ZNF706

Summary

ZNF706 (zinc finger protein 706, HGNC:24992) is a protein-coding gene on chromosome 8q22.3, encoding Zinc finger protein 706 (Q9Y5V0). Transcription repressor involved in the exit of embryonic stem cells (ESCs) from self-renewal.

Predicted to enable zinc ion binding activity. Predicted to be involved in negative regulation of DNA-templated transcription and negative regulation of stem cell population maintenance. Predicted to be located in cytoplasm and nucleus.

Source: NCBI Gene 51123 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 9 total
• MANE Select transcript: NM_016096

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24992
Approved symbol	ZNF706
Name	zinc finger protein 706
Location	8q22.3
Locus type	gene with protein product
Status	Approved
Aliases	HSPC038
Ensembl gene	ENSG00000120963
Ensembl biotype	protein_coding
OMIM	619526
Entrez	51123

Gene structure

Transcript identifiers

Ensembl transcripts: 45 — 41 protein_coding, 2 nonsense_mediated_decay, 2 retained_intron

ENST00000311212, ENST00000517844, ENST00000518071, ENST00000518336, ENST00000519103, ENST00000519744, ENST00000519882, ENST00000519916, ENST00000520347, ENST00000520454, ENST00000520498, ENST00000520984, ENST00000521272, ENST00000523146, ENST00000523922, ENST00000873571, ENST00000873572, ENST00000873573, ENST00000873574, ENST00000873575, ENST00000873576, ENST00000873577, ENST00000873578, ENST00000873579, ENST00000873580, ENST00000873581, ENST00000873582, ENST00000873583, ENST00000873584, ENST00000873585, ENST00000873586, ENST00000873587, ENST00000873588, ENST00000873589, ENST00000873590, ENST00000912817, ENST00000912818, ENST00000912819, ENST00000912820, ENST00000912821, ENST00000912822, ENST00000971565, ENST00000971566, ENST00000971567, ENST00000971568

RefSeq mRNA: 4 — MANE Select: NM_016096 NM_001042510, NM_001267708, NM_001267709, NM_016096

CCDS: CCDS6291

Canonical transcript exons

ENST00000311212 — 4 exons

Exon	Start	End
ENSE00000819088	101199990	101200097
ENSE00001193308	101201607	101201743
ENSE00002093511	101205435	101205673
ENSE00002121322	101197052	101199239

Expression profiles

Bgee: expression breadth ubiquitous, 257 present calls, max score 99.33.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 56.8075 / max 312.3710, expressed in 1825 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
94224	51.4241	1825
94223	4.0189	1529
94221	0.4846	188
94226	0.4177	102
94222	0.1793	65
94220	0.1428	73
94227	0.1267	52
94225	0.0134	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
body of pancreas	UBERON:0001150	99.33	gold quality
skin of abdomen	UBERON:0001416	98.95	gold quality
skin of leg	UBERON:0001511	98.85	gold quality
nerve	UBERON:0001021	98.72	gold quality
tibial nerve	UBERON:0001323	98.72	gold quality
lower esophagus mucosa	UBERON:0035834	98.41	gold quality
right testis	UBERON:0004534	98.35	gold quality
left testis	UBERON:0004533	98.31	gold quality
adenohypophysis	UBERON:0002196	98.27	gold quality
minor salivary gland	UBERON:0001830	98.17	gold quality
small intestine Peyer’s patch	UBERON:0003454	98.03	gold quality
mucosa of transverse colon	UBERON:0004991	98.02	gold quality
rectum	UBERON:0001052	97.99	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	97.91	gold quality
embryo	UBERON:0000922	97.83	gold quality
ganglionic eminence	UBERON:0004023	97.83	gold quality
ectocervix	UBERON:0012249	97.83	gold quality
transverse colon	UBERON:0001157	97.81	gold quality
left lobe of thyroid gland	UBERON:0001120	97.77	gold quality
body of stomach	UBERON:0001161	97.72	gold quality
mucosa of stomach	UBERON:0001199	97.72	gold quality
gall bladder	UBERON:0002110	97.71	gold quality
pancreas	UBERON:0001264	97.70	gold quality
esophagus mucosa	UBERON:0002469	97.68	gold quality
body of uterus	UBERON:0009853	97.58	gold quality
cortical plate	UBERON:0005343	97.57	gold quality
right lobe of thyroid gland	UBERON:0001119	97.55	gold quality
right lung	UBERON:0002167	97.51	gold quality
endocervix	UBERON:0000458	97.50	gold quality
omental fat pad	UBERON:0010414	97.50	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-HCAD-1	yes	40.20
E-CURD-46	yes	11.51
E-GEOD-125970	yes	4.91
E-HCAD-13	no	3.18
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

135 targeting ZNF706, 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-3163	100.00	77.23	8605
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-223-3P	99.99	70.14	1140
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-4496	99.88	68.89	2236

Literature-anchored findings (GeneRIF, showing 3)

• functional interaction between ICln and HSPC038 (PMID:21917931)
• Protein G-quadruplex interactions and their effects on phase transitions and protein aggregation. (PMID:38572746)
• A novel MYC-ZNF706-SLC7A11 regulatory circuit contributes to cancer progression and redox balance in human hepatocellular carcinoma. (PMID:38862581)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	znf706	ENSDARG00000056307
mus_musculus	Zfp706	ENSMUSG00000062397
rattus_norvegicus	Zfp706	ENSRNOG00000060956
drosophila_melanogaster	CG18081	FBGN0036537
drosophila_melanogaster	CG15715	FBGN0036538
caenorhabditis_elegans		WBGENE00007223
caenorhabditis_elegans		WBGENE00019609

Protein

Protein identifiers

Zinc finger protein 706 — Q9Y5V0 (reviewed: Q9Y5V0)

All UniProt accessions (7): A0A1D5RMS7, E5RHR6, E5RHV4, E5RIY7, Q9Y5V0, H0YAP1, H0YC70

UniProt curated annotations — full annotation on UniProt →

Function. Transcription repressor involved in the exit of embryonic stem cells (ESCs) from self-renewal. Acts by repressing expression of KLF4.

Subcellular location. Cytoplasm. Nucleus.

RefSeq proteins (4): NP_001035975, NP_001254637, NP_001254638, NP_057180* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007513	SERF-like_N	Domain
IPR013087	Znf_C2H2_type	Domain
IPR026939	ZNF706/At2g23090_sf	Homologous_superfamily
IPR045230	MBS1/2-like	Family

Pfam: PF04419, PF12874

UniProt features (7 total): compositionally biased region 3, region of interest 2, chain 1, zinc finger region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y5V0-F1	70.90	0.00

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 181 (showing top): MODULE_151, GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, PATIL_LIVER_CANCER, GOBP_TRANSLATION, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, GOBP_NEGATIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS, ONKEN_UVEAL_MELANOMA_UP, AAAGACA_MIR511, GOBP_MAINTENANCE_OF_CELL_NUMBER, GOBP_REGULATION_OF_STEM_CELL_POPULATION_MAINTENANCE, NIKOLSKY_BREAST_CANCER_8Q12_Q22_AMPLICON, chr8q22, AACTTT_UNKNOWN, RYTTCCTG_ETS2_B

GO Biological Process (3): regulation of translation (GO:0006417), negative regulation of DNA-templated transcription (GO:0045892), negative regulation of stem cell population maintenance (GO:1902455)

GO Molecular Function (2): zinc ion binding (GO:0008270), metal ion binding (GO:0046872)

GO Cellular Component (2): nucleus (GO:0005634), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
RNA Polymerase II Transcription	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
translation	1
post-transcriptional regulation of gene expression	1
regulation of protein metabolic process	1
DNA-templated transcription	1
regulation of DNA-templated transcription	1
negative regulation of RNA biosynthetic process	1
stem cell population maintenance	1
negative regulation of developmental process	1
negative regulation of multicellular organismal process	1
regulation of stem cell population maintenance	1
transition metal ion binding	1
cation binding	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

650 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF706	ANKRD9	Q96BM1	549
ZNF706	IQCF1	Q8N6M8	539
ZNF706	SERPINE3	A8MV23	518
ZNF706	PRR15L	Q9BU68	508
ZNF706	RUNDC3A	Q59EK9	464
ZNF706	WDR81	Q562E7	444
ZNF706	CCDC181	Q5TID7	434
ZNF706	AZIN1	O14977	421
ZNF706	ZNF407	Q9C0G0	392
ZNF706	TIMM17A	Q99595	392
ZNF706	UBR5	O95071	390
ZNF706	TSSK6	Q9BXA6	374
ZNF706	CLNS1A	P54105	370
ZNF706	NCALD	P29554	369
ZNF706	RASSF3	Q86WH2	362

IntAct

6 interactions, top by confidence:

A	B	Type	Score
	ZNF706	psi-mi:“MI:0407”(direct interaction)	0.440
ZNF706	SP100	psi-mi:“MI:0915”(physical association)	0.400
MAPT	SHTN1	psi-mi:“MI:0914”(association)	0.350
RAC3	ZNF706	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (10): SP100 (Affinity Capture-MS), ZNF706 (Affinity Capture-RNA), ZNF706 (Affinity Capture-RNA), ZNF706 (Co-fractionation), ZNF706 (Affinity Capture-MS), ZNF706 (Affinity Capture-RNA), APP (Reconstituted Complex), ZNF706 (Co-fractionation), ZNF706 (Co-fractionation), ZNF706 (Co-fractionation)

ESM2 similar proteins: A1C646, A1DGS2, A2R7Z2, A6SGN8, A7EWN6, B0XS28, B3MSP2, B3NYY7, B4J4G8, B4L710, B4MA85, B4N1L0, B4NFY1, B4PP90, C8V330, F8RP11, G1SE28, O64818, O70333, P38666, P46301, P61122, P83731, P83732, Q0CPF9, Q0U6E7, Q1DPD9, Q1WCC0, Q2U002, Q3ZC66, Q42347, Q4X1I3, Q567Z6, Q5ZKB6, Q5ZMM5, Q66WF5, Q6NU28, Q6V291, Q6Y263, Q792Q4

Diamond homologs: Q5ZMM5, Q9D115, Q9Y5V0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

1093 predictions. Top by Δscore:

Variant	Effect	Δscore
8:101178387:CCT:C	acceptor_gain	1.0000
8:101201605:AC:A	donor_gain	1.0000
8:101201606:CC:C	donor_gain	1.0000
8:101201606:CCCTA:C	donor_gain	1.0000
8:101201739:CATAT:C	acceptor_gain	1.0000
8:101201740:ATAT:A	acceptor_gain	1.0000
8:101201741:TAT:T	acceptor_gain	1.0000
8:101201742:AT:A	acceptor_gain	1.0000
8:101201742:ATCTA:A	acceptor_loss	1.0000
8:101201744:C:CC	acceptor_gain	1.0000
8:101201744:C:T	acceptor_loss	1.0000
8:101201745:T:C	acceptor_loss	1.0000
8:101178389:T:C	acceptor_gain	0.9900
8:101178389:T:TC	acceptor_gain	0.9900
8:101199072:CAT:C	donor_gain	0.9900
8:101199137:AGCC:A	donor_gain	0.9900
8:101201646:AGCAG:A	donor_gain	0.9900
8:101201751:C:CT	acceptor_gain	0.9900
8:101205113:T:TA	donor_gain	0.9900
8:101205429:GCTCA:G	donor_loss	0.9900
8:101205430:CTCAC:C	donor_loss	0.9900
8:101205431:TCA:T	donor_loss	0.9900
8:101205432:CACC:C	donor_loss	0.9900
8:101205433:A:AT	donor_loss	0.9900
8:101205434:C:G	donor_loss	0.9900
8:101178386:CC:C	acceptor_gain	0.9800
8:101178386:CCCT:C	acceptor_gain	0.9800
8:101178388:C:T	acceptor_gain	0.9800
8:101201600:CCCTT:C	donor_loss	0.9800
8:101201601:CCTTA:C	donor_loss	0.9800

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000151254 (8:101197130 A>G), RS1000661161 (8:101206165 C>A,T), RS1000941955 (8:101201811 A>G), RS1001103202 (8:101200187 A>G), RS1001488223 (8:101203022 A>G), RS1001992514 (8:101200636 G>C,T), RS1002026448 (8:101206218 G>A), RS1002080360 (8:101206473 T>C), RS1002259688 (8:101200323 C>T), RS1002291678 (8:101207605 T>G), RS1002438533 (8:101201185 C>T), RS1002491107 (8:101201581 G>A), RS1002750705 (8:101208005 T>G), RS1002937392 (8:101203593 TAA>T), RS1002966718 (8:101196876 T>C)

Disease associations

OMIM: gene MIM:619526 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST000885_7	Response to antipsychotic treatment in schizophrenia (reasoning)	2.000000e-06
GCST005951_63	Body mass index	2.000000e-08
GCST007576_178	Chronotype	3.000000e-11
GCST010396_307	Gut microbiota (bacterial taxa, hurdle binary method)	6.000000e-06

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004350	reasoning
EFO:0004340	body mass index
EFO:0008328	chronotype measurement
EFO:0007874	gut microbiome measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

34 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
trichostatin A	affects cotreatment, decreases expression	3
Valproic Acid	affects expression, increases expression, increases methylation	3
sodium arsenite	decreases expression, increases abundance, increases expression	2
Arsenic	decreases expression, increases abundance, increases expression	2
Benzo(a)pyrene	affects methylation, decreases expression	2
bisphenol F	affects cotreatment, increases expression	1
methylmercuric chloride	decreases expression	1
sodium arsenate	decreases expression, increases abundance	1
beta-lapachone	increases expression	1
butyraldehyde	decreases expression	1
pentanal	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Capecitabine	increases response to substance	1
Resveratrol	affects cotreatment, increases expression	1
Air Pollutants	increases abundance, decreases expression	1
Atrazine	decreases expression	1
Cisplatin	increases expression	1
Dexamethasone	increases expression, affects cotreatment	1
Indomethacin	affects cotreatment, increases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Smoke	decreases expression	1
Dihydrotestosterone	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Cyclosporine	increases expression	1
Aflatoxin B1	decreases expression, decreases methylation	1

Cellosaurus cell lines

3 cell lines: 3 embryonic stem cell

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_A8J7	SEES3-1V human ZNF706, clone1	Embryonic stem cell	Male
CVCL_A8J8	SEES3-1V human ZNF706, clone2	Embryonic stem cell	Male
CVCL_A8J9	SEES3-1V human ZNF706, clone3	Embryonic stem cell	Male

Clinical trials (associated diseases)

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