ZNF682

Summary

ZNF682 (zinc finger protein 682, HGNC:28857) is a protein-coding gene on chromosome 19p12, encoding Zinc finger protein 682 (O95780). May be involved in transcriptional regulation.

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

Source: NCBI Gene 91120 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 69 total
• MANE Select transcript: NM_033196

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28857
Approved symbol	ZNF682
Name	zinc finger protein 682
Location	19p12
Locus type	gene with protein product
Status	Approved
Aliases	BC39498_3
Ensembl gene	ENSG00000197124
Ensembl biotype	protein_coding
Entrez	91120

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 10 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000358523, ENST00000397162, ENST00000397165, ENST00000593468, ENST00000594127, ENST00000595534, ENST00000595736, ENST00000596019, ENST00000597972, ENST00000599240, ENST00000601100, ENST00000601365, ENST00000602079

RefSeq mRNA: 2 — MANE Select: NM_033196 NM_001077349, NM_033196

CCDS: CCDS42533, CCDS42534

Canonical transcript exons

ENST00000397165 — 4 exons

Exon	Start	End
ENSE00001527566	20004418	20007275
ENSE00001687174	20023004	20023099
ENSE00003043790	20039343	20039505
ENSE00003496184	20024250	20024376

Expression profiles

Bgee: expression breadth ubiquitous, 228 present calls, max score 93.77.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.7417 / max 198.4478, expressed in 1429 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
180176	2.6722	993
180175	2.3254	779
180174	1.2079	637
180177	0.5363	287

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	93.77	gold quality
secondary oocyte	CL:0000655	92.92	gold quality
cortical plate	UBERON:0005343	87.51	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.91	gold quality
ganglionic eminence	UBERON:0004023	85.22	gold quality
epithelial cell of pancreas	CL:0000083	84.62	silver quality
visceral pleura	UBERON:0002401	84.47	gold quality
endothelial cell	CL:0000115	84.29	gold quality
ventricular zone	UBERON:0003053	83.14	gold quality
right lobe of thyroid gland	UBERON:0001119	82.08	gold quality
tibia	UBERON:0000979	81.99	gold quality
apex of heart	UBERON:0002098	81.87	gold quality
left lobe of thyroid gland	UBERON:0001120	81.38	gold quality
thyroid gland	UBERON:0002046	81.33	gold quality
amniotic fluid	UBERON:0000173	80.89	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.56	gold quality
putamen	UBERON:0001874	79.40	gold quality
upper arm skin	UBERON:0004263	79.03	silver quality
caudate nucleus	UBERON:0001873	78.80	gold quality
heart left ventricle	UBERON:0002084	78.72	gold quality
parietal pleura	UBERON:0002400	78.13	gold quality
cardiac ventricle	UBERON:0002082	78.09	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	78.02	gold quality
sperm	CL:0000019	77.94	gold quality
cerebellar hemisphere	UBERON:0002245	77.94	gold quality
cerebellar cortex	UBERON:0002129	77.88	gold quality
skin of abdomen	UBERON:0001416	77.61	gold quality
right uterine tube	UBERON:0001302	77.46	gold quality
Brodmann (1909) area 23	UBERON:0013554	77.25	gold quality
cerebellum	UBERON:0002037	76.77	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-89232	yes	338.06
E-ANND-3	yes	5.09
E-MTAB-6058	no	236.39

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA1599.1	ZNF682	More than 3 adjacent zinc fingers
MA1599.2	ZNF682	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:28092692

miRNA regulators (miRDB)

62 targeting ZNF682, 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-3925-3P	100.00	69.95	1237
HSA-MIR-3064-3P	100.00	70.09	1254
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-LET-7C-3P	99.95	73.42	2862
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-3119	99.92	71.34	2390
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-3686	99.90	70.53	2432
HSA-MIR-380-3P	99.89	70.18	1978

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp738	ENSMUSG00000048280
mus_musculus	Zfp457	ENSMUSG00000055341
mus_musculus	Zfp595	ENSMUSG00000057842
mus_musculus	Zfp953	ENSMUSG00000098905
rattus_norvegicus	AABR07009105.1	ENSRNOG00000053325

Paralogs (176): ZNF195 (ENSG00000005801), ZNF112 (ENSG00000062370), ZNF275 (ENSG00000063587), ZNF37A (ENSG00000075407), ZNF510 (ENSG00000081386), ZNF506 (ENSG00000081665), ZNF268 (ENSG00000090612), MZF1 (ENSG00000099326), ZNF629 (ENSG00000102870), ZNF175 (ENSG00000105497), ZNF85 (ENSG00000105750), ZFP30 (ENSG00000120784), ZNF45 (ENSG00000124459), ZNF391 (ENSG00000124613), ZNF436 (ENSG00000125945), ZNF484 (ENSG00000127081), ZNF835 (ENSG00000127903), ZNF780B (ENSG00000128000), ZSCAN10 (ENSG00000130182), ZNF317 (ENSG00000130803), ZNF331 (ENSG00000130844), ZNF227 (ENSG00000131115), ZNF141 (ENSG00000131127), ZNF132 (ENSG00000131849), ZNF189 (ENSG00000136870), ZIM3 (ENSG00000141946), ZFP14 (ENSG00000142065), ZNF514 (ENSG00000144026), ZNF300 (ENSG00000145908), RBAK (ENSG00000146587), ZNF157 (ENSG00000147117), ZNF182 (ENSG00000147118), ZNF41 (ENSG00000147124), ZNF7 (ENSG00000147789), ZNF117 (ENSG00000152926), ZNF221 (ENSG00000159905), ZNF235 (ENSG00000159917), ZNF714 (ENSG00000160352), ZNF577 (ENSG00000161551), ZNF12 (ENSG00000164631)

Protein

Protein identifiers

Zinc finger protein 682 — O95780 (reviewed: O95780)

All UniProt accessions (8): B9EG95, O95780, M0QXB8, M0QYJ5, M0QZ56, M0R067, M0R1A6, M0R2B6

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.

Isoforms (3)

UniProt ID	Names	Canonical?
O95780-1	1	yes
O95780-2	2
O95780-3	3

RefSeq proteins (2): NP_001070817, NP_149973* (*=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
IPR050826	Krueppel_C2H2_ZnFinger	Family

Pfam: PF00096, PF01352

UniProt features (18 total): zinc finger region 11, sequence variant 3, splice variant 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O95780-F1	70.14	0.11

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 70 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_UP, GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_UP, chr19p12, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, LU_EZH2_TARGETS_DN, GOBP_NEGATIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, BRCA1_DN.V1_UP, MTOR_UP.N4.V1_DN, TAVAZOIE_METASTASIS, STK33_SKM_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, CBX7_TARGET_GENES, HAND1_TARGET_GENES

GO Biological Process (2): negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (5): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), 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 transcription by RNA polymerase II	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
transcription by RNA polymerase II	1
negative regulation of DNA-templated transcription	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
transition metal ion binding	1
nucleic acid binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

348 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF682	VAV3	Q9UKW4	400
ZNF682	JHY	Q6NUN7	377
ZNF682	C9JR48	C9JR48	324
ZNF682	CFAP74	Q9C0B2	324
ZNF682	MCMDC2	Q4G0Z9	323
ZNF682	CAPZB	P47756	302
ZNF682	TCAF2	A6NFQ2	292
ZNF682	EXO5	Q9H790	290
ZNF682	NDRG4	Q9ULP0	281
ZNF682	OCIAD1	Q9NX40	276
ZNF682	MYO3B	Q8WXR4	274
ZNF682	PTGR2	Q8N8N7	270
ZNF682	HYPK	Q9NX55	269
ZNF682	CATSPER2	Q96P56	253
ZNF682	CLPTM1	O96005	252

IntAct

4 interactions, top by confidence:

A	B	Type	Score
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.530
ZNF682	ECE1	psi-mi:“MI:0915”(physical association)	0.370
ZNF682		psi-mi:“MI:0915”(physical association)	0.000

BioGRID (5): ZNF682 (Affinity Capture-MS), ZNF682 (Affinity Capture-MS), ZNF682 (Affinity Capture-MS), ZNF682 (Cross-Linking-MS (XL-MS)), ZNF682 (Affinity Capture-RNA)

ESM2 similar proteins: A0A1W2PQL4, A0JPL0, A2RRD8, A6NHJ4, A6NP11, B4DX44, O75346, O95780, P0CB33, P21506, P51508, P52738, Q0D2J5, Q0VGE8, Q12901, Q13360, Q14593, Q15973, Q2M218, Q2M3X9, Q2VY69, Q3SXZ3, Q5HY98, Q5RCJ2, Q5VIY5, Q6J6I6, Q7L2R6, Q86XU0, Q86Y25, Q8IW36, Q8IYN0, Q8IYX0, Q8N782, Q8N883, Q8N9Z0, Q8NDP4, Q95K49, Q969W8, Q96H40, Q96N58

Diamond homologs: A0A1W2PQL4, A6NK75, A6NN14, A6NNF4, A6NP11, A8MQ14, A8MTY0, A8MUV8, A8MXY4, B4DX44, B4DXR9, E9PYI1, O14628, O43345, O75290, O75346, O75373, O75437, O95780, P0CB33, P0DKX0, P0DPD5, P16373, P17019, P17038, P21506, P35789, P52736, P52738, P52744, Q03923, Q03924, Q03936, Q03938, Q05481, Q14586, Q14593, Q14929, Q15928, Q3KNS6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	61
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1230 predictions. Top by Δscore:

Variant	Effect	Δscore
19:20024244:TCTCA:T	donor_loss	1.0000
19:20024245:CTCAC:C	donor_loss	1.0000
19:20024246:TCACC:T	donor_loss	1.0000
19:20024247:CAC:C	donor_loss	1.0000
19:20024248:A:AC	donor_gain	1.0000
19:20024248:A:C	donor_loss	1.0000
19:20024248:AC:A	donor_gain	1.0000
19:20024249:C:CC	donor_gain	1.0000
19:20024249:C:CG	donor_loss	1.0000
19:20024249:CC:C	donor_gain	1.0000
19:20024289:T:A	donor_gain	1.0000
19:20024372:AGTTC:A	acceptor_gain	1.0000
19:20024373:GTTC:G	acceptor_gain	1.0000
19:20024374:TTC:T	acceptor_gain	1.0000
19:20024375:TC:T	acceptor_gain	1.0000
19:20024375:TCCTG:T	acceptor_loss	1.0000
19:20024376:CC:C	acceptor_gain	1.0000
19:20024377:C:CC	acceptor_gain	1.0000
19:20024378:T:C	acceptor_loss	1.0000
19:20039338:CTCA:C	donor_loss	1.0000
19:20039339:TCAC:T	donor_loss	1.0000
19:20039341:ACC:A	donor_loss	1.0000
19:20039342:C:CA	donor_loss	1.0000
19:20007283:A:C	acceptor_gain	0.9900
19:20024248:ACC:A	donor_gain	0.9900
19:20024249:CCC:C	donor_gain	0.9900
19:20024386:A:T	acceptor_gain	0.9900
19:20039341:A:AC	donor_gain	0.9900
19:20039341:AC:A	donor_gain	0.9900
19:20039342:C:CC	donor_gain	0.9900

AlphaMissense

3307 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:20006284:A:C	F406L	0.990
19:20006284:A:T	F406L	0.990
19:20006286:A:G	F406L	0.990
19:20006620:A:C	F294L	0.990
19:20006620:A:T	F294L	0.990
19:20006622:A:G	F294L	0.990
19:20006704:A:C	F266L	0.987
19:20006704:A:T	F266L	0.987
19:20006706:A:G	F266L	0.987
19:20006200:A:C	F434L	0.985
19:20006200:A:T	F434L	0.985
19:20006202:A:G	F434L	0.985
19:20006788:A:C	F238L	0.985
19:20006788:A:T	F238L	0.985
19:20006790:A:G	F238L	0.985
19:20006452:A:C	F350L	0.981
19:20006452:A:T	F350L	0.981
19:20006454:A:G	F350L	0.981
19:20006536:A:C	F322L	0.980
19:20006536:A:T	F322L	0.980
19:20006538:A:G	F322L	0.980
19:20006615:C:G	R296P	0.977
19:20006195:C:G	R436P	0.971
19:20024341:G:C	F13L	0.963
19:20024341:G:T	F13L	0.963
19:20024343:A:G	F13L	0.963
19:20006368:A:C	F378L	0.956
19:20006368:A:T	F378L	0.956
19:20006370:A:G	F378L	0.956
19:20006448:A:G	S352P	0.946

dbSNP variants (sampled 300 via entrez): RS1000014811 (19:20002046 C>G), RS1000048855 (19:20004523 T>C), RS1000113674 (19:20004336 C>T), RS1000115836 (19:20017616 AT>A), RS1000145777 (19:20008136 T>C), RS1000308928 (19:20040742 T>C), RS1000337870 (19:20017187 G>A), RS1000428693 (19:20007824 G>A), RS1000485633 (19:20023379 C>T), RS1000582394 (19:20029750 A>C), RS1000701555 (19:20001559 A>C), RS1000726370 (19:20036037 A>T), RS1000900875 (19:19999539 C>T), RS1000910767 (19:20034213 T>C), RS1001136631 (19:19996878 C>T)

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
GCST90007007_8	Gut microbiota relative abundance (Sutterella)	2.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
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
sodium arsenite	decreases expression, increases expression	2
Air Pollutants	decreases expression, increases abundance, increases expression, affects cotreatment	2
Tobacco Smoke Pollution	decreases expression, increases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
bisphenol F	affects cotreatment, decreases expression	1
methylmercuric chloride	decreases expression	1
alpha-pinene	affects cotreatment, decreases expression, increases abundance	1
bisphenol A	decreases expression	1
arsenite	decreases methylation	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
methacrylaldehyde	decreases expression, increases abundance, affects cotreatment	1
di-n-butylphosphoric acid	affects expression	1
erucylphospho-N,N,N-trimethylpropylammonium	increases expression	1
ICG 001	increases expression	1
picoxystrobin	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Arsenic Trioxide	increases expression	1
Leflunomide	decreases expression	1
Acrolein	affects cotreatment, decreases expression, increases abundance	1
Benzo(a)pyrene	affects methylation	1
Dexamethasone	affects cotreatment, decreases expression	1
Succimer	affects cotreatment, increases expression	1
Hydrogen Peroxide	affects expression	1
Indomethacin	affects cotreatment, decreases expression	1
Ozone	decreases expression, increases abundance, affects cotreatment	1
Rotenone	increases expression	1
Silicon Dioxide	increases expression	1
Tretinoin	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Asbestos, Crocidolite	decreases expression	1

Clinical trials (associated diseases)

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