CT55

Summary

CT55 (cancer/testis antigen 55, HGNC:26047) is a protein-coding gene on chromosome Xq26.3, encoding Cancer/testis antigen 55 (Q8WUE5). Plays a role in spermatogenesis, possibly acting in the regulation of the autophagy pathway.

Involved in spermatogenesis. Located in acrosomal vesicle and sperm flagellum. Implicated in X-linked spermatogenic failure 7.

Source: NCBI Gene 54967 — RefSeq curated summary.

At a glance

• Gene–disease (curated): spermatogenic failure, X-linked, 7 (Limited, GenCC)
• Clinical variants (ClinVar): 17 total — 1 pathogenic
• Phenotypes (HPO): 14
• MANE Select transcript: NM_001031705

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26047
Approved symbol	CT55
Name	cancer/testis antigen 55
Location	Xq26.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20527
Ensembl gene	ENSG00000169551
Ensembl biotype	protein_coding
OMIM	301105
Entrez	54967

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000276241, ENST00000344129

RefSeq mRNA: 2 — MANE Select: NM_001031705 NM_001031705, NM_017863

CCDS: CCDS14647, CCDS35400

Canonical transcript exons

ENST00000276241 — 6 exons

Exon	Start	End
ENSE00001126635	135156540	135157028
ENSE00001300814	135157316	135157503
ENSE00001309025	135171078	135171398
ENSE00001644388	135160411	135160555
ENSE00001663689	135158199	135158311
ENSE00001670525	135169594	135169778

Expression profiles

Bgee: expression breadth broad, 59 present calls, max score 81.22.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	81.22	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.33	gold quality
right testis	UBERON:0004534	66.44	gold quality
testis	UBERON:0000473	65.09	gold quality
left testis	UBERON:0004533	63.89	gold quality
superior frontal gyrus	UBERON:0002661	56.11	gold quality
primary visual cortex	UBERON:0002436	50.98	gold quality
ventricular zone	UBERON:0003053	48.41	gold quality
Brodmann (1909) area 9	UBERON:0013540	47.89	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	47.70	gold quality
prefrontal cortex	UBERON:0000451	47.65	gold quality
sural nerve	UBERON:0015488	47.64	gold quality
frontal cortex	UBERON:0001870	46.37	gold quality
cerebral cortex	UBERON:0000956	46.30	gold quality
anterior cingulate cortex	UBERON:0009835	46.16	gold quality
putamen	UBERON:0001874	45.97	gold quality
temporal lobe	UBERON:0001871	44.53	gold quality
nucleus accumbens	UBERON:0001882	44.52	gold quality
amygdala	UBERON:0001876	44.40	gold quality
adrenal tissue	UBERON:0018303	44.38	silver quality
Ammon’s horn	UBERON:0001954	43.89	gold quality
cortex of kidney	UBERON:0001225	43.73	gold quality
caudate nucleus	UBERON:0001873	43.63	gold quality
right frontal lobe	UBERON:0002810	43.49	gold quality
bone marrow cell	CL:0002092	43.30	gold quality
brain	UBERON:0000955	41.83	gold quality
right adrenal gland cortex	UBERON:0035827	40.98	gold quality
hypothalamus	UBERON:0001898	40.96	gold quality
adrenal gland	UBERON:0002369	40.35	silver quality
left adrenal gland cortex	UBERON:0035825	40.31	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.97

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

46 targeting CT55, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-6748-5P	100.00	65.81	1057
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-302A-3P	99.89	71.23	1777
HSA-MIR-302B-3P	99.89	71.23	1777
HSA-MIR-302C-3P	99.89	71.20	1778
HSA-MIR-302D-3P	99.89	71.25	1777
HSA-MIR-9902	99.89	69.15	2250
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-30A-3P	99.87	69.74	2928
HSA-MIR-30D-3P	99.87	69.92	2917
HSA-MIR-30E-3P	99.87	69.68	2942
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349
HSA-MIR-373-3P	99.84	70.68	1668
HSA-MIR-520E-3P	99.84	70.55	1698
HSA-MIR-1323	99.83	69.89	2471
HSA-MIR-372-3P	99.83	70.58	1691
HSA-MIR-520A-3P	99.83	70.59	1687
HSA-MIR-520B-3P	99.83	70.56	1699
HSA-MIR-520C-3P	99.83	70.56	1699
HSA-MIR-520D-3P	99.83	70.78	1676
HSA-MIR-8076	99.78	68.52	1170
HSA-MIR-548O-3P	99.74	69.30	2228
HSA-MIR-8084	99.73	69.57	1760

Literature-anchored findings (GeneRIF, showing 3)

• A novel BRCA2-interacting protein, BJ-HCC-20A, which is reported to be a potential cancer-testis antigen, was identified. (PMID:18307534)
• the relapse rate of CXorf48-specific CTL-negative patients was 63.6%, compared to 0% in CXorf48-specific CTL-positive patients. These results indicate that CXorf48 could be a promising therapeutic target of LSCs for immunotherapy to obtain durable treatment-free remission in CML patients. (PMID:28862699)
• Deficiency of cancer/testis antigen gene CT55 causes male infertility in humans and mice. (PMID:36481789)

Cross-species orthologs

16 orthologs

Organism	Symbol	Gene ID
danio_rerio	setx	ENSDARG00000022996
danio_rerio	dna2	ENSDARG00000078759
rattus_norvegicus	LOC120099287	ENSRNOG00000070753
rattus_norvegicus		ENSRNOG00000074002
rattus_norvegicus		ENSRNOG00000082477
rattus_norvegicus		ENSRNOG00000090738
rattus_norvegicus		ENSRNOG00000090861
rattus_norvegicus		ENSRNOG00000091088
drosophila_melanogaster	CG6701	FBGN0033889
drosophila_melanogaster	Mov10	FBGN0034187
drosophila_melanogaster	armi	FBGN0041164
drosophila_melanogaster	Dna2	FBGN0288690
caenorhabditis_elegans		WBGENE00001016
caenorhabditis_elegans	Y106G6D.5	WBGENE00014965
caenorhabditis_elegans	sosi-1	WBGENE00016565
caenorhabditis_elegans	eri-7	WBGENE00016566

Paralogs (10): UPF1 (ENSG00000005007), AQR (ENSG00000021776), MOV10L1 (ENSG00000073146), SETX (ENSG00000107290), ZNFX1 (ENSG00000124201), HELZ2 (ENSG00000130589), IGHMBP2 (ENSG00000132740), DNA2 (ENSG00000138346), MOV10 (ENSG00000155363), HELZ (ENSG00000198265)

Protein

Protein identifiers

Cancer/testis antigen 55 — Q8WUE5 (reviewed: Q8WUE5)

Alternative names: Tumor antigen BJ-HCC-20

All UniProt accessions (1): Q8WUE5

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in spermatogenesis, possibly acting in the regulation of the autophagy pathway.

Subunit / interactions. Interacts with GABARAP; this interaction may be important for GABARAP protein stability. Isoform 1 interacts with LAMP2; this interaction may be important for LAMP2 protein stability.

Subcellular location. Cytoplasm. Cytoplasmic vesicle. Secretory vesicle. Acrosome. Cell projection. Cilium. Flagellum.

Tissue specificity. Testis-specific. Expressed in spermatozoa (at protein level).

Disease relevance. Spermatogenic failure, X-linked, 7 (SPGFX7) [MIM:301106] A male infertility disorder characterized by a significant reduction in sperm count and motility, and aberrant sperm morphology with abnormalities of the head and flagella. Patient sperm show insufficient individualization, excessive residual cytoplasm, and defects in acrosome development. The disease is caused by variants affecting the gene represented in this entry.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8WUE5-1	1, BJ-HCC-20A	yes
Q8WUE5-2	2, BJ-HCC-20B

RefSeq proteins (2): NP_001026875, NP_060333 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR012340	NA-bd_OB-fold	Homologous_superfamily
IPR025223	S1-like_RNA-bd_dom	Domain

Pfam: PF14444

UniProt features (5 total): chain 1, region of interest 1, compositionally biased region 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WUE5-F1	75.60	0.36

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 68 (showing top): GOCC_SECRETORY_GRANULE, GOBP_MALE_GAMETE_GENERATION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, GOCC_SECRETORY_VESICLE, GOCC_MOTILE_CILIUM, GOCC_ACROSOMAL_VESICLE, GOCC_CILIUM, chrXq26, GOCC_9PLUS2_MOTILE_CILIUM, KRAS.600_UP.V1_DN, ZHONG_RESPONSE_TO_AZACITIDINE_AND_TSA_UP, MIR6780B_5P, MIR4725_3P, MIR6853_3P, MIR12120

GO Biological Process (1): spermatogenesis (GO:0007283)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (7): acrosomal vesicle (GO:0001669), cytoplasm (GO:0005737), sperm flagellum (GO:0036126), cilium (GO:0005929), cytoplasmic vesicle (GO:0031410), motile cilium (GO:0031514), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
developmental process involved in reproduction	1
male gamete generation	1
binding	1
secretory granule	1
intracellular anatomical structure	1
9+2 motile cilium	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
cytoplasm	1
intracellular vesicle	1
cilium	1

Protein interactions and networks

STRING

658 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CT55	CT45A1	Q5HYN5	525
CT55	CT47A11	Q5JQC4	522
CT55	GAGE2A	Q6NT46	507
CT55	ACTL8	Q9H568	507
CT55	EPPIN	O95925	506
CT55	XAGE1B	Q9HD64	506
CT55	A0A1W2PQG5	A0A1W2PQG5	505
CT55	PASD1	Q8IV76	493
CT55	MAGEA10	P43363	480
CT55	SAGE1	Q9NXZ1	480
CT55	CSAG2	Q9Y5P2	479
CT55	MAGEC1	O60732	476
CT55	FTHL17	Q9BXU8	476
CT55	SSX4	O60224	447
CT55	SPANXN1	Q5VSR9	447

IntAct

105 interactions, top by confidence:

A	B	Type	Score
CT55	TXLNB	psi-mi:“MI:0915”(physical association)	0.670
KIAA0753	CT55	psi-mi:“MI:0915”(physical association)	0.560
KLHL42	CT55	psi-mi:“MI:0915”(physical association)	0.560
PIH1D2	CT55	psi-mi:“MI:0915”(physical association)	0.560
SHC3	CT55	psi-mi:“MI:0915”(physical association)	0.560
SAMD11	CT55	psi-mi:“MI:0915”(physical association)	0.560
C2CD6	CT55	psi-mi:“MI:0915”(physical association)	0.560
KLC3	CT55	psi-mi:“MI:0915”(physical association)	0.560
KYNU	CT55	psi-mi:“MI:0915”(physical association)	0.560
EXOC7	CT55	psi-mi:“MI:0915”(physical association)	0.560
MEMO1	CT55	psi-mi:“MI:0915”(physical association)	0.560
FAAP20	CT55	psi-mi:“MI:0915”(physical association)	0.560
SNF8	CT55	psi-mi:“MI:0915”(physical association)	0.560
LYPLAL1	CT55	psi-mi:“MI:0915”(physical association)	0.560
BFSP2	CT55	psi-mi:“MI:0915”(physical association)	0.560
TLE5	CT55	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (73): CT55 (Two-hybrid), TXLNB (Two-hybrid), USP4 (Affinity Capture-MS), SYNM (Affinity Capture-MS), UHRF1BP1L (Affinity Capture-MS), VPS33A (Affinity Capture-MS), VPS41 (Affinity Capture-MS), VPS18 (Affinity Capture-MS), VPS16 (Affinity Capture-MS), CNOT1 (Affinity Capture-MS), C12orf45 (Affinity Capture-MS), CNOT8 (Affinity Capture-MS), CNOT10 (Affinity Capture-MS), RQCD1 (Affinity Capture-MS), LRBA (Affinity Capture-MS)

ESM2 similar proteins: A0JNQ6, A2RT67, A2RUS2, A6NC42, A6NGQ2, A9X185, O75031, O75817, O94955, O95267, P50747, Q06VW1, Q0II25, Q0ZFW8, Q1RMS8, Q1RMZ1, Q29108, Q2TBA3, Q3T0J1, Q3TYS2, Q4VX76, Q568D5, Q568M3, Q587J7, Q5JSQ8, Q5T9G4, Q5ZLS2, Q62522, Q69ZK0, Q6AYA6, Q6P5G6, Q7Z7H3, Q80X86, Q86WV5, Q8BXK4, Q8C0Q9, Q8CHQ0, Q8TCU6, Q8WUE5, Q91Z62

Diamond homologs: Q14BQ3, Q8WUE5, Q99MV5, Q9BXT6, P23249, P30771, P34243, P39369, P42694, Q09820, Q0V8H6, Q1LXK4, Q1LXK5, Q54I89, Q5ZKD7, Q6DFV5, Q6J5K9, Q6NYU2, Q86AS0, Q86YA3, Q8GYD9, Q92900, Q9EPU0, Q9FJR0, Q9HCE1, Q9HEH1, Q9VYS3, B6SFA4, F1RCY6, O76512, O94387, Q0VGT4, Q6ZQJ5, Q7Z333, Q9BYK8

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 35 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

GO biological processes:

GO term	Partners	Fold	FDR
intermediate filament organization	5	36.5×	4e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	13
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
2499997	NM_001031705.3(CT55):c.465T>A (p.Tyr155Ter)	Pathogenic

SpliceAI

899 predictions. Top by Δscore:

Variant	Effect	Δscore
X:135160487:T:TA	donor_gain	1.0000
X:135169588:TCTCA:T	donor_loss	1.0000
X:135169589:CTCA:C	donor_loss	1.0000
X:135169590:TCA:T	donor_loss	1.0000
X:135169591:CACCT:C	donor_loss	1.0000
X:135169774:GTCAC:G	acceptor_gain	1.0000
X:135169775:TCAC:T	acceptor_gain	1.0000
X:135169776:CAC:C	acceptor_gain	1.0000
X:135169776:CACC:C	acceptor_gain	1.0000
X:135169777:AC:A	acceptor_gain	1.0000
X:135169777:ACC:A	acceptor_gain	1.0000
X:135169777:ACCT:A	acceptor_loss	1.0000
X:135169778:CC:C	acceptor_gain	1.0000
X:135169778:CCT:C	acceptor_gain	1.0000
X:135169778:CCTA:C	acceptor_loss	1.0000
X:135169779:C:CC	acceptor_gain	1.0000
X:135169783:A:T	acceptor_gain	1.0000
X:135169786:A:C	acceptor_gain	1.0000
X:135157347:T:A	donor_gain	0.9900
X:135158198:CCT:C	donor_gain	0.9900
X:135158312:C:CC	acceptor_gain	0.9900
X:135160464:T:C	donor_gain	0.9900
X:135160505:T:TA	donor_gain	0.9900
X:135169592:A:AC	donor_gain	0.9900
X:135169593:C:CC	donor_gain	0.9900
X:135169775:TCACC:T	acceptor_gain	0.9900
X:135169776:CACCT:C	acceptor_gain	0.9900
X:135169779:C:A	acceptor_gain	0.9900
X:135169780:T:A	acceptor_gain	0.9900
X:135169782:CAAGA:C	acceptor_gain	0.9900

AlphaMissense

1728 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:135157447:G:C	F198L	0.981
X:135157447:G:T	F198L	0.981
X:135157449:A:G	F198L	0.981
X:135157345:T:A	R232S	0.980
X:135157345:T:G	R232S	0.980
X:135157391:A:T	V217D	0.979
X:135169696:G:C	F59L	0.971
X:135169696:G:T	F59L	0.971
X:135169698:A:G	F59L	0.971
X:135158307:A:C	F143L	0.969
X:135158307:A:T	F143L	0.969
X:135158309:A:G	F143L	0.969
X:135157346:C:G	R232T	0.962
X:135157448:A:G	F198S	0.960
X:135157409:G:T	P211H	0.957
X:135157343:G:T	A233E	0.955
X:135169745:A:T	V43D	0.955
X:135157472:C:T	G190E	0.950
X:135158290:T:G	D149A	0.950
X:135158290:T:C	D149G	0.949
X:135157369:G:C	S224R	0.947
X:135157369:G:T	S224R	0.947
X:135157371:T:G	S224R	0.947
X:135157347:T:C	R232G	0.944
X:135158291:C:G	D149H	0.943
X:135158284:A:G	L151S	0.939
X:135158302:G:T	P145H	0.939
X:135157410:G:A	P211S	0.938
X:135157450:A:C	F197L	0.937
X:135157450:A:T	F197L	0.937

dbSNP variants (sampled 300 via entrez): RS111378411 (X:135158618 T>G), RS111527783 (X:135159600 T>C), RS111593484 (X:135164100 G>A), RS111629738 (X:135158131 T>G), RS112085692 (X:135169968 T>A), RS112336234 (X:135164126 C>G,T), RS113172956 (X:135169811 G>A), RS1156375591 (X:135171846 A>G), RS1156678956 (X:135169010 T>A), RS1156888676 (X:135159971 G>A), RS1157160436 (X:135162747 C>T), RS1157167110 (X:135157717 G>A), RS1157587313 (X:135159058 C>T), RS1157729350 (X:135159551 C>T), RS1157950505 (X:135158452 CT>C)

Disease associations

OMIM: gene MIM:301105 | disease phenotypes: MIM:301106

GenCC curated gene-disease

Disease	Classification	Inheritance
spermatogenic failure, X-linked, 7	Limited	Unknown

Mondo (1): spermatogenic failure, X-linked, 7 (MONDO:0957202)

Orphanet (0):

HPO phenotypes

14 total (14 of 14 shown, HPO-id order):

HPO	Term
HP:0000027	Azoospermia
HP:0000118	Phenotypic abnormality
HP:0000837	Increased circulating gonadotropin level
HP:0001417	X-linked inheritance
HP:0003251	Male infertility
HP:0008669	Abnormal spermatogenesis
HP:0008734	Decreased testicular size
HP:0011462	Young adult onset
HP:0011961	Non-obstructive azoospermia
HP:0011962	Obstructive azoospermia
HP:0012205	Globozoospermia
HP:0012207	Reduced sperm motility
HP:0034309	Multiflagellar spermatozoa
HP:0034795	Excess residual spermatozoal cytoplasm

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Resveratrol	affects cotreatment, decreases expression	1
Acetaminophen	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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