CT45A9

Summary

CT45A9 (cancer/testis antigen family 45 member A9, HGNC:51262) is a protein-coding gene on chromosome Xq26.3, encoding Cancer/testis antigen family 45 member A9 (P0DMV2).

At a glance

• Clinical variants (ClinVar): 3 total — 1 pathogenic
• MANE Select transcript: NM_001291540

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:51262
Approved symbol	CT45A9
Name	cancer/testis antigen family 45 member A9
Location	Xq26.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000270946
Ensembl biotype	protein_coding
Entrez	102723680

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000604569, ENST00000620704

RefSeq mRNA: 2 — MANE Select: NM_001291540 NM_001291540, NM_001321271

CCDS: CCDS76034

Canonical transcript exons

ENST00000620704 — 5 exons

Exon	Start	End
ENSE00001616460	135871574	135871812
ENSE00003586474	135865725	135865973
ENSE00003684760	135865251	135865344
ENSE00003734331	135867893	135868067
ENSE00003740932	135863418	135864028

Expression profiles

Bgee: expression breadth broad, 27 present calls, max score 85.12.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.12	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.47	gold quality
testis	UBERON:0000473	49.10	gold quality
right testis	UBERON:0004534	47.99	gold quality
left testis	UBERON:0004533	47.38	gold quality
bone marrow cell	CL:0002092	38.58	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
prefrontal cortex	UBERON:0000451	36.64	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
hypothalamus	UBERON:0001898	35.73	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	34.50	gold quality
nucleus accumbens	UBERON:0001882	34.25	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
bone marrow	UBERON:0002371	32.98	gold quality
caudate nucleus	UBERON:0001873	32.20	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
substantia nigra	UBERON:0002038	31.47	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
temporal lobe	UBERON:0001871	30.93	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
amygdala	UBERON:0001876	30.91	gold quality
frontal cortex	UBERON:0001870	30.25	gold quality
Ammon’s horn	UBERON:0001954	30.11	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
tonsil	UBERON:0002372	29.28	gold quality
brain	UBERON:0000955	29.27	gold quality
putamen	UBERON:0001874	29.08	gold quality
cerebral cortex	UBERON:0000956	29.05	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.33

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

34 targeting CT45A9, 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-450A-1-3P	100.00	69.33	1837
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-3133	99.81	70.92	3506
HSA-MIR-4668-5P	99.79	70.58	3782
HSA-MIR-586	99.65	70.40	2051
HSA-MIR-6716-5P	99.56	68.62	1244
HSA-MIR-190A-5P	99.54	71.45	933
HSA-MIR-190B-5P	99.54	71.40	925
HSA-MIR-4506	99.34	67.47	526
HSA-MIR-5006-5P	98.79	66.92	1246
HSA-MIR-501-5P	98.77	68.88	1328
HSA-MIR-4755-3P	98.77	65.59	1915
HSA-MIR-5572	98.55	65.84	970
HSA-MIR-3689A-5P	98.35	70.12	1049
HSA-MIR-3689B-5P	98.35	70.12	1049
HSA-MIR-3689E	98.35	70.12	1049
HSA-MIR-3689F	98.35	70.08	1052
HSA-MIR-4518	98.12	66.82	1030
HSA-MIR-6819-5P	97.96	66.59	1071
HSA-MIR-3151-3P	97.80	66.16	479
HSA-MIR-6737-5P	97.75	66.54	1044
HSA-MIR-1266-5P	97.71	66.92	1052

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ct45a	ENSMUSG00000064016
rattus_norvegicus	Ct45a9	ENSRNOG00000048059
drosophila_melanogaster	IntS6	FBGN0261383
caenorhabditis_elegans		WBGENE00000994

Paralogs (11): INTS6 (ENSG00000102786), INTS6L (ENSG00000165359), SAGE1 (ENSG00000181433), CT45A5 (ENSG00000228836), CT45A1 (ENSG00000268940), CT45A3 (ENSG00000269096), CT45A10 (ENSG00000269586), CT45A2 (ENSG00000271449), CT45A7 (ENSG00000273696), CT45A8 (ENSG00000278085), CT45A6 (ENSG00000278289)

Protein

Protein identifiers

Cancer/testis antigen family 45 member A9 — P0DMV2 (reviewed: P0DMV2)

Alternative names: Cancer/testis antigen 45A9

All UniProt accessions (1): P0DMV2

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the CT45 family.

RefSeq proteins (2): NP_001278469, NP_001308200 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029307	INT_SG_DDX_CT_C	Domain
IPR051113	Integrator_subunit6	Family

Pfam: PF15300

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0DMV2-F1	68.99	0.17

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 5 (showing top): chrXq26, MIR450A_1_3P, MIR501_5P, HE_LIM_SUN_FETAL_LUNG_C0_MYOFIBROBLAST_1_CELL, HE_LIM_SUN_FETAL_LUNG_C0_MYOFIBROBLAST_2_CELL

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

2 interactions, top by confidence:

A	B	Type	Score
PPP4R2	METTL15	psi-mi:“MI:0914”(association)	0.350

ESM2 similar proteins: A0A097I2D0, A0A1W2PP81, A0A1W2PPE2, A0A1W2PPH5, A0A1W2PPL8, A0A1W2PPW3, A0A1W2PQ09, A0A1W2PR64, A0A1W2PRV1, A6NLC8, F4HR03, O54825, O75461, P0C1H6, P0CV38, P0DMV1, P0DMV2, P0DW11, P0DW12, P0DW13, P0DW14, P40914, P49585, P49906, P81195, Q0MTC0, Q13895, Q15544, Q2N2K6, Q3SZB8, Q5DJT8, Q5RA91, Q5U1X0, Q6CER9, Q6RG77, Q6XL73, Q75DE4, Q7XHR2, Q7Z2G1, Q80WL2

Diamond homologs: A6NJ88, P0DMU7, P0DMU8, P0DMU9, P0DMV0, P0DMV1, P0DMV2, Q2TAF4, Q5DJT8, Q5HYN5, Q5JSJ4, Q5U4W6, Q6PCM2, Q7SYD9, Q8BND4, Q8NHU0, Q9NXZ1, Q9UL03, Q54Z23, Q9W485

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
144465	GRCh38/hg38 Xp22.33-q28(chrX:10701-156003242)x1	Pathogenic

SpliceAI

774 predictions. Top by Δscore:

Variant	Effect	Δscore
X:135865247:CCA:C	donor_loss	1.0000
X:135865248:CACCT:C	donor_loss	1.0000
X:135865249:A:AC	donor_gain	1.0000
X:135865249:A:AG	donor_loss	1.0000
X:135865250:C:A	donor_loss	1.0000
X:135865250:C:CC	donor_gain	1.0000
X:135865250:CCTTG:C	donor_gain	1.0000
X:135865260:T:TA	donor_gain	1.0000
X:135865340:ATATT:A	acceptor_gain	1.0000
X:135865341:TATT:T	acceptor_gain	1.0000
X:135865342:ATT:A	acceptor_gain	1.0000
X:135865342:ATTC:A	acceptor_loss	1.0000
X:135865343:TT:T	acceptor_gain	1.0000
X:135865344:TCTG:T	acceptor_loss	1.0000
X:135865345:C:CC	acceptor_gain	1.0000
X:135865345:CTG:C	acceptor_loss	1.0000
X:135865351:A:AC	acceptor_gain	1.0000
X:135865351:A:C	acceptor_gain	1.0000
X:135865353:G:C	acceptor_gain	1.0000
X:135865353:G:GC	acceptor_gain	1.0000
X:135865354:T:C	acceptor_gain	1.0000
X:135865354:T:TC	acceptor_gain	1.0000
X:135865721:TTA:T	donor_loss	1.0000
X:135865721:TTACT:T	donor_loss	1.0000
X:135865722:TACTT:T	donor_loss	1.0000
X:135865723:A:AC	donor_gain	1.0000
X:135865723:ACTT:A	donor_loss	1.0000
X:135865723:ACTTT:A	donor_loss	1.0000
X:135865724:C:A	donor_loss	1.0000
X:135865724:C:CA	donor_gain	1.0000

AlphaMissense

1265 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:135865258:C:G	A169P	0.896
X:135865762:T:A	K127N	0.845
X:135865762:T:G	K127N	0.845
X:135868014:A:C	F16L	0.845
X:135868014:A:T	F16L	0.845
X:135868016:A:G	F16L	0.845
X:135865328:G:C	F145L	0.844
X:135865328:G:T	F145L	0.844
X:135865330:A:G	F145L	0.844
X:135865306:C:G	G153R	0.843
X:135865306:C:T	G153R	0.843
X:135865277:A:C	F162L	0.816
X:135865277:A:T	F162L	0.816
X:135865279:A:G	F162L	0.816
X:135865774:A:C	N123K	0.776
X:135865774:A:T	N123K	0.776
X:135865754:A:G	L130S	0.774
X:135865320:A:T	L148H	0.769
X:135865280:A:C	F161L	0.755
X:135865280:A:T	F161L	0.755
X:135865282:A:G	F161L	0.755
X:135863999:A:G	L181P	0.745
X:135865281:A:G	F161S	0.730
X:135863999:A:T	L181H	0.728
X:135865273:A:G	S164P	0.725
X:135864010:A:C	F177L	0.722
X:135864010:A:T	F177L	0.722
X:135864012:A:G	F177L	0.722
X:135867972:C:A	R30S	0.711
X:135867972:C:G	R30S	0.711

dbSNP variants (sampled 300 via entrez): RS1157611383 (X:135868285 A>G), RS1159113857 (X:135863379 A>C), RS1162791841 (X:135863609 C>A,T), RS1164191457 (X:135872023 G>A), RS1167683711 (X:135863130 C>G), RS1168044244 (X:135867300 G>A,C,T), RS1168659002 (X:135867335 T>C), RS1175789706 (X:135867718 A>T), RS1175946003 (X:135867882 G>A), RS1180895442 (X:135868372 A>C), RS1182751748 (X:135863398 C>T), RS1183860574 (X:135863677 C>T), RS1185433119 (X:135869539 A>G), RS1193997562 (X:135863853 G>A), RS1196166448 (X:135863214 G>A)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (1): congenital portosystemic shunt (MONDO:0018811)

Orphanet (1): Congenital portosystemic shunt (Orphanet:480531)

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

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT06041906	Not specified	ENROLLING_BY_INVITATION	International Registry of Congenital Portosystemic Shunt (IRCPSS)
NCT07314814	Not specified	NOT_YET_RECRUITING	Genetic Hallmarks of Patients With Congenital Portosystemic Shunts and Portopulmonary Hypertension