CT47A6

Summary

CT47A6 (cancer/testis antigen family 47 member A6, HGNC:33287) 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.

Source: NCBI Gene 728062 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 4 total
• MANE Select transcript: NM_001080141

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33287
Approved symbol	CT47A6
Name	cancer/testis antigen family 47 member A6
Location	Xq24
Locus type	gene with protein product
Status	Approved
Aliases	CT47.6
Ensembl gene	ENSG00000226023
Ensembl biotype	protein_coding
OMIM	300785
Entrez	728062

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000419194

RefSeq mRNA: 1 — MANE Select: NM_001080141 NM_001080141

CCDS: CCDS35386

Canonical transcript exons

ENST00000419194 — 3 exons

Exon	Start	End
ENSE00001872210	120958165	120958305
ENSE00003723497	120960487	120961487
ENSE00003724229	120959444	120959599

Expression profiles

Bgee: expression breadth tissue_specific, 6 present calls, max score 76.69.

Top tissues by expression

132 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	76.69	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	72.16	gold quality
bone marrow cell	CL:0002092	38.30	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	32.84	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
left testis	UBERON:0004533	30.85	gold quality
testis	UBERON:0000473	30.09	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
prefrontal cortex	UBERON:0000451	29.19	gold quality
placenta	UBERON:0001987	29.10	gold quality
liver	UBERON:0002107	29.04	gold quality
urinary bladder	UBERON:0001255	28.58	gold quality
tonsil	UBERON:0002372	28.52	gold quality
duodenum	UBERON:0002114	28.14	gold quality
lymph node	UBERON:0000029	27.57	gold quality
islet of Langerhans	UBERON:0000006	26.55	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
blood	UBERON:0000178	26.18	gold quality
gall bladder	UBERON:0002110	25.98	gold quality
pancreas	UBERON:0001264	25.91	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	25.89	gold quality
leukocyte	CL:0000738	25.22	gold quality
muscle of leg	UBERON:0001383	25.00	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 CT47A6, 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), CT47A9 (ENSG00000226600), CT47A12 (ENSG00000226685), CT47A11 (ENSG00000226929), CT47A7 (ENSG00000228517), CT47A8 (ENSG00000230347), CT47A4 (ENSG00000230594), CT47A3 (ENSG00000236126), CT47A1 (ENSG00000236371), 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_001073610* (*=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: 4 (showing top): chrXq24, MIR5696, MIR12123, MIR664A_3P

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
CT47A6	GPHRA	B7ZAQ6	952
CT47A6	TAF11L5	A0A1W2PP81	654
CT47A6	TAF11L4	A0A1W2PPE2	654
CT47A6	TAF11L3	A0A1W2PRV1	654
CT47A6	TAF11L2	A6NLC8	620
CT47A6	CTAG2	O75638	616
CT47A6	CT45A1	Q5HYN5	602
CT47A6	MAGEA1	P43355	584
CT47A6	A0A1W2PRN6	A0A1W2PRN6	544
CT47A6	CT55	Q8WUE5	522
CT47A6	PRR20A	P86496	522
CT47A6	A0A1W2PQG5	A0A1W2PQG5	520
CT47A6	SPANXA1	Q9NS26	507
CT47A6	CSAG2	Q9Y5P2	507
CT47A6	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	4
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

387 predictions. Top by Δscore:

Variant	Effect	Δscore
X:120958203:A:C	donor_gain	1.0000
X:120958206:TGA:T	donor_gain	1.0000
X:120960485:AC:A	donor_gain	1.0000
X:120960486:CC:C	donor_gain	1.0000
X:120960486:CCCT:C	donor_gain	1.0000
X:120960504:T:TA	donor_gain	1.0000
X:120958206:TGAAC:T	donor_gain	0.9900
X:120958221:ACAT:A	donor_gain	0.9900
X:120958222:CAT:C	donor_gain	0.9900
X:120958222:CATC:C	donor_gain	0.9900
X:120958224:T:TA	donor_gain	0.9900
X:120958250:A:AC	donor_gain	0.9900
X:120960481:CCTTA:C	donor_loss	0.9900
X:120960482:CTTA:C	donor_loss	0.9900
X:120960483:TTAC:T	donor_loss	0.9900
X:120960484:TA:T	donor_loss	0.9900
X:120959597:CTT:C	acceptor_gain	0.9800
X:120959602:T:C	acceptor_gain	0.9800
X:120959602:T:TC	acceptor_gain	0.9800
X:120960485:A:AC	donor_gain	0.9800
X:120960486:C:CC	donor_gain	0.9800
X:120960485:ACC:A	donor_gain	0.9700
X:120960485:ACCCT:A	donor_gain	0.9700
X:120960486:CCC:C	donor_gain	0.9700
X:120960486:CCCTC:C	donor_gain	0.9700
X:120958221:A:AC	donor_gain	0.9600
X:120958222:C:CC	donor_gain	0.9600
X:120959600:C:CC	acceptor_gain	0.9600
X:120959601:T:C	acceptor_gain	0.9600
X:120959460:TC:T	donor_gain	0.9500

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 87 via entrez): RS112187612 (X:120961549 T>C), RS1161215653 (X:120960524 TGTGGCTGG>T), RS1173923429 (X:120960523 C>A), RS1178078523 (X:120960530 T>C), RS1197669488 (X:120960565 C>T), RS1225955136 (X:120960538 C>G), RS1233264210 (X:120960545 T>C), RS1238535920 (X:120960571 G>A), RS1244521626 (X:120960502 C>A,T), RS1253712605 (X:120960478 G>A), RS1264478689 (X:120960559 C>T), RS1299893650 (X:120960541 C>T), RS1309004824 (X:120960437 G>A), RS1337478774 (X:120960530 TG>T,TGG), RS1408498044 (X:120960531 G>A)

Disease associations

OMIM: gene MIM:300785 | 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: no

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

CTD chemical–gene interactions

1 total (human), top 1 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression	1

Clinical trials (associated diseases)

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