ZNF709

Summary

ZNF709 (zinc finger protein 709, HGNC:20629) is a protein-coding gene on chromosome 19p13.2, encoding Zinc finger protein 709 (Q8N972). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus.

Source: NCBI Gene 163051 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 59 total
• MANE Select transcript: NM_152601

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20629
Approved symbol	ZNF709
Name	zinc finger protein 709
Location	19p13.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ38281
Ensembl gene	ENSG00000242852
Ensembl biotype	protein_coding
Entrez	163051

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000397732, ENST00000455490, ENST00000493776, ENST00000926406, ENST00000966691

RefSeq mRNA: 1 — MANE Select: NM_152601 NM_152601

CCDS: CCDS42504

Canonical transcript exons

ENST00000397732 — 4 exons

Exon	Start	End
ENSE00001529914	12484655	12484816
ENSE00001893054	12461184	12465733
ENSE00003596659	12466724	12466850
ENSE00003682762	12466462	12466519

Expression profiles

Bgee: expression breadth ubiquitous, 171 present calls, max score 86.97.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.0497 / max 97.5973, expressed in 1313 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
179312	4.6024	1289
179311	0.3602	170
179313	0.0871	54

Top tissues by expression

220 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	86.97	gold quality
right testis	UBERON:0004534	83.37	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.09	gold quality
left testis	UBERON:0004533	82.81	gold quality
testis	UBERON:0000473	80.12	gold quality
ganglionic eminence	UBERON:0004023	75.85	gold quality
ventricular zone	UBERON:0003053	75.41	gold quality
sperm	CL:0000019	75.16	gold quality
right uterine tube	UBERON:0001302	72.63	gold quality
islet of Langerhans	UBERON:0000006	70.78	gold quality
oocyte	CL:0000023	70.64	silver quality
cerebellar hemisphere	UBERON:0002245	70.25	gold quality
cerebellar cortex	UBERON:0002129	70.21	gold quality
cortical plate	UBERON:0005343	70.11	gold quality
vena cava	UBERON:0004087	70.10	silver quality
skeletal muscle tissue	UBERON:0001134	70.01	gold quality
cerebellum	UBERON:0002037	69.32	gold quality
right hemisphere of cerebellum	UBERON:0014890	69.11	gold quality
muscle tissue	UBERON:0002385	69.09	gold quality
calcaneal tendon	UBERON:0003701	68.71	gold quality
adrenal tissue	UBERON:0018303	68.19	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	67.73	gold quality
left ovary	UBERON:0002119	67.61	gold quality
nucleus accumbens	UBERON:0001882	67.22	gold quality
right ovary	UBERON:0002118	67.10	gold quality
biceps brachii	UBERON:0001507	66.89	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	66.63	gold quality
nasal cavity epithelium	UBERON:0005384	66.18	gold quality
body of uterus	UBERON:0009853	65.68	gold quality
apex of heart	UBERON:0002098	65.53	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.04

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

111 targeting ZNF709, 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-3613-3P	100.00	76.36	7965
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-4493	99.90	66.48	977
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-4302	99.89	67.94	1187
HSA-MIR-4496	99.88	68.89	2236
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-383-3P	99.85	65.84	1359

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
rattus_norvegicus	Znf709l	ENSRNOG00000069976

Paralogs (15): ZNF14 (ENSG00000105708), ZNF57 (ENSG00000171970), ZNF791 (ENSG00000173875), ZNF443 (ENSG00000180855), ZNF101 (ENSG00000181896), ZNF563 (ENSG00000188868), ZNF799 (ENSG00000196466), ZNF700 (ENSG00000196757), ZNF441 (ENSG00000197044), ZNF433 (ENSG00000197647), ZNF44 (ENSG00000197857), ZNF823 (ENSG00000197933), ZNF442 (ENSG00000198342), ZNF844 (ENSG00000223547), ZNF878 (ENSG00000257446)

Protein

Protein identifiers

Zinc finger protein 709 — Q8N972 (reviewed: Q8N972)

All UniProt accessions (2): Q8N972, H7C129

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

Similarity. Belongs to the krueppel C2H2-type zinc-finger protein family.

RefSeq proteins (1): NP_689814* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001909	KRAB	Domain
IPR013087	Znf_C2H2_type	Domain
IPR036051	KRAB_dom_sf	Homologous_superfamily
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF00096, PF01352

UniProt features (21 total): zinc finger region 19, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N972-F1	80.37	0.31

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 41 (showing top): JAATINEN_HEMATOPOIETIC_STEM_CELL_UP, chr19p13, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, DODD_NASOPHARYNGEAL_CARCINOMA_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, BARX1_TARGET_GENES, PCGF1_TARGET_GENES, SOX3_TARGET_GENES, MIR616_5P, MIR371B_5P, MIR373_5P, MIR651_3P, MIR3121_3P, MIR7159_5P, MIR548AT_5P

GO Biological Process (2): regulation of transcription by RNA polymerase II (GO:0006357), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (5): RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), zinc ion binding (GO:0008270), DNA binding (GO:0003677), metal ion binding (GO:0046872)

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

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
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
transcription cis-regulatory region binding	1
chromatin	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	1
DNA-binding transcription factor activity	1
regulation of transcription by RNA polymerase II	1
transition metal ion binding	1
nucleic acid binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

180 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF709	PCBP4	P57723	407
ZNF709	DENND4B	O75064	392
ZNF709	PRTFDC1	Q9NRG1	388
ZNF709	KBTBD6	Q86V97	348
ZNF709	PODXL2	Q9NZ53	300
ZNF709	RABL6	Q3YEC7	297
ZNF709	HELB	Q8NG08	296
ZNF709	DDX52	Q9Y2R4	279
ZNF709	A0A0A6YYI9	A0A0A6YYI9	255
ZNF709	ACTMAP	Q5BKX5	254
ZNF709	GTF2IRD1	Q9UHL9	246
ZNF709	JPH3	Q8WXH2	241
ZNF709	NOB1	Q9ULX3	234
ZNF709	ZNF414	Q96IQ9	231
ZNF709	RBM14	Q96PK6	229

IntAct

15 interactions, top by confidence:

A	B	Type	Score
EN1	NFIB	psi-mi:“MI:2364”(proximity)	0.470
ECE1	ZNF709	psi-mi:“MI:0915”(physical association)	0.370
S100B	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
NOTCH2	ZNF320	psi-mi:“MI:0914”(association)	0.350
LTBP2	ZNF320	psi-mi:“MI:0914”(association)	0.350
FBLN2	ZNF316	psi-mi:“MI:0914”(association)	0.350
MRFAP1L1	MYO9A	psi-mi:“MI:0914”(association)	0.350
PTX3	POLRMT	psi-mi:“MI:0914”(association)	0.350
OR52B2	PCCA	psi-mi:“MI:0914”(association)	0.350
KAZALD1	ZNF865	psi-mi:“MI:0914”(association)	0.350
GATA3	BCL9	psi-mi:“MI:2364”(proximity)	0.270
MYB	KMT2D	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (12): ZNF709 (Affinity Capture-MS), ZNF709 (Affinity Capture-MS), ZNF709 (Affinity Capture-MS), ZNF709 (Affinity Capture-MS), ZNF709 (Affinity Capture-MS), ZNF709 (Affinity Capture-MS), ZNF709 (Affinity Capture-MS), ZNF709 (Affinity Capture-MS), ZNF709 (Proximity Label-MS), ZNF709 (Proximity Label-MS), ZNF709 (Proximity Label-MS), ZNF709 (Affinity Capture-RNA)

ESM2 similar proteins: A2VDQ7, A6NNF4, A8MQ14, A8MTY0, E9QAG8, O75290, O75373, P08043, P0CJ79, P10751, P17017, P17027, P17039, P35789, P51522, P51523, Q08AN1, Q14585, Q14587, Q3SYV7, Q3ZCX4, Q4R4C7, Q52M93, Q5MCW4, Q5R5U3, Q5R8X1, Q5R9F0, Q5SXM1, Q6ECI4, Q6JLC9, Q6P3V2, Q6P5C7, Q6ZN57, Q86UE3, Q86XN6, Q86YE8, Q8C827, Q8IYB9, Q8N4W9, Q8N7M2

Diamond homologs: A0JPK3, A8MT65, C9JN71, E9QAG8, G3X9G7, O75820, P16373, P16374, P16415, P17017, P17024, P17025, P51815, P52737, Q08AG5, Q08ER8, Q0D2J5, Q15973, Q2M218, Q3KP31, Q3V080, Q494X3, Q4R4C7, Q5MYW4, Q5R9F0, Q5R9S5, Q5REI6, Q5REK1, Q68EA5, Q6P560, Q6P5C7, Q6ZQV5, Q7L945, Q86T29, Q8BGV5, Q8C6P8, Q8IYI8, Q8IZC7, Q8N7K0, Q8N972

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	51
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1156 predictions. Top by Δscore:

Variant	Effect	Δscore
19:12466861:CCACA:C	acceptor_gain	1.0000
19:12466862:CACA:C	acceptor_gain	1.0000
19:12466865:A:C	acceptor_gain	1.0000
19:12465731:CTT:C	acceptor_gain	0.9900
19:12465732:TT:T	acceptor_gain	0.9900
19:12465734:C:CC	acceptor_gain	0.9900
19:12466457:CTCA:C	donor_loss	0.9900
19:12466458:TCACC:T	donor_loss	0.9900
19:12466459:CAC:C	donor_loss	0.9900
19:12466459:CACC:C	donor_loss	0.9900
19:12466460:A:C	donor_loss	0.9900
19:12466460:A:T	donor_loss	0.9900
19:12466461:C:CA	donor_loss	0.9900
19:12466718:TCTTA:T	donor_loss	0.9900
19:12466719:CTTAC:C	donor_loss	0.9900
19:12466720:TTAC:T	donor_loss	0.9900
19:12466720:TTACC:T	donor_loss	0.9900
19:12466721:T:TG	donor_loss	0.9900
19:12466722:A:AG	donor_loss	0.9900
19:12466722:A:C	donor_loss	0.9900
19:12466723:C:A	donor_loss	0.9900
19:12466723:C:G	donor_loss	0.9900
19:12466862:C:T	acceptor_gain	0.9900
19:12484651:TTA:T	donor_loss	0.9900
19:12484652:TA:T	donor_loss	0.9900
19:12484653:A:AC	donor_gain	0.9900
19:12484653:A:AG	donor_loss	0.9900
19:12484653:AC:A	donor_gain	0.9900
19:12484654:C:CG	donor_gain	0.9900
19:12484654:C:CT	donor_loss	0.9900

AlphaMissense

4321 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:12464383:G:C	F513L	0.994
19:12464383:G:T	F513L	0.994
19:12464385:A:G	F513L	0.994
19:12464551:G:C	F457L	0.993
19:12464551:G:T	F457L	0.993
19:12464553:A:G	F457L	0.993
19:12465139:G:C	F261L	0.993
19:12465139:G:T	F261L	0.993
19:12465141:A:G	F261L	0.993
19:12464467:A:C	F485L	0.992
19:12464467:A:T	F485L	0.992
19:12464469:A:G	F485L	0.992
19:12464299:A:C	F541L	0.991
19:12464299:A:T	F541L	0.991
19:12464301:A:G	F541L	0.991
19:12464215:G:C	F569L	0.990
19:12464215:G:T	F569L	0.990
19:12464217:A:G	F569L	0.990
19:12464635:G:C	F429L	0.990
19:12464635:G:T	F429L	0.990
19:12464637:A:G	F429L	0.990
19:12465391:G:C	F177L	0.989
19:12465391:G:T	F177L	0.989
19:12465393:A:G	F177L	0.989
19:12464131:G:C	F597L	0.988
19:12464131:G:T	F597L	0.988
19:12464133:A:G	F597L	0.988
19:12464803:A:C	F373L	0.988
19:12464803:A:T	F373L	0.988
19:12464805:A:G	F373L	0.988

dbSNP variants (sampled 300 via entrez): RS1000089549 (19:12468166 C>G), RS1000125533 (19:12461619 G>T), RS1000145934 (19:12472928 C>T), RS1000279050 (19:12466196 C>T), RS1000339841 (19:12480540 G>A), RS1000366507 (19:12473189 C>T), RS1000637374 (19:12467314 A>AT), RS1000795697 (19:12465881 G>A), RS1000855150 (19:12470942 A>G), RS1001002988 (19:12486435 A>G,T), RS1001136633 (19:12486235 G>A,C), RS1001153632 (19:12473397 T>C), RS1001345943 (19:12460929 CAT>C), RS1001528006 (19:12474656 C>T), RS1001563562 (19:12486542 GAAAAA>G,GAAAA,GAAAAAA)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression	4
aristolochic acid I	increases expression	1
methylmercuric chloride	decreases expression	1
methyleugenol	increases expression	1
propionaldehyde	increases expression	1
trichostatin A	decreases expression	1
pentabromodiphenyl ether	decreases expression	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
Sunitinib	decreases expression	1
Benzo(a)pyrene	affects methylation	1
Cadmium	increases expression	1
Formaldehyde	decreases expression	1
Phenylmercuric Acetate	affects cotreatment, decreases expression	1
Phthalic Acids	increases methylation	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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