ZNF662

Summary

ZNF662 (zinc finger protein 662, HGNC:31930) is a protein-coding gene on chromosome 3p22.1, encoding Zinc finger protein 662 (Q6ZS27). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity 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 located in nucleus.

Source: NCBI Gene 389114 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 93 total
• MANE Select transcript: NM_207404

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31930
Approved symbol	ZNF662
Name	zinc finger protein 662
Location	3p22.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ45880
Ensembl gene	ENSG00000182983
Ensembl biotype	protein_coding
Entrez	389114

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 11 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000328199, ENST00000422021, ENST00000430067, ENST00000440367, ENST00000475386, ENST00000856443, ENST00000856444, ENST00000856445, ENST00000856446, ENST00000928117, ENST00000928118, ENST00000958960, ENST00000958961

RefSeq mRNA: 2 — MANE Select: NM_207404 NM_001134656, NM_207404

CCDS: CCDS2708, CCDS46807

Canonical transcript exons

ENST00000440367 — 5 exons

Exon	Start	End
ENSE00001372910	42913201	42913302
ENSE00001417605	42906142	42906168
ENSE00001953502	42914327	42919334
ENSE00003660358	42908793	42908909
ENSE00003661500	42908022	42908148

Expression profiles

Bgee: expression breadth ubiquitous, 201 present calls, max score 94.32.

FANTOM5 (CAGE): breadth broad, TPM avg 1.1845 / max 37.8725, expressed in 433 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
36295	1.1845	433

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oviduct epithelium	UBERON:0004804	94.32	gold quality
pancreatic ductal cell	CL:0002079	89.57	silver quality
left ovary	UBERON:0002119	86.61	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.84	gold quality
right ovary	UBERON:0002118	85.67	gold quality
ovary	UBERON:0000992	85.23	gold quality
body of uterus	UBERON:0009853	84.09	gold quality
body of pancreas	UBERON:0001150	84.01	gold quality
colonic epithelium	UBERON:0000397	83.30	gold quality
secondary oocyte	CL:0000655	83.03	gold quality
mucosa of stomach	UBERON:0001199	82.59	gold quality
endocervix	UBERON:0000458	82.39	gold quality
skin of leg	UBERON:0001511	82.29	gold quality
ectocervix	UBERON:0012249	82.13	gold quality
tibial nerve	UBERON:0001323	81.76	gold quality
right hemisphere of cerebellum	UBERON:0014890	81.61	gold quality
right uterine tube	UBERON:0001302	81.53	gold quality
skin of abdomen	UBERON:0001416	81.50	gold quality
cerebellar hemisphere	UBERON:0002245	81.44	gold quality
vagina	UBERON:0000996	81.34	gold quality
minor salivary gland	UBERON:0001830	81.33	gold quality
cerebellar cortex	UBERON:0002129	81.27	gold quality
fallopian tube	UBERON:0003889	81.12	gold quality
left uterine tube	UBERON:0001303	80.93	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	80.91	gold quality
oocyte	CL:0000023	80.79	gold quality
right lobe of thyroid gland	UBERON:0001119	80.71	gold quality
ventricular zone	UBERON:0003053	80.64	gold quality
ganglionic eminence	UBERON:0004023	80.64	gold quality
tendon of biceps brachii	UBERON:0008188	80.42	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.17

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

120 targeting ZNF662, 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-450A-1-3P	100.00	69.33	1837
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-219A-5P	99.91	73.36	735
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-5682	99.89	72.56	1005
HSA-MIR-4782-3P	99.88	73.31	735
HSA-MIR-6766-3P	99.88	73.38	732
HSA-MIR-5003-3P	99.85	69.29	2517
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-4728-5P	99.85	69.39	4718

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	znf574	ENSDARG00000087074
drosophila_melanogaster	CG11902	FBGN0028647
drosophila_melanogaster	CG11696	FBGN0030314
drosophila_melanogaster	CG10631	FBGN0032817

Paralogs (7): ZNF671 (ENSG00000083814), ZNF710 (ENSG00000140548), ZNF212 (ENSG00000170260), ZNF366 (ENSG00000178175), ZNF667 (ENSG00000198046), ZNF783 (ENSG00000204946), ZNF865 (ENSG00000261221)

Protein

Protein identifiers

Zinc finger protein 662 — Q6ZS27 (reviewed: Q6ZS27)

All UniProt accessions (2): Q6ZS27, F8WE97

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?
Q6ZS27-1	1	yes
Q6ZS27-2	2
Q6ZS27-3	3

RefSeq proteins (2): NP_001128128, NP_997287* (*=MANE)

Domains & families (InterPro)

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

Pfam: PF00096

UniProt features (16 total): zinc finger region 8, splice variant 4, chain 1, domain 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZS27-F1	63.75	0.28

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 42 (showing top): chr3p22, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, DODD_NASOPHARYNGEAL_CARCINOMA_DN, FIGUEROA_AML_METHYLATION_CLUSTER_1_UP, FIGUEROA_AML_METHYLATION_CLUSTER_3_UP, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, MIR10527_5P, MIR561_3P, MIR4306, MIR3120_3P, MIR4644, MIR185_5P, MIR4524A_3P, MIR450A_1_3P

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

GO Molecular Function (7): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity (GO:0003700), zinc ion binding (GO:0008270), DNA binding (GO:0003677), protein binding (GO:0005515), sequence-specific DNA binding (GO:0043565), 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	2
transcription by RNA polymerase II	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	1
cis-regulatory region sequence-specific DNA binding	1
transcription cis-regulatory region binding	1
transcription regulator activity	1
transition metal ion binding	1
nucleic acid binding	1
binding	1
DNA binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

194 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF662	GASK1A	Q9UFP1	595
ZNF662	ARMC7	Q9H6L4	546
ZNF662	ZNF511	Q8NB15	507
ZNF662	HEXD	Q8WVB3	491
ZNF662	LSG1	Q9H089	442
ZNF662	UROS	P10746	368
ZNF662	ACOX2	Q99424	367
ZNF662	ACKR2	O00590	358
ZNF662	CYP8B1	Q9UNU6	357
ZNF662	ATP13A3	Q9H7F0	356
ZNF662	PCDHA5	Q9Y5H7	348
ZNF662	TDRD5	Q8NAT2	324
ZNF662	SLC27A5	Q9Y2P5	308
ZNF662	BAIAP2	Q9UQB8	298
ZNF662	ACADSB	P45954	298

IntAct

7 interactions, top by confidence:

A	B	Type	Score
ZNF662	H1-3	psi-mi:“MI:0915”(physical association)	0.590
EPHA1	ZNF662	psi-mi:“MI:0915”(physical association)	0.000
NDEL1	ZNF662	psi-mi:“MI:0915”(physical association)	0.000
HUNK	ZNF662	psi-mi:“MI:0915”(physical association)	0.000
RSPH1	ZNF662	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (10): ZNF662 (Two-hybrid), ZNF662 (Two-hybrid), HIST1H1D (Affinity Capture-MS), HIST1H1D (Affinity Capture-MS), ZNF662 (Two-hybrid), ZNF662 (Two-hybrid), CTNNA3 (Two-hybrid), HIST1H1D (Affinity Capture-MS), ZNF662 (Two-hybrid), ZNF662 (Two-hybrid)

ESM2 similar proteins: A1L1L7, A3KN36, D3ZVT0, O43296, P08042, P13682, P16373, P17023, P17097, P52738, P85977, Q02975, Q12901, Q14590, Q14592, Q2M3W8, Q2VY69, Q4V8A8, Q571J5, Q5CZA5, Q5R7I8, Q5RB33, Q5RBX0, Q61751, Q61967, Q6GQR8, Q6PF04, Q6ZNG0, Q6ZS27, Q86Y25, Q8BFS8, Q8BQC8, Q8IZ26, Q8N782, Q8N9Z0, Q8R1D1, Q8TF47, Q8WTR7, Q96LW1, Q9BS31

Diamond homologs: A6NFI3, A7MBI1, P17097, Q5RBX0, Q6PGE4, Q6ZS27, Q6ZSS3, Q96N20

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	75
Likely benign	8
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1276 predictions. Top by Δscore:

Variant	Effect	Δscore
3:42908109:G:T	donor_gain	1.0000
3:42914325:AGAG:A	acceptor_gain	1.0000
3:42914326:GAGG:G	acceptor_gain	1.0000
3:42906437:GCCGG:G	donor_gain	0.9900
3:42906438:CCGGG:C	donor_loss	0.9900
3:42906440:GG:G	donor_gain	0.9900
3:42906441:GG:G	donor_gain	0.9900
3:42906441:GGTG:G	donor_loss	0.9900
3:42906442:G:GC	donor_loss	0.9900
3:42906443:TGAG:T	donor_loss	0.9900
3:42906444:GAGT:G	donor_loss	0.9900
3:42907940:G:GG	donor_gain	0.9900
3:42908109:G:GT	donor_gain	0.9900
3:42908147:GG:G	donor_gain	0.9900
3:42908148:GG:G	donor_gain	0.9900
3:42908148:GGT:G	donor_loss	0.9900
3:42908149:G:A	donor_loss	0.9900
3:42908150:T:TC	donor_loss	0.9900
3:42914326:GA:G	acceptor_gain	0.9900
3:42906442:G:GG	donor_gain	0.9800
3:42906445:AGTG:A	donor_loss	0.9800
3:42907939:A:AG	donor_gain	0.9800
3:42908016:TTTCA:T	acceptor_loss	0.9800
3:42908017:TTCAG:T	acceptor_loss	0.9800
3:42908018:TCA:T	acceptor_loss	0.9800
3:42908020:A:AC	acceptor_loss	0.9800
3:42908021:G:GC	acceptor_loss	0.9800
3:42908021:GGA:G	acceptor_gain	0.9800
3:42908145:CTGGG:C	donor_loss	0.9800
3:42908146:TGGG:T	donor_loss	0.9800

AlphaMissense

2840 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:42914842:T:C	F257L	0.999
3:42914844:T:A	F257L	0.999
3:42914844:T:G	F257L	0.999
3:42914926:T:C	F285L	0.999
3:42914928:T:A	F285L	0.999
3:42914928:T:G	F285L	0.999
3:42915262:T:C	F397L	0.999
3:42915264:C:A	F397L	0.999
3:42915264:C:G	F397L	0.999
3:42915010:T:C	F313L	0.998
3:42915012:T:A	F313L	0.998
3:42915012:T:G	F313L	0.998
3:42915094:T:C	F341L	0.998
3:42915096:C:A	F341L	0.998
3:42915096:C:G	F341L	0.998
3:42915197:T:C	L375P	0.998
3:42914758:T:C	F229L	0.997
3:42914760:C:A	F229L	0.997
3:42914760:C:G	F229L	0.997
3:42914869:C:G	H266D	0.997
3:42914871:C:A	H266Q	0.997
3:42914871:C:G	H266Q	0.997
3:42914955:T:A	H294Q	0.997
3:42914955:T:G	H294Q	0.997
3:42914960:G:C	R296P	0.997
3:42915207:T:A	H378Q	0.997
3:42915207:T:G	H378Q	0.997
3:42915209:A:C	Q379P	0.997
3:42914861:T:C	L263P	0.996
3:42914867:G:C	R265P	0.996

dbSNP variants (sampled 300 via entrez): RS1000008088 (3:42909835 C>T), RS1000051805 (3:42915324 C>T), RS1000292566 (3:42909200 G>A,C), RS1000293316 (3:42915203 G>A,T), RS1000627680 (3:42913547 C>T), RS1000973065 (3:42913525 A>G), RS1001134960 (3:42907393 G>C), RS1001466598 (3:42913849 A>G), RS1001560456 (3:42907748 A>G), RS1001578871 (3:42913862 C>T), RS1001966391 (3:42911992 A>G), RS1001989723 (3:42907374 A>C,G), RS1002175424 (3:42918687 G>C), RS1002495731 (3:42919021 A>G), RS1002508807 (3:42917414 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
GCST002595_14	Clozapine-induced agranulocytosis	3.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases expression, increases methylation	2
TAK-243	increases sumoylation	1
methyleugenol	decreases expression	1
bisphenol A	decreases methylation	1
sodium arsenate	decreases expression, increases abundance	1
terbufos	increases methylation	1
dimethylselenide	increases expression, increases oxidation	1
hydroquinone	increases expression	1
CGP 52608	affects binding, increases reaction	1
Air Pollutants	increases abundance, affects expression	1
Arsenic	decreases expression, increases abundance	1
Fonofos	increases methylation	1
Ozone	affects expression, increases abundance	1
Parathion	increases methylation	1
Phthalic Acids	increases methylation	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Reactive Oxygen Species	increases expression, increases oxidation	1
Antirheumatic Agents	increases expression	1
Okadaic Acid	decreases expression	1
Lactic Acid	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_XW74	HEK293 eGFP-ZNF662	Transformed cell line	Female

Clinical trials (associated diseases)

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