1UN	HAP1 CT83 (-) 1	Cancer cell line	Male
CVCL_E1UP	HAP1 CT83 (-) 2	Cancer cell line	Male
CVCL_E1UQ	HAP1 CT83 (-) 3	Cancer cell line	Male

Clinical trials (associated diseases)

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