ZNF2

Summary

ZNF2 (zinc finger protein 2, HGNC:12991) is a protein-coding gene on chromosome 2q11.1, encoding Zinc finger protein 2 (Q9BSG1). May be involved in transcriptional regulation.

The protein encoded by this gene belongs to the C2H2-type zinc-finger protein family. The exact function of this gene is not known, however, zinc-finger proteins are known to interact with DNA and function as transcription regulators. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 7549 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 19 total
• MANE Select transcript: NM_021088

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:12991
Approved symbol	ZNF2
Name	zinc finger protein 2
Location	2q11.1
Locus type	gene with protein product
Status	Approved
Aliases	A1-5, ZNF661, Zfp661
Ensembl gene	ENSG00000275111
Ensembl biotype	protein_coding
OMIM	194500
Entrez	7549

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 protein_coding

ENST00000611147, ENST00000611463, ENST00000614034, ENST00000617923, ENST00000622059, ENST00000876804

RefSeq mRNA: 5 — MANE Select: NM_021088 NM_001017396, NM_001282398, NM_001291604, NM_001291605, NM_021088

CCDS: CCDS42712, CCDS42713, CCDS62957, CCDS77434, CCDS77435

Canonical transcript exons

ENST00000614034 — 5 exons

Exon	Start	End
ENSE00003712550	95181103	95184317
ENSE00003715158	95176188	95176259
ENSE00003726469	95177483	95177609
ENSE00003734368	95180159	95180272
ENSE00003749171	95165809	95165860

Expression profiles

Bgee: expression breadth ubiquitous, 189 present calls, max score 82.69.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.8723 / max 44.3196, expressed in 1599 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
21416	3.7768	1587
21417	0.0955	32

Top tissues by expression

242 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	82.69	gold quality
secondary oocyte	CL:0000655	82.48	gold quality
endothelial cell	CL:0000115	79.67	gold quality
oocyte	CL:0000023	78.96	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	78.77	gold quality
ileal mucosa	UBERON:0000331	78.44	gold quality
pancreatic ductal cell	CL:0002079	75.37	silver quality
stromal cell of endometrium	CL:0002255	75.10	gold quality
granulocyte	CL:0000094	74.85	gold quality
islet of Langerhans	UBERON:0000006	74.46	gold quality
cortical plate	UBERON:0005343	74.27	gold quality
ganglionic eminence	UBERON:0004023	74.20	gold quality
ventricular zone	UBERON:0003053	73.41	gold quality
tibialis anterior	UBERON:0001385	72.66	silver quality
hindlimb stylopod muscle	UBERON:0004252	72.15	gold quality
smooth muscle tissue	UBERON:0001135	71.39	gold quality
muscle of leg	UBERON:0001383	70.85	gold quality
gastrocnemius	UBERON:0001388	70.59	gold quality
right adrenal gland cortex	UBERON:0035827	70.29	gold quality
right adrenal gland	UBERON:0001233	70.21	gold quality
apex of heart	UBERON:0002098	70.17	gold quality
left adrenal gland	UBERON:0001234	69.93	gold quality
sperm	CL:0000019	69.62	silver quality
prefrontal cortex	UBERON:0000451	69.47	gold quality
left adrenal gland cortex	UBERON:0035825	69.45	gold quality
leukocyte	CL:0000738	68.97	gold quality
adrenal gland	UBERON:0002369	68.89	gold quality
pigmented layer of retina	UBERON:0001782	68.55	gold quality
descending thoracic aorta	UBERON:0002345	68.52	gold quality
adrenal cortex	UBERON:0001235	68.42	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.69

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

Target	Regulation
SULT1A1

miRNA regulators (miRDB)

90 targeting ZNF2, 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-4481	100.00	66.42	1669
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4745-5P	99.98	65.95	1028
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-6753-3P	99.93	66.57	637
HSA-MIR-7107-3P	99.93	66.73	627
HSA-MIR-106A-5P	99.90	73.94	2683
HSA-MIR-17-5P	99.89	73.83	2665
HSA-MIR-302A-3P	99.89	71.23	1777
HSA-MIR-302B-3P	99.89	71.23	1777
HSA-MIR-302C-3P	99.89	71.20	1778
HSA-MIR-302D-3P	99.89	71.25	1777
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-106B-5P	99.88	74.72	2795
HSA-MIR-20A-5P	99.88	74.76	2769
HSA-MIR-20B-5P	99.88	74.01	2621
HSA-MIR-519D-3P	99.88	73.97	2607
HSA-MIR-526B-3P	99.88	74.06	2587
HSA-MIR-93-5P	99.88	73.98	2606
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-6857-5P	99.87	65.32	985
HSA-MIR-373-3P	99.84	70.68	1668
HSA-MIR-520E-3P	99.84	70.55	1698
HSA-MIR-3663-3P	99.84	70.39	798
HSA-MIR-372-3P	99.83	70.58	1691
HSA-MIR-520A-3P	99.83	70.59	1687

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp661	ENSMUSG00000034800
rattus_norvegicus	LOC100909998	ENSRNOG00000068677

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 2 — Q9BSG1 (reviewed: Q9BSG1)

Alternative names: Zinc finger protein 2.2, Zinc finger protein 661

All UniProt accessions (3): Q9BSG1, A0A087WYR5, Q68CY6

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?
Q9BSG1-2	2	yes
Q9BSG1-3	3
Q9BSG1-4	4

RefSeq proteins (5): NP_001017396, NP_001269327, NP_001278533, NP_001278534, NP_066574* (*=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
IPR050758	Znf_C2H2-type	Family

Pfam: PF00096, PF01352

UniProt features (20 total): zinc finger region 9, sequence conflict 3, region of interest 2, compositionally biased region 2, splice variant 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BSG1-F1	74.43	0.47

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 48 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_DN, GTGCCTT_MIR506, CREB_Q3, chr2q11, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A, WAKABAYASHI_ADIPOGENESIS_PPARG_BOUND_8D, ZWANG_CLASS_1_TRANSIENTLY_INDUCED_BY_EGF, BARX1_TARGET_GENES, DACH1_TARGET_GENES, DIDO1_TARGET_GENES, HES4_TARGET_GENES, NFE2L1_TARGET_GENES, ZBTB18_TARGET_GENES, ZNF563_TARGET_GENES, ZNF618_TARGET_GENES

GO Biological Process (1): regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (4): DNA binding (GO:0003677), zinc ion binding (GO:0008270), 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
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
nucleic acid binding	1
transition metal ion binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

616 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF2	CNBP	P20694	723
ZNF2	KMT2C	Q8NEZ4	642
ZNF2	MBNL2	Q5VZF2	572
ZNF2	MBNL3	Q9NUK0	565
ZNF2	MBNL1	Q9NR56	512
ZNF2	MAT2A	P31153	480
ZNF2	PUM1	Q14671	446
ZNF2	SLC7A8	Q9UHI5	425
ZNF2	CRBN	Q96SW2	404
ZNF2	GPD1	P21695	372
ZNF2	GLIS2	Q9BZE0	360
ZNF2	CLCN1	P35523	355
ZNF2	PAXIP1	Q6ZW49	340
ZNF2	DMPK	Q09013	334
ZNF2	YIPF2	Q9BWQ6	321
ZNF2	TBRG4	Q969Z0	321

IntAct

18 interactions, top by confidence:

A	B	Type	Score
DVL3	ZNF2	psi-mi:“MI:0915”(physical association)	0.560
TRIM41	ZNF2	psi-mi:“MI:0915”(physical association)	0.560
SPANXN2	ZNF2	psi-mi:“MI:0915”(physical association)	0.560
HTT	ZNF2	psi-mi:“MI:0915”(physical association)	0.560
ZNF2	MPHOSPH10	psi-mi:“MI:0914”(association)	0.530
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.530
ZNF2	PRMT5	psi-mi:“MI:0915”(physical association)	0.370
ZNF2	TRIM24	psi-mi:“MI:0914”(association)	0.350
ZNF2	APOBEC3DE	psi-mi:“MI:0914”(association)	0.350
ZNF2	DVL3	psi-mi:“MI:0915”(physical association)	0.000
ZNF2	TRIM41	psi-mi:“MI:0915”(physical association)	0.000
SPANXN2	ZNF2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (122): TSGA10 (Two-hybrid), KRTAP10-7 (Two-hybrid), ZNF2 (Affinity Capture-MS), ZNF2 (Reconstituted Complex), KIAA0020 (Affinity Capture-MS), ZFP62 (Affinity Capture-MS), TAF1B (Affinity Capture-MS), ZNF800 (Affinity Capture-MS), RRP8 (Affinity Capture-MS), BUD13 (Affinity Capture-MS), RPF2 (Affinity Capture-MS), ZNF770 (Affinity Capture-MS), GLYR1 (Affinity Capture-MS), RPL37A (Affinity Capture-MS), DDX10 (Affinity Capture-MS)

ESM2 similar proteins: A2A761, A2T7D2, A3KN32, A3KN36, A7MBI1, B2RXC5, E9PYI1, O43296, P0CG31, P10072, P10078, P17023, P17097, P18725, P18728, P52738, Q02525, Q07231, Q0VCB0, Q12901, Q14592, Q49AA0, Q4V8A8, Q571J5, Q5CZA5, Q5JNZ3, Q5R7I8, Q5RB33, Q5RBX0, Q5RBY9, Q61967, Q62396, Q6PF04, Q6ZNG0, Q6ZS27, Q7Z398, Q80YP6, Q8BIQ3, Q8IZ26, Q96N20

Diamond homologs: A0JPL0, A1L1L7, A2A761, A2VDP4, A3KN36, A6QLU5, A6QPT6, A7MBI1, A8MT65, B2RXC5, E9PYI1, E9Q8G5, O75290, O94892, O95780, P10076, P17014, P17023, P17025, P17030, P17032, P17098, P51523, P51814, P52736, P52742, P58317, Q02975, Q06730, Q06732, Q08DG8, Q0VCB0, Q13360, Q14584, Q14587, Q14590, Q147U1, Q16587, Q29RZ4, Q2M218

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	12
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

833 predictions. Top by Δscore:

Variant	Effect	Δscore
2:95177570:G:GT	donor_gain	1.0000
2:95165839:TCCC:T	donor_gain	0.9900
2:95165858:G:GT	donor_gain	0.9900
2:95177481:A:AG	acceptor_gain	0.9900
2:95177481:A:AT	acceptor_loss	0.9900
2:95177481:AG:A	acceptor_gain	0.9900
2:95177482:G:GG	acceptor_gain	0.9900
2:95177482:GG:G	acceptor_gain	0.9900
2:95177576:A:AG	donor_loss	0.9900
2:95177607:TGGGT:T	donor_loss	0.9900
2:95177608:GG:G	donor_gain	0.9900
2:95177609:GG:G	donor_gain	0.9900
2:95177610:G:GA	donor_loss	0.9900
2:95177611:T:G	donor_loss	0.9900
2:95181101:A:AG	acceptor_gain	0.9900
2:95181102:G:GG	acceptor_gain	0.9900
2:95181102:GACT:G	acceptor_gain	0.9900
2:95165858:GAGG:G	donor_loss	0.9800
2:95165859:AG:A	donor_loss	0.9800
2:95165860:GG:G	donor_loss	0.9800
2:95166018:A:T	donor_gain	0.9800
2:95170178:A:T	donor_gain	0.9800
2:95177482:GGA:G	acceptor_gain	0.9800
2:95177610:G:GG	donor_gain	0.9800
2:95181101:AGACT:A	acceptor_gain	0.9800
2:95181102:GACTG:G	acceptor_gain	0.9800
2:95170177:G:GT	donor_gain	0.9700
2:95177616:G:T	donor_gain	0.9700
2:95180243:A:T	donor_gain	0.9700
2:95165737:G:GT	donor_gain	0.9600

AlphaMissense

2806 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:95181960:T:C	F378L	0.998
2:95181962:T:A	F378L	0.998
2:95181962:T:G	F378L	0.998
2:95181624:T:C	F266L	0.997
2:95181626:T:A	F266L	0.997
2:95181626:T:G	F266L	0.997
2:95181708:T:C	F294L	0.997
2:95181710:T:A	F294L	0.997
2:95181710:T:G	F294L	0.997
2:95181792:T:C	F322L	0.997
2:95181794:C:A	F322L	0.997
2:95181794:C:G	F322L	0.997
2:95181456:T:C	F210L	0.996
2:95181458:C:A	F210L	0.996
2:95181458:C:G	F210L	0.996
2:95181574:G:C	R249P	0.996
2:95181643:T:C	L272P	0.996
2:95181597:T:C	F257L	0.995
2:95181599:T:A	F257L	0.995
2:95181599:T:G	F257L	0.995
2:95181639:T:C	S271P	0.995
2:95181653:C:A	H275Q	0.995
2:95181653:C:G	H275Q	0.995
2:95181733:G:C	R302P	0.995
2:95181876:T:C	F350L	0.995
2:95181878:C:A	F350L	0.995
2:95181878:C:G	F350L	0.995
2:95181540:T:C	F238L	0.994
2:95181542:C:A	F238L	0.994
2:95181542:C:G	F238L	0.994

dbSNP variants (sampled 300 via entrez): RS1000000009 (2:95169763 A>G), RS1000276023 (2:95183192 G>A), RS1000562308 (2:95170049 C>T), RS1000983508 (2:95175552 A>G), RS1001410772 (2:95168290 T>C), RS1001530780 (2:95178152 TAG>T), RS1001553788 (2:95184705 G>T), RS1001646757 (2:95178420 T>A), RS1001830513 (2:95171547 TA>T), RS1001836086 (2:95184256 G>A), RS1001945366 (2:95165069 T>C), RS1002435775 (2:95182732 A>T), RS1002580297 (2:95168172 A>G,T), RS1003208028 (2:95179328 G>A), RS1003317588 (2:95179617 T>A)

Disease associations

OMIM: gene MIM:194500 | 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

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects cotreatment, increases abundance, increases expression	2
Arsenic	affects methylation, affects cotreatment, increases abundance, increases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
FR900359	increases phosphorylation	1
bisphenol F	increases expression, affects cotreatment	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, increases expression	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
resorcinol	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
bisphenol S	affects cotreatment, increases expression	1
(+)-JQ1 compound	increases expression	1
Sunitinib	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Atrazine	decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Indomethacin	affects cotreatment, increases expression	1
Manganese	increases abundance, increases expression, affects cotreatment	1
T-2 Toxin	increases expression	1
Testosterone	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Particulate Matter	decreases expression, increases abundance	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_XW16	HEK293 eGFP-ZNF2	Transformed cell line	Female

Clinical trials (associated diseases)

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