CTAGE9

Summary

CTAGE9 (CTAGE family member 9, HGNC:37275) is a protein-coding gene on chromosome 6q23.2, encoding cTAGE family member 9 (A4FU28). It is a selective cancer dependency (DepMap: 41.8% of cell lines).

Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport; protein secretion; and vesicle cargo loading. Predicted to be located in membrane. Predicted to be active in endoplasmic reticulum exit site and endoplasmic reticulum membrane.

Source: NCBI Gene 643854 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 113 total
• Cancer dependency (DepMap): dependent in 41.8% of screened cell lines
• MANE Select transcript: NM_001145659

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:37275
Approved symbol	CTAGE9
Name	CTAGE family member 9
Location	6q23.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000236761
Ensembl biotype	protein_coding
Entrez	643854

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000314099

RefSeq mRNA: 1 — MANE Select: NM_001145659 NM_001145659

CCDS: CCDS47475

Canonical transcript exons

ENST00000314099 — 1 exons

Exon	Start	End
ENSE00002507203	131708441	131711017

Expression profiles

Bgee: expression breadth broad, 74 present calls, max score 81.14.

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	81.14	gold quality
right testis	UBERON:0004534	73.74	gold quality
left testis	UBERON:0004533	73.13	gold quality
testis	UBERON:0000473	72.59	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	65.50	gold quality
adrenal tissue	UBERON:0018303	54.13	gold quality
lower esophagus mucosa	UBERON:0035834	52.04	gold quality
mucosa of transverse colon	UBERON:0004991	50.60	gold quality
endometrium	UBERON:0001295	50.01	gold quality
tonsil	UBERON:0002372	48.91	silver quality
colonic epithelium	UBERON:0000397	48.56	silver quality
bone marrow cell	CL:0002092	47.97	gold quality
cortex of kidney	UBERON:0001225	47.93	gold quality
ganglionic eminence	UBERON:0004023	46.42	silver quality
skin of abdomen	UBERON:0001416	45.85	gold quality
minor salivary gland	UBERON:0001830	45.48	gold quality
zone of skin	UBERON:0000014	44.76	gold quality
saliva-secreting gland	UBERON:0001044	44.72	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	44.71	gold quality
esophagus mucosa	UBERON:0002469	44.17	gold quality
right lobe of liver	UBERON:0001114	44.10	gold quality
skin of leg	UBERON:0001511	43.91	gold quality
kidney	UBERON:0002113	43.67	gold quality
left lobe of thyroid gland	UBERON:0001120	43.33	gold quality
bone marrow	UBERON:0002371	43.04	gold quality
adult mammalian kidney	UBERON:0000082	42.97	gold quality
thyroid gland	UBERON:0002046	42.83	gold quality
metanephros cortex	UBERON:0010533	42.21	silver quality
liver	UBERON:0002107	42.01	gold quality
mucosa of stomach	UBERON:0001199	41.73	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.79

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

20 targeting CTAGE9, 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-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-1200	99.71	70.42	1838
HSA-MIR-4699-3P	99.71	70.15	3142
HSA-MIR-519A-3P	99.67	71.67	1868
HSA-MIR-519B-3P	99.67	71.67	1868
HSA-MIR-519C-3P	99.67	71.67	1870
HSA-MIR-3934-5P	99.67	64.04	846
HSA-MIR-6126	99.62	68.09	996
HSA-MIR-1252-3P	99.55	67.71	2862
HSA-MIR-548G-3P	99.48	68.67	2159
HSA-MIR-548AV-3P	99.43	68.50	1721
HSA-MIR-302A-5P	99.39	68.21	1913
HSA-MIR-4324	99.04	70.14	1569
HSA-MIR-5701	98.97	69.54	1502
HSA-MIR-6715B-3P	98.80	68.07	1204
HSA-MIR-6864-5P	98.38	66.59	1079
HSA-MIR-152-5P	96.42	66.59	960
HSA-MIR-431-5P	96.16	66.50	652

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 41.8% of screened cell lines.

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Mia2	ENSMUSG00000021000
rattus_norvegicus	Mia2	ENSRNOG00000005101
drosophila_melanogaster	Tango1	FBGN0286898

Paralogs (10): OTOR (ENSG00000125879), MIA2 (ENSG00000150527), MIA3 (ENSG00000154305), SPZ1 (ENSG00000164299), CTAGE1 (ENSG00000212710), MIA (ENSG00000261857), CTAGE15 (ENSG00000271079), CTAGE6 (ENSG00000271321), CTAGE4 (ENSG00000288784), CTAGE8 (ENSG00000289604)

Protein

Protein identifiers

cTAGE family member 9 — A4FU28 (reviewed: A4FU28)

All UniProt accessions (1): A4FU28

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the cTAGE family.

RefSeq proteins (1): NP_001139131* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR051500	cTAGE_MIA/OTOR	Family

UniProt features (9 total): compositionally biased region 3, region of interest 2, coiled-coil region 2, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A4FU28-F1	69.37	0.44

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 36 (showing top): GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_ENDOPLASMIC_RETICULUM_TO_GOLGI_VESICLE_MEDIATED_TRANSPORT, GOBP_SECRETION, LIU_SOX4_TARGETS_UP, GOCC_NUCLEAR_OUTER_MEMBRANE_ENDOPLASMIC_RETICULUM_MEMBRANE_NETWORK, GOCC_ORGANELLE_SUBCOMPARTMENT, GOBP_GOLGI_VESICLE_TRANSPORT, chr6q23, MOREAUX_MULTIPLE_MYELOMA_BY_TACI_UP, TIEN_INTESTINE_PROBIOTICS_24HR_DN, CHEMNITZ_RESPONSE_TO_PROSTAGLANDIN_E2_DN, GOBP_VESICLE_CARGO_LOADING, GOBP_INTRACELLULAR_TRANSPORT, GOCC_ENDOPLASMIC_RETICULUM_EXIT_SITE, KRAS.DF.V1_DN

GO Biological Process (3): endoplasmic reticulum to Golgi vesicle-mediated transport (GO:0006888), protein secretion (GO:0009306), vesicle cargo loading (GO:0035459)

GO Molecular Function (0):

GO Cellular Component (3): endoplasmic reticulum membrane (GO:0005789), endoplasmic reticulum exit site (GO:0070971), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
cytoplasm	1
intercellular transport	1
intracellular transport	1
Golgi vesicle transport	1
protein transport	1
secretion by cell	1
establishment of protein localization to extracellular region	1
protein localization to extracellular region	1
transport	1
vesicle-mediated transport	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
endoplasmic reticulum	1

Protein interactions and networks

STRING

435 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CTAGE9	OTOR	Q9NRC9	509
CTAGE9	NDST1	P52848	365
CTAGE9	TMEM131	Q92545	355
CTAGE9	PREB	Q9HCU5	311
CTAGE9	NUS1	Q96E22	298
CTAGE9	STX18	Q9P2W9	287
CTAGE9	KLHL12	Q53G59	278
CTAGE9	TRAPPC2	P0DI81	265
CTAGE9	TRAPPC6A	O75865	258
CTAGE9	SEC16A	O15027	257
CTAGE9	CCDC68	Q9H2F9	257
CTAGE9	PAPLN	O95428	247
CTAGE9	TRAPPC4	Q9Y296	245
CTAGE9	BNIP1	Q12981	233
CTAGE9	SCFD1	Q8WVM8	216

IntAct

3 interactions, top by confidence:

A	B	Type	Score
Prdm16	ESYT2	psi-mi:“MI:0914”(association)	0.350

ESM2 similar proteins: A0JMQ7, A2BGP7, A4D2H0, A4FU28, B4F7A7, O75665, P0C219, P0CG41, Q05D60, Q15025, Q28BZ7, Q28C41, Q2T9X8, Q32LC2, Q499E4, Q4PJT6, Q4R7I4, Q5FWP9, Q5U3Z6, Q5U465, Q5XIA0, Q5XJA2, Q5ZJA3, Q6AXZ4, Q6NRH3, Q6P926, Q6PCG6, Q7M6Y5, Q80Z25, Q865V0, Q86UF2, Q86W54, Q86XR8, Q86YF9, Q86Z20, Q8BMD2, Q8CEE0, Q8IX94, Q8IYJ2, Q8IYX8

Diamond homologs: A4D2H0, A4FU28, P0CG41, Q86UF2, Q8IX94, Q8IX95, Q91ZV0, Q96PC5, Q96RT6, Q9I8P5, Q9I8P6, Q9JIE3, Q9NRC9, Q16674, Q61865, Q62946

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	113
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

74 predictions. Top by Δscore:

Variant	Effect	Δscore
6:131710216:TCTTG:T	donor_gain	0.9100
6:131710199:C:T	donor_gain	0.8900
6:131709149:T:TA	acceptor_gain	0.7300
6:131709797:A:AG	donor_gain	0.7000
6:131710204:GTCC:G	donor_gain	0.6800
6:131709798:T:G	donor_gain	0.6000
6:131710885:C:CT	donor_gain	0.5600
6:131710227:T:G	donor_gain	0.5400
6:131710226:A:AG	donor_gain	0.5300
6:131710214:GGTCT:G	donor_gain	0.5000
6:131710940:T:TA	donor_gain	0.4400
6:131710941:A:AA	donor_gain	0.4400
6:131710194:ATT:A	donor_gain	0.4200
6:131710882:A:T	donor_gain	0.4000
6:131709259:G:T	donor_gain	0.3800
6:131709143:CCTT:C	acceptor_gain	0.3600
6:131710886:C:CT	donor_gain	0.3500
6:131709149:TGG:T	acceptor_gain	0.3400
6:131709296:ATT:A	acceptor_gain	0.3300
6:131709449:GGGAC:G	donor_gain	0.3100
6:131709146:T:C	acceptor_gain	0.3000
6:131709219:G:T	acceptor_gain	0.3000
6:131710942:G:GG	donor_gain	0.3000
6:131709142:CCCTT:C	acceptor_gain	0.2900
6:131709298:T:A	acceptor_gain	0.2900
6:131710887:A:T	donor_gain	0.2900
6:131709144:CTT:C	acceptor_gain	0.2800
6:131709145:TTT:T	acceptor_gain	0.2800
6:131709151:G:C	acceptor_gain	0.2800
6:131710920:T:C	donor_gain	0.2800

AlphaMissense

5117 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:131710447:C:G	A191P	0.928
6:131709879:A:G	L380P	0.915
6:131709867:A:G	L384P	0.910
6:131709613:C:G	A469P	0.894
6:131710384:C:G	A212P	0.891
6:131710752:T:A	K89I	0.890
6:131709604:C:G	A472P	0.884
6:131710832:A:C	S62R	0.881
6:131710832:A:T	S62R	0.881
6:131710834:T:G	S62R	0.881
6:131709942:A:G	L359P	0.877
6:131709591:A:G	L476P	0.874
6:131710867:C:G	G51R	0.866
6:131710867:C:T	G51R	0.866
6:131709699:A:G	L440P	0.859
6:131710866:C:T	G51E	0.854
6:131710572:A:G	L149P	0.841
6:131710743:A:G	L92P	0.839
6:131709963:A:G	L352P	0.830
6:131709825:A:G	L398P	0.825
6:131710477:A:G	S181P	0.812
6:131709609:C:G	R470P	0.804
6:131710614:A:G	L135P	0.801
6:131709612:G:T	A469D	0.800
6:131709709:C:G	A437P	0.798
6:131710829:A:C	F63L	0.790
6:131710829:A:T	F63L	0.790
6:131710831:A:G	F63L	0.790
6:131710764:A:G	L85P	0.786
6:131709873:T:G	Q382P	0.782

dbSNP variants (sampled 300 via entrez): RS1004057491 (6:131708866 C>G), RS1008409859 (6:131712330 A>C), RS1008462519 (6:131711335 T>A), RS1024686606 (6:131712770 GGT>G), RS1026620306 (6:131712548 T>C), RS1027088955 (6:131711453 A>G), RS1028949504 (6:131710691 C>T), RS1033100350 (6:131710650 T>C), RS1038140733 (6:131710522 A>G), RS1039758276 (6:131708565 G>C), RS1042302391 (6:131710992 T>C), RS1049808636 (6:131712980 T>C), RS1050187908 (6:131710839 CACAAAAAAAGGAGAACA>C), RS1050290463 (6:131712238 T>A,C), RS1054443084 (6:131712111 T>A)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST90013406_118	Liver enzyme levels (alkaline phosphatase)	3.000000e-13

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004533	alkaline phosphatase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

Clinical trials (associated diseases)

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