CT47A1

Summary

CT47A1 (cancer/testis antigen family 47 member A1, HGNC:33282) is a protein-coding gene on chromosome Xq24, encoding Cancer/testis antigen 47A (Q5JQC4).

This locus represents a member of the cancer/testis gene family 47. This family, also known as CT47, is comprised of 13 nearly identical loci clustered at Xq24. This locus is the most telomeric of the cluster.

Source: NCBI Gene 728096 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 4 total
• MANE Select transcript: NM_001080146

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33282
Approved symbol	CT47A1
Name	cancer/testis antigen family 47 member A1
Location	Xq24
Locus type	gene with protein product
Status	Approved
Aliases	CT47.1
Ensembl gene	ENSG00000236371
Ensembl biotype	protein_coding
OMIM	300780
Entrez	728096

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000433030

RefSeq mRNA: 1 — MANE Select: NM_001080146 NM_001080146

CCDS: CCDS35391

Canonical transcript exons

ENST00000433030 — 3 exons

Exon	Start	End
ENSE00001620868	120984788	120985760
ENSE00001671378	120982476	120982606
ENSE00001691035	120983745	120983900

Expression profiles

Bgee: expression breadth tissue_specific, 9 present calls, max score 78.11.

Top tissues by expression

131 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	78.11	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	74.53	gold quality
bone marrow cell	CL:0002092	37.95	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
bone marrow	UBERON:0002371	32.66	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
placenta	UBERON:0001987	29.91	silver quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
right testis	UBERON:0004534	29.79	gold quality
testis	UBERON:0000473	29.39	gold quality
prefrontal cortex	UBERON:0000451	29.04	gold quality
liver	UBERON:0002107	28.40	gold quality
blood	UBERON:0000178	28.18	silver quality
duodenum	UBERON:0002114	28.14	gold quality
left testis	UBERON:0004533	27.78	gold quality
lymph node	UBERON:0000029	27.57	gold quality
tonsil	UBERON:0002372	27.05	gold quality
islet of Langerhans	UBERON:0000006	26.55	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
gall bladder	UBERON:0002110	25.98	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	25.89	gold quality
urinary bladder	UBERON:0001255	25.72	gold quality
leukocyte	CL:0000738	25.26	gold quality
monocyte	CL:0000576	25.03	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

14 targeting CT47A1, 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-5696	99.98	72.36	4487
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-6505-5P	99.73	69.25	1595
HSA-MIR-1290	99.59	69.90	2079
HSA-MIR-190A-5P	99.54	71.45	933
HSA-MIR-190B-5P	99.54	71.40	925
HSA-MIR-12123	99.52	71.79	2990
HSA-MIR-664A-3P	99.22	71.08	2696
HSA-MIR-653-3P	98.31	67.71	1542
HSA-MIR-6773-3P	98.17	65.51	1213
HSA-MIR-6839-5P	96.74	68.29	1088
HSA-MIR-378J	96.44	66.20	1020
HSA-MIR-6760-3P	96.35	68.31	1001

Cross-species orthologs

0 orthologs

Paralogs (13): CT47A10 (ENSG00000224089), CT47A6 (ENSG00000226023), CT47A9 (ENSG00000226600), CT47A12 (ENSG00000226685), CT47A11 (ENSG00000226929), CT47A7 (ENSG00000228517), CT47A8 (ENSG00000230347), CT47A4 (ENSG00000230594), CT47A3 (ENSG00000236126), CT47B1 (ENSG00000236446), CT47A5 (ENSG00000237957), CT47A2 (ENSG00000242362), CT47C1 (ENSG00000277535)

Protein

Protein identifiers

Cancer/testis antigen 47A — Q5JQC4 (reviewed: Q5JQC4)

Alternative names: Cancer/testis antigen 47

All UniProt accessions (1): Q5JQC4

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Strongly expressed in testis, low expression in placenta, and very low expression in brain.

RefSeq proteins (1): NP_001073615* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR028930	CT47	Family

Pfam: PF15623

UniProt features (14 total): compositionally biased region 9, region of interest 2, chain 1, sequence conflict 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5JQC4-F1	53.93	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 5 (showing top): chrXq24, MIR5696, MIR12123, MIR664A_3P, FOURATI_BLOOD_TWINRIX_AGE_25_83YO_RESPONDERS_VS_POOR_RESPONDERS_0DY_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

350 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CT47A1	GPHRA	B7ZAQ6	952
CT47A1	TAF11L5	A0A1W2PP81	654
CT47A1	TAF11L4	A0A1W2PPE2	654
CT47A1	TAF11L3	A0A1W2PRV1	654
CT47A1	TAF11L2	A6NLC8	620
CT47A1	CTAG2	O75638	616
CT47A1	CT45A1	Q5HYN5	602
CT47A1	MAGEA1	P43355	584
CT47A1	A0A1W2PRN6	A0A1W2PRN6	544
CT47A1	CT55	Q8WUE5	522
CT47A1	PRR20A	P86496	522
CT47A1	A0A1W2PQG5	A0A1W2PQG5	520
CT47A1	SPANXA1	Q9NS26	507
CT47A1	CSAG2	Q9Y5P2	507
CT47A1	USP17L23	D6RBM5	506

IntAct

3 interactions, top by confidence:

A	B	Type	Score
CSAG2	CAMK2D	psi-mi:“MI:0914”(association)	0.350
NXT2	MYO1G	psi-mi:“MI:0914”(association)	0.350

BioGRID (15): CT47A3 (Positive Genetic), CT47A2 (Positive Genetic), CT47A6 (Positive Genetic), CT47A5 (Positive Genetic), CT47A1 (Positive Genetic), CT47A7 (Positive Genetic), CT47A11 (Positive Genetic), CT47A4 (Positive Genetic), CT47A10 (Positive Genetic), CT47A12 (Positive Genetic), CT47A9 (Positive Genetic), CT47A8 (Positive Genetic), CT47A6 (Negative Genetic), CT47A3 (Negative Genetic), CT47A1 (Affinity Capture-MS)

ESM2 similar proteins: A0A0U1RQG5, A1L429, A6NDE8, A6NER3, A6NGK3, E1AZ71, O08664, O60829, O75459, O76087, P0C2W7, P0CL80, P0CL81, P0CL82, P0DSO3, P0DTW1, P52651, P62521, P86478, P86479, P86480, P86481, P86496, Q13066, Q13069, Q13070, Q17QW4, Q28181, Q2T9P9, Q32PA2, Q4V321, Q4V326, Q5JQC4, Q5U2Y8, Q62100, Q63803, Q64256, Q6NT46, Q6X7S9, Q7Z2X7

Diamond homologs: A0A0U1RQG5, P0C2W7, Q5JQC4

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	3
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

352 predictions. Top by Δscore:

Variant	Effect	Δscore
X:120984805:T:TA	donor_gain	1.0000
X:120983898:CTT:C	acceptor_gain	0.9900
X:120983903:T:C	acceptor_gain	0.9900
X:120983903:T:TC	acceptor_gain	0.9900
X:120984786:AC:A	donor_gain	0.9900
X:120984787:CC:C	donor_gain	0.9900
X:120984787:CCCT:C	donor_gain	0.9900
X:120983901:C:CC	acceptor_gain	0.9800
X:120983902:T:C	acceptor_gain	0.9800
X:120983896:GACTT:G	acceptor_gain	0.9700
X:120984782:CCTTA:C	donor_loss	0.9700
X:120984783:CTTAC:C	donor_loss	0.9700
X:120984784:TTAC:T	donor_loss	0.9700
X:120984785:TA:T	donor_loss	0.9700
X:120984787:C:G	donor_loss	0.9700
X:120983924:A:C	acceptor_gain	0.9600
X:120983932:C:CT	acceptor_gain	0.9600
X:120983761:TC:T	donor_gain	0.9500
X:120984258:T:TG	acceptor_gain	0.9500
X:120983899:TT:T	acceptor_gain	0.9400
X:120984786:A:AC	donor_gain	0.9400
X:120984787:C:CC	donor_gain	0.9400
X:120984781:T:A	donor_gain	0.9300
X:120983900:TC:T	acceptor_loss	0.9200
X:120983901:CTTT:C	acceptor_loss	0.9200
X:120983902:T:A	acceptor_loss	0.9200
X:120984786:ACC:A	donor_gain	0.9200
X:120984787:CCC:C	donor_gain	0.9200
X:120982605:ATCTG:A	acceptor_loss	0.9100
X:120982606:TCT:T	acceptor_loss	0.9100

AlphaMissense

1866 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:120985111:A:G	I140T	0.913
X:120985141:A:G	L130P	0.877
X:120985150:A:T	V127D	0.855
X:120984964:A:G	I189T	0.845
X:120985174:A:G	I119T	0.845
X:120985167:G:C	F121L	0.841
X:120985167:G:T	F121L	0.841
X:120985169:A:G	F121L	0.841
X:120983872:C:A	W257C	0.838
X:120983872:C:G	W257C	0.838
X:120985117:T:A	D138V	0.838
X:120985111:A:C	I140S	0.832
X:120985190:A:C	Y114D	0.815
X:120983874:A:G	W257R	0.799
X:120983874:A:T	W257R	0.799
X:120985145:A:G	S129P	0.792
X:120985138:A:G	L131P	0.789
X:120985120:T:A	N137I	0.757
X:120985473:G:C	S19R	0.753
X:120985473:G:T	S19R	0.753
X:120985475:T:G	S19R	0.753
X:120985113:G:C	H139Q	0.749
X:120985113:G:T	H139Q	0.749
X:120985525:G:C	S2C	0.748
X:120985525:G:A	S2F	0.747
X:120985525:G:T	S2Y	0.745
X:120985111:A:T	I140N	0.742
X:120985174:A:C	I119S	0.742
X:120985129:A:G	L134P	0.736
X:120985132:C:G	R133P	0.734

dbSNP variants (sampled 300 via entrez): RS1002455564 (X:120987738 G>A,T), RS1002609875 (X:120987378 G>T), RS1002898131 (X:120987464 C>A,G,T), RS1004304081 (X:120987445 C>A,G,T), RS1006608188 (X:120987133 A>C), RS1008192801 (X:120987115 C>G,T), RS1008725143 (X:120986897 C>G,T), RS1009499701 (X:120986881 G>A,T), RS1010791353 (X:120987370 G>A,T), RS1011344080 (X:120987207 A>G), RS1018392796 (X:120986906 C>T), RS1018692306 (X:120987129 A>T), RS1022267159 (X:120987228 T>G), RS1025101073 (X:120987452 G>A), RS1026353915 (X:120987694 T>G)

Disease associations

OMIM: gene MIM:300780 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): male infertility (MONDO:0005372)

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D007248	Infertility, Male	C12.100.500.430; C12.100.750.700; C12.200.294.430

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT02202382	PHASE4	COMPLETED	Effects of Korean Red Ginseng on Male Infertility
NCT02204826	PHASE4	COMPLETED	Effects of Korean Red Ginseng on Semen Parameters in Male Infertility Patients: a Randomized, Placebo-controlled, Double-blind Clinical Study
NCT03802864	PHASE4	COMPLETED	Post-operative Pain Control of Testicular Sperm Extraction Using Liposomal Bupivacaine
NCT06100432	PHASE4	ACTIVE_NOT_RECRUITING	Effect of Eurycoma Longifolia (DLBS5055) and Multivitamins (Vitamin C+Vitamin E+ β-carotene) for Infertile Males
NCT07523022	PHASE4	ENROLLING_BY_INVITATION	Comparison of the Effect of Gonadotropin and Clomiphene Citrate Treatment on Sperm Parameters and the Outcome of Assisted Reproductive Procedures in Subfertile Men Based on the APHRODITE Groups
NCT00975117	PHASE3	COMPLETED	Spermotrend in the Treatment of Male Infertility
NCT01407432	PHASE3	COMPLETED	Impact of Folates in the Care of the Male Infertility
NCT01895816	PHASE3	COMPLETED	Herbal Tonic Fertile Supplement(ZO2C5)
NCT02605070	PHASE3	TERMINATED	Pilot Study on the Effects of FSH Treatment on the Epigenetic Characteristics of Spermatozoa in Infertile Patients With Severe Oligozoospermia
NCT07402759	PHASE3	ACTIVE_NOT_RECRUITING	Impact of tdrd9 Gene Mutations in the Therapeutic Response to L-carnitine in Oligoasthenozoospermic Men
NCT01880086	PHASE2	COMPLETED	Clomiphene Citrate for the Treatment of Low Testosterone Associated With Chronic Opioid Pain Medication Administration
NCT02061384	PHASE2	COMPLETED	RA-2 13-cis Retinoic Acid (Isotretinoin)
NCT02421887	PHASE2	COMPLETED	Males, Antioxidants, and Infertility Trial
NCT05200663	PHASE2	UNKNOWN	Efficacy Comparison of Tamoxifen and Tamoxifen With Antioxidants on Semen Quality of Male With Idiopathic Infertility
NCT05290558	PHASE2	ACTIVE_NOT_RECRUITING	The Therapeutic Effects of Bu Shen Yi Jing Pill on Semen Quality in Sub Fertile Males: a Randomized Controlled Trial
NCT06091969	PHASE2	NOT_YET_RECRUITING	Supplementation for Male Subfertility
NCT01595308	PHASE1	COMPLETED	A Pilot Study to Evaluate the Effect of Pomegranate Juice on Semen Parameters in Healthy Male Volunteers
NCT02122211	PHASE1	COMPLETED	Choline Dehydrogenase and Sperm Function: Effects of Betaine
NCT02575924	PHASE1	UNKNOWN	Influence of Culture Media on Clinical Outcomes in Poor Responders or Severe Male Infertility
NCT01304927	PHASE2/PHASE3	COMPLETED	Vitamin D Supplementation and Male Infertility: The CBG-study a Randomized Clinical Trial
NCT02349945	PHASE2/PHASE3	COMPLETED	FSH Receptor Polymorphism p.N680S and Efficacy of FSH Therapy
NCT05222841	PHASE2/PHASE3	COMPLETED	The Effectiveness of Spermotrend Food Supplement in the Treatment of Male Infertility
NCT05616598	PHASE2/PHASE3	COMPLETED	Effect of New Oral Treatment for Hepatitis C Virus on Seminal Parameters
NCT02025270	PHASE1/PHASE2	COMPLETED	MSCs For Treatment of Azoospermic Patients
NCT04541459	EARLY_PHASE1	UNKNOWN	Validation of New Devices Against Ambient Electromagnetic Radiation
NCT05792813	EARLY_PHASE1	UNKNOWN	Efficacy and Safety of Linggui Yangyuan Paste in Patients With Male Infertility
NCT06188936	EARLY_PHASE1	COMPLETED	Home Semen Analysis Tests As a Screening Tool for Fertility Patients
NCT00012480	Not specified	COMPLETED	Effect of Environmental Exposures on the Egg Fertilizing Ability of Human Sperm
NCT00044369	Not specified	COMPLETED	Role of the Toxic Metal Cadmium in the Mechanism Producing Infertility With a Varicocele
NCT00119925	Not specified	UNKNOWN	‘SPRING’-Study: Subfertility Guidelines: Patient Related Implementation in the Netherlands Among Gynaecologists
NCT00178516	Not specified	COMPLETED	Vitamin E and Male Infertility
NCT00315029	Not specified	COMPLETED	Patient-Centered Implementation Trial for Single Embryo Transfer
NCT00341120	Not specified	COMPLETED	Genetic Causes of Male Infertility
NCT00481403	Not specified	COMPLETED	Study of Sperm Molecular Factors Implicated in Male Fertility
NCT00548977	Not specified	COMPLETED	Genetic Studies Spermatogenic Failure
NCT00596739	Not specified	COMPLETED	A Study of the Pre- and Post-operative Semen Analyses and Reproductive Hormone Levels of Men Undergoing Weight-reduction Surgery
NCT00756561	Not specified	COMPLETED	HOP-2A - Intratesticular Hormone Levels
NCT00961558	Not specified	TERMINATED	Canadian Varicocelectomy Initiative (CVI): Effects on Male Fertility and Testicular Function of Varicocelectomy
NCT01075334	Not specified	UNKNOWN	Is a Carnitine Based Food Supplement (PorimoreTM) for Infertile Men Superior to Folate and Zinc With Regard to Pregnancy Rates in Intrauterine Insemination Cycles?
NCT01178463	Not specified	UNKNOWN	Spermatogonial Stem Cells in Azoospermic Patients: a Comparison Between Obstructive and Non-obstructive Azoospermia