ZIM3

Summary

ZIM3 (zinc finger imprinted 3, HGNC:16366) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger imprinted 3 (Q96PE6). 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 transcription by RNA polymerase II. Predicted to be active in nucleus.

Source: NCBI Gene 114026 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 84 total
• MANE Select transcript: NM_052882

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16366
Approved symbol	ZIM3
Name	zinc finger imprinted 3
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Aliases	ZNF657
Ensembl gene	ENSG00000141946
Ensembl biotype	protein_coding
Entrez	114026

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000269834

RefSeq mRNA: 1 — MANE Select: NM_052882 NM_052882

CCDS: CCDS33125

Canonical transcript exons

ENST00000269834 — 5 exons

Exon	Start	End
ENSE00000951383	57138472	57138598
ENSE00000951384	57136873	57136971
ENSE00000951385	57134096	57136095
ENSE00001177825	57142629	57142685
ENSE00001177828	57144859	57145202

Expression profiles

Bgee: expression breadth tissue_specific, 7 present calls, max score 78.91.

Top tissues by expression

244 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	78.91	gold quality
lower lobe of lung	UBERON:0008949	50.59	silver quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
vastus lateralis	UBERON:0001379	41.41	gold quality
quadriceps femoris	UBERON:0001377	41.37	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality
palpebral conjunctiva	UBERON:0001812	41.10	gold quality
mucosa of paranasal sinus	UBERON:0005030	40.98	gold quality
amniotic fluid	UBERON:0000173	40.69	gold quality
jejunal mucosa	UBERON:0000399	40.59	gold quality
biceps brachii	UBERON:0001507	40.57	gold quality
epithelium of nasopharynx	UBERON:0001951	40.45	gold quality
myocardium	UBERON:0002349	40.45	gold quality
gingival epithelium	UBERON:0001949	40.43	gold quality
germinal epithelium of ovary	UBERON:0001304	40.33	gold quality
esophagus squamous epithelium	UBERON:0006920	40.29	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	40.27	gold quality
jejunum	UBERON:0002115	40.18	gold quality
cartilage tissue	UBERON:0002418	40.06	gold quality
oviduct epithelium	UBERON:0004804	40.03	gold quality
mammary duct	UBERON:0001765	39.98	gold quality
mucosa of sigmoid colon	UBERON:0004993	39.95	gold quality
deltoid	UBERON:0001476	39.83	gold quality
saphenous vein	UBERON:0007318	39.83	gold quality
parotid gland	UBERON:0001831	39.81	gold quality
oocyte	CL:0000023	39.80	gold quality
urethra	UBERON:0000057	39.80	gold quality
heart right ventricle	UBERON:0002080	39.79	gold quality
pericardium	UBERON:0002407	39.77	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.12

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA1709.1	ZIM3	More than 3 adjacent zinc fingers
MA1709.2	ZIM3	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:27852650

miRNA regulators (miRDB)

43 targeting ZIM3, 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-4673	100.00	66.64	1490
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-106B-5P	99.88	74.72	2795
HSA-MIR-20A-5P	99.88	74.76	2769
HSA-MIR-137-3P	99.87	74.74	2401
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-3934-3P	99.76	65.51	1351
HSA-MIR-4679	99.76	69.19	1229
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-4802-3P	99.72	70.13	1273
HSA-MIR-5197-5P	99.64	69.08	1494
HSA-MIR-141-5P	99.57	67.86	897
HSA-MIR-143-3P	99.49	69.05	1457
HSA-MIR-4770	99.49	69.09	1451
HSA-MIR-4318	99.38	66.94	1505
HSA-MIR-185-5P	99.35	68.60	2497
HSA-MIR-4644	99.35	69.12	2514
HSA-MIR-504-3P	99.30	67.18	1745
HSA-MIR-6088	99.29	68.45	1284
HSA-MIR-8077	99.17	66.67	862
HSA-MIR-548L	99.06	70.90	2560
HSA-MIR-7151-3P	99.04	69.72	2370
HSA-MIR-6876-3P	98.97	65.69	765
HSA-MIR-3926	98.95	69.26	1438
HSA-MIR-626	98.89	66.21	762
HSA-MIR-3190-5P	98.87	64.89	1345

Cross-species orthologs

0 orthologs

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), 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), ZNF3 (ENSG00000166526)

Protein

Protein identifiers

Zinc finger imprinted 3 — Q96PE6 (reviewed: Q96PE6)

Alternative names: Zinc finger protein 657

All UniProt accessions (1): Q96PE6

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_443114* (*=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
IPR050717	C2H2-ZF_Transcription_Reg	Family

Pfam: PF00096, PF01352

UniProt features (19 total): zinc finger region 11, sequence variant 6, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96PE6-F1	75.82	0.24

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 43 (showing top): GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, PKCA_DN.V1_UP, GSE5503_MLN_DC_VS_SPLEEN_DC_ACTIVATED_ALLOGENIC_TCELL_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, MIR548N, MIR1305, MIR548AN, MIR7151_3P, MIR653_3P, MIR4693_5P, MIR585_5P, MIR3934_3P, MIR6823_5P, GSE13306_TREG_VS_TCONV_LAMINA_PROPRIA_DN, GSE17721_CTRL_VS_LPS_2H_BMDC_UP

GO Biological Process (4): regulation of transcription by RNA polymerase II (GO:0006357), regulation of DNA-templated transcription (GO:0006355), regulation of gene expression (GO:0010468), regulation of primary metabolic process (GO:0080090)

GO Molecular Function (6): 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), protein binding (GO:0005515), 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
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
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
gene expression	1
regulation of macromolecule biosynthetic process	1
regulation of metabolic process	1
primary metabolic process	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
regulation of transcription by RNA polymerase II	1
transition metal ion binding	1
nucleic acid binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

440 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZIM3	USP29	Q9HBJ7	713
ZIM3	ZIM2	Q9NZV7	575
ZIM3	IGF2R	P11717	453
ZIM3	ZNF641	Q96N77	399
ZIM3	SUN1	O94901	398
ZIM3	FBXL4	Q9UKA2	395
ZIM3	SMOX	Q9NWM0	386
ZIM3	SNRPN	P14648	384
ZIM3	GARNL3	Q5VVW2	381
ZIM3	DUXA	A6NLW8	376
ZIM3	TERB1	Q8NA31	365
ZIM3	ODAD4	Q96NG3	338
ZIM3	RALGPS1	Q5JS13	337
ZIM3	KRTAP10-1	P60331	324
ZIM3	CNTD1	Q8N815	323

IntAct

8 interactions, top by confidence:

A	B	Type	Score
ZIM3	RING1	psi-mi:“MI:0915”(physical association)	0.560
RING1	ZIM3	psi-mi:“MI:0915”(physical association)	0.560
LMO3	ZIM3	psi-mi:“MI:0915”(physical association)	0.560
ZIM3	IPO8	psi-mi:“MI:0914”(association)	0.350
LMO3	ZIM3	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (5): ZIM3 (Affinity Capture-MS), ZIM3 (Synthetic Lethality), ZIM3 (Two-hybrid), RING1 (Two-hybrid), ZIM3 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0JPL0, A2A761, A3KN36, A7MBI1, A8MT65, B2RXC5, G3X9G7, P08042, P17023, P18728, P52738, Q02525, Q0D2J5, Q0VCB0, Q12901, Q2M3W8, Q2M3X9, Q49AA0, Q4R6J4, Q4V8A8, Q5FWF6, Q5JNZ3, Q5R7I8, Q5RB33, Q5REF1, Q5T5D7, Q61967, Q62396, Q6ZN11, Q6ZNG0, Q86XU0, Q8BGV5, Q8IZ26, Q8N782, Q8N859, Q8N9Z0, Q8NE65, Q8R2V3, Q8TF39, Q96BR6

Diamond homologs: A0JPL0, A2VDP4, A6QLU5, A6QPT6, A8MQ14, A8MUZ8, A8MWA4, B1APH4, B2RXC5, E9PYI1, E9Q8G5, O75290, O94892, P08042, P0CH99, P0CI00, P17014, P17025, P17030, P17031, P17032, P17098, P21506, P51508, P51523, P51786, P51814, P52736, P52738, Q02525, Q03923, Q03936, Q06730, Q06732, Q0VCB0, Q13401, Q14587, Q16587, Q2M218, Q2M3X9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	81
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

481 predictions. Top by Δscore:

Variant	Effect	Δscore
19:57138466:CCTTA:C	donor_loss	1.0000
19:57138467:CTT:C	donor_loss	1.0000
19:57138468:TTA:T	donor_loss	1.0000
19:57138469:TA:T	donor_loss	1.0000
19:57138470:A:AC	donor_gain	1.0000
19:57138470:AC:A	donor_gain	1.0000
19:57138470:ACC:A	donor_gain	1.0000
19:57138471:C:CC	donor_gain	1.0000
19:57138471:CC:C	donor_gain	1.0000
19:57138471:CCC:C	donor_gain	1.0000
19:57138471:CCCA:C	donor_gain	1.0000
19:57138511:C:A	donor_gain	1.0000
19:57138594:CTTCC:C	acceptor_gain	1.0000
19:57138595:TTCC:T	acceptor_gain	1.0000
19:57138597:CC:C	acceptor_gain	1.0000
19:57138597:CCCTG:C	acceptor_loss	1.0000
19:57138598:CC:C	acceptor_gain	1.0000
19:57138598:CCTG:C	acceptor_loss	1.0000
19:57138599:C:CC	acceptor_gain	1.0000
19:57138599:C:G	acceptor_loss	1.0000
19:57142623:GCTCA:G	donor_loss	1.0000
19:57142624:CTCA:C	donor_loss	1.0000
19:57142625:TCAC:T	donor_loss	1.0000
19:57142626:CAC:C	donor_loss	1.0000
19:57142627:A:T	donor_loss	1.0000
19:57142681:CAGAT:C	acceptor_gain	1.0000
19:57142686:C:CC	acceptor_gain	1.0000
19:57142686:CTGAG:C	acceptor_loss	1.0000
19:57142687:T:A	acceptor_loss	1.0000
19:57136094:TT:T	acceptor_gain	0.9900

AlphaMissense

3161 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:57135137:G:C	F400L	0.998
19:57135137:G:T	F400L	0.998
19:57135139:A:G	F400L	0.998
19:57135389:G:C	F316L	0.998
19:57135389:G:T	F316L	0.998
19:57135391:A:G	F316L	0.998
19:57135557:A:C	F260L	0.998
19:57135557:A:T	F260L	0.998
19:57135559:A:G	F260L	0.998
19:57134969:G:C	F456L	0.997
19:57134969:G:T	F456L	0.997
19:57134971:A:G	F456L	0.997
19:57135053:G:C	F428L	0.997
19:57135053:G:T	F428L	0.997
19:57135055:A:G	F428L	0.997
19:57135305:A:C	F344L	0.997
19:57135305:A:T	F344L	0.997
19:57135307:A:G	F344L	0.997
19:57135473:G:C	F288L	0.997
19:57135473:G:T	F288L	0.997
19:57135475:A:G	F288L	0.997
19:57135725:G:C	F204L	0.997
19:57135725:G:T	F204L	0.997
19:57135727:A:G	F204L	0.997
19:57135110:A:C	H409Q	0.996
19:57135110:A:T	H409Q	0.996
19:57135120:A:G	L406P	0.996
19:57135360:T:G	Q326P	0.996
19:57135362:G:C	H325Q	0.996
19:57135362:G:T	H325Q	0.996

dbSNP variants (sampled 300 via entrez): RS1000267113 (19:57136022 T>A,C), RS1000576906 (19:57133598 A>G), RS1000754016 (19:57138442 G>A), RS1000926292 (19:57143451 C>G), RS1001581241 (19:57140743 A>T), RS1001632236 (19:57141063 G>A,C), RS1002108665 (19:57145762 G>A), RS1002476730 (19:57137464 G>A), RS1002565744 (19:57145480 G>A), RS1003209946 (19:57139770 A>C,G), RS1003232479 (19:57140309 T>C), RS1003411859 (19:57145511 T>C), RS1003767459 (19:57145291 A>C,G), RS1003898201 (19:57134574 G>A,T), RS1004041808 (19:57143126 G>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
GCST004858_25	Dupuytren’s disease	2.000000e-17

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004229	Dupuytren Contracture

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation	1
Cadmium	decreases expression	1
Smoke	increases expression	1

Clinical trials (associated diseases)

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