ZFTA

Summary

ZFTA (zinc finger translocation associated, HGNC:28449) is a protein-coding gene on chromosome 11q13.1, encoding Zinc finger translocation-associated protein (C9JLR9).

Predicted to be involved in negative regulation of DNA-templated transcription. Predicted to be located in nucleus.

Source: NCBI Gene 65998 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 14 total
• Phenotypes (HPO): 15
• MANE Select transcript: NM_001144936

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28449
Approved symbol	ZFTA
Name	zinc finger translocation associated
Location	11q13.1
Locus type	gene with protein product
Status	Approved
Aliases	MGC3032
Ensembl gene	ENSG00000188070
Ensembl biotype	protein_coding
OMIM	615699
Entrez	65998

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 7 protein_coding

ENST00000338498, ENST00000433688, ENST00000445014, ENST00000546282, ENST00000918476, ENST00000918477, ENST00000948030

RefSeq mRNA: 1 — MANE Select: NM_001144936 NM_001144936

CCDS: CCDS44636

Canonical transcript exons

ENST00000433688 — 5 exons

Exon	Start	End
ENSE00001608436	63764038	63764598
ENSE00001665435	63765807	63766304
ENSE00001739347	63759892	63763869
ENSE00003591278	63768484	63768775
ENSE00003671616	63764868	63765254

Expression profiles

Bgee: expression breadth ubiquitous, 259 present calls, max score 96.95.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.7846 / max 160.4231, expressed in 1641 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
120336	8.0056	1611
120337	1.7789	1042

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	96.95	gold quality
ganglionic eminence	UBERON:0004023	96.34	gold quality
tendon of biceps brachii	UBERON:0008188	93.64	gold quality
embryo	UBERON:0000922	92.83	gold quality
parietal pleura	UBERON:0002400	91.78	gold quality
ventricular zone	UBERON:0003053	91.60	gold quality
tibia	UBERON:0000979	91.26	gold quality
pleura	UBERON:0000977	90.42	gold quality
germinal epithelium of ovary	UBERON:0001304	89.43	gold quality
periodontal ligament	UBERON:0008266	89.27	gold quality
visceral pleura	UBERON:0002401	89.07	gold quality
heart right ventricle	UBERON:0002080	87.97	gold quality
ovary	UBERON:0000992	87.18	gold quality
choroid plexus epithelium	UBERON:0003911	86.96	gold quality
hair follicle	UBERON:0002073	86.87	silver quality
right ovary	UBERON:0002118	86.49	gold quality
left ovary	UBERON:0002119	86.28	gold quality
metanephros	UBERON:0000081	86.26	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	86.19	gold quality
body of uterus	UBERON:0009853	85.95	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.75	gold quality
metanephric glomerulus	UBERON:0004736	85.17	gold quality
myometrium	UBERON:0001296	85.14	gold quality
tendon	UBERON:0000043	84.97	gold quality
middle temporal gyrus	UBERON:0002771	84.97	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	84.97	gold quality
renal glomerulus	UBERON:0000074	84.80	gold quality
CA1 field of hippocampus	UBERON:0003881	84.65	gold quality
mucosa of stomach	UBERON:0001199	84.49	gold quality
stromal cell of endometrium	CL:0002255	84.29	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.40

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA2603.1	ZFTA	Factors with multiple dispersed zinc fingers

JASPAR matrix evidence (PMIDs): PMID:33741710

miRNA regulators (miRDB)

86 targeting ZFTA, 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-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-6740-5P	100.00	65.64	932
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-519D-3P	99.88	73.97	2607
HSA-MIR-526B-3P	99.88	74.06	2587
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-548AZ-5P	99.83	69.94	3230
HSA-MIR-548T-5P	99.83	69.91	3220

Literature-anchored findings (GeneRIF, showing 7)

• Based on a recurrent translocation t(11;16)(q13;p13), the C11orf95-MKL2 fusion gene has been found in eight further cases of chondroid lipomas. (PMID:23672313)
• C11orf95-RELA fusions represent a unique novel mechanism leading to pathological activation of NF-kappaB signaling in supratentorial ependymomas. (PMID:24562983)
• C11orf95-RELA fusion transcript is thought to be the driver genetic alteration leading to activation of the NFkB pathway in supratentorial ependymomas. (PMID:25388523)
• Ependymoma with C11orf95-MAML2 fusion: presenting with granular cell and ganglion cell features. (PMID:33221956)
• Ependymoma-like tumor with mesenchymal differentiation harboring C11orf95-NCOA1/2 or -RELA fusion: A hitherto unclassified tumor related to ependymoma. (PMID:33576087)
• C11orf95-RELA fusion drives aberrant gene expression through the unique epigenetic regulation for ependymoma formation. (PMID:33685520)
• CNS tumors with PLAGL1-fusion: beyond ZFTA and YAP1 in the genetic spectrum of supratentorial ependymomas. (PMID:38581034)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	zfta	ENSDARG00000088036
mus_musculus	Zfta	ENSMUSG00000053080
rattus_norvegicus	Zfta	ENSRNOG00000032042

Protein

Protein identifiers

Zinc finger translocation-associated protein — C9JLR9 (reviewed: C9JLR9)

All UniProt accessions (4): C9JLR9, A0A087WU89, A0A087WZS6, A0A087X051

UniProt curated annotations — full annotation on UniProt →

Disease relevance. A chromosomal aberration involving MRTFB is found in 3 chondroid lipomas. Translocation t(11;16)(q13;p13) with MRTFB produces a ZFTA-MRTFB fusion protein. A chromosomal aberration involving RELA is found in more than two-thirds of supratentorial ependymomas. Translocation with RELA produces a ZFTA-RELA fusion protein. ZFTA-RELA translocations are potent oncogenes that probably transform neural stem cells by driving an aberrant NF-kappa-B transcription program.

RefSeq proteins (1): NP_001138408* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR040647	SPIN-DOC_Znf-C2H2	Domain
IPR052675	ZnF_transloc-Spindlin_int	Family

Pfam: PF18658

UniProt features (16 total): compositionally biased region 9, region of interest 4, chain 1, site 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-C9JLR9-F1	57.63	0.03

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 138 (breakpoint for translocation to form zfta-mlk2 fusion protein)

Post-translational modifications (1): 375

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 151 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_UP, GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_UP, TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP, GCM_PPM1D, chr11q13, CAIRO_HEPATOBLASTOMA_UP, JAATINEN_HEMATOPOIETIC_STEM_CELL_UP, GCM_RBM8A, MEISSNER_NPC_HCP_WITH_H3K4ME2, MIKKELSEN_MEF_HCP_WITH_H3_UNMETHYLATED, TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_DN, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, KRIEG_HYPOXIA_NOT_VIA_KDM3A, MYC_UP.V1_DN, MEK_UP.V1_UP

GO Biological Process (1): negative regulation of DNA-templated transcription (GO:0045892)

GO Molecular Function (0):

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
DNA-templated transcription	1
regulation of DNA-templated transcription	1
negative regulation of RNA biosynthetic process	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

576 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZFTA	SIRAL1	Q9BPY3	808
ZFTA	MAMLD1	Q13495	738
ZFTA	RELA	Q04206	717
ZFTA	MRTFB	Q9ULH7	644
ZFTA	YAP1	P46937	594
ZFTA	KIAA1549	Q9HCM3	572
ZFTA	L1CAM	P32004	524
ZFTA	MN1	Q10571	495
ZFTA	EZHIP	Q86X51	486
ZFTA	FOXR2	Q6PJQ5	421
ZFTA	MARCKSL1	P49006	404
ZFTA	BEND2	Q8NDZ0	397
ZFTA	MYBL1	P10243	381
ZFTA	NF2	P35240	350
ZFTA	NCOA1	Q15788	350

IntAct

0 interactions, top by confidence:

BioGRID (4): C11orf95 (Affinity Capture-RNA), C11orf95 (Affinity Capture-RNA), C11orf95 (Affinity Capture-MS), C11orf95 (Affinity Capture-MS)

ESM2 similar proteins: A0A8I5KY20, A2A9T0, A2IDD5, B0BNK9, B8ZZ34, C9JI98, C9JLR9, F5GYI3, O18734, P0CG25, P84157, Q0IIA6, Q0PHV7, Q0X0E2, Q13387, Q1RMK9, Q2M3D2, Q2TAM9, Q3ZCQ3, Q4VA45, Q673H1, Q69YZ2, Q6NS60, Q6P6N5, Q6PJ61, Q7Z6J2, Q80ZJ8, Q810I0, Q86SX3, Q86UD0, Q86XT2, Q8BNN1, Q8IUW3, Q8N4Y2, Q8N6N2, Q8QZV0, Q8R4T5, Q8TF61, Q8VCR9, Q8WXF8

Diamond homologs: C9JLR9, Q05AH6, Q4VA45, Q9BUA3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	9
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

767 predictions. Top by Δscore:

Variant	Effect	Δscore
11:63763870:C:CC	acceptor_gain	1.0000
11:63764496:T:TA	donor_gain	1.0000
11:63764975:T:TA	donor_gain	1.0000
11:63765946:G:C	donor_gain	1.0000
11:63765962:T:TA	donor_gain	1.0000
11:63768478:TCTTA:T	donor_loss	1.0000
11:63768479:CTTA:C	donor_loss	1.0000
11:63768482:A:AC	donor_gain	1.0000
11:63768482:A:C	donor_loss	1.0000
11:63768482:ACCGC:A	donor_gain	1.0000
11:63768483:C:CC	donor_gain	1.0000
11:63768483:C:CT	donor_loss	1.0000
11:63768483:CCG:C	donor_gain	1.0000
11:63768483:CCGCC:C	donor_gain	1.0000
11:63768495:T:TA	donor_gain	1.0000
11:63763866:TCGC:T	acceptor_gain	0.9900
11:63763866:TCGCC:T	acceptor_loss	0.9900
11:63763867:CGC:C	acceptor_gain	0.9900
11:63763867:CGCC:C	acceptor_gain	0.9900
11:63763867:CGCCT:C	acceptor_loss	0.9900
11:63763868:GCCTA:G	acceptor_loss	0.9900
11:63763870:C:A	acceptor_loss	0.9900
11:63763871:T:G	acceptor_loss	0.9900
11:63764188:C:CA	donor_gain	0.9900
11:63764448:T:TA	donor_gain	0.9900
11:63764451:T:TA	donor_gain	0.9900
11:63764503:CGT:C	donor_gain	0.9900
11:63765941:T:TA	donor_gain	0.9900
11:63765942:C:A	donor_gain	0.9900
11:63765963:C:A	donor_gain	0.9900

AlphaMissense

4323 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:63763593:A:T	I621N	1.000
11:63763595:G:C	H620Q	1.000
11:63763595:G:T	H620Q	1.000
11:63763597:G:C	H620D	1.000
11:63763597:G:T	H620N	1.000
11:63763599:C:G	R619P	1.000
11:63763600:G:T	R619S	1.000
11:63763601:C:A	K618N	1.000
11:63763601:C:G	K618N	1.000
11:63763605:A:C	I617S	1.000
11:63763605:A:G	I617T	1.000
11:63763605:A:T	I617N	1.000
11:63763608:G:A	T616I	1.000
11:63763610:G:C	S615R	1.000
11:63763610:G:T	S615R	1.000
11:63763612:T:G	S615R	1.000
11:63763616:C:A	K613N	1.000
11:63763616:C:G	K613N	1.000
11:63763620:A:T	L612H	1.000
11:63763641:C:T	C605Y	1.000
11:63763642:A:G	C605R	1.000
11:63763649:A:C	C602W	1.000
11:63763650:C:T	C602Y	1.000
11:63763651:A:G	C602R	1.000
11:63763656:A:G	L600P	1.000
11:63763686:A:G	L590P	1.000
11:63763700:C:A	W585C	1.000
11:63763700:C:G	W585C	1.000
11:63763701:C:G	W585S	1.000
11:63763702:A:G	W585R	1.000

dbSNP variants (sampled 300 via entrez): RS1000232889 (11:63761520 A>G), RS1000263763 (11:63761228 T>C), RS1000419927 (11:63767560 G>A), RS1000533666 (11:63770681 G>A,T), RS1000592709 (11:63765146 C>A), RS1000599644 (11:63762529 A>T), RS1000644947 (11:63764815 C>A,T), RS1000829172 (11:63769312 C>T), RS1000893217 (11:63767360 T>G), RS1001158227 (11:63769532 G>A,T), RS1001228991 (11:63761190 CAAA>C,CAAAA), RS1001231904 (11:63760371 T>A), RS1001252335 (11:63767826 A>C,G), RS1001616961 (11:63760871 G>A), RS1001779450 (11:63761847 G>A)

Disease associations

OMIM: gene MIM:615699 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

15 total (15 of 15 shown, HPO-id order):

HPO	Term
HP:0001250	Seizure
HP:0001288	Gait disturbance
HP:0002013	Vomiting
HP:0002076	Migraine
HP:0002460	Distal muscle weakness
HP:0002888	Ependymoma
HP:0002896	Neoplasm of the liver
HP:0010302	Spinal cord tumor
HP:0012531	Pain
HP:0012534	Dysesthesia
HP:0025461	Abnormal cell morphology
HP:0030693	Supratentorial neoplasm
HP:0100013	Neoplasm of the breast
HP:0100526	Neoplasm of the lung
HP:0100615	Ovarian neoplasm

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

17 total (human), top 17 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, increases methylation	4
Cyclosporine	decreases expression	2
sodium arsenite	decreases expression	1
butyraldehyde	decreases expression	1
N,N,N’,N’-tetrakis(2-pyridylmethyl)ethylenediamine	decreases expression	1
Sunitinib	increases expression	1
Vorinostat	decreases expression	1
Acetaminophen	decreases expression	1
Doxorubicin	decreases expression	1
Estradiol	decreases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Aflatoxin B1	increases methylation	1
Antirheumatic Agents	increases expression	1
Zinc Sulfate	increases expression	1
Particulate Matter	increases expression	1

Clinical trials (associated diseases)

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