ZNF233

Summary

ZNF233 (zinc finger protein 233, HGNC:30946) is a protein-coding gene on chromosome 19q13.31, encoding Zinc finger protein 233 (A6NK53). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity. Predicted to be involved in regulation of DNA-templated transcription. Predicted to be located in nucleus.

Source: NCBI Gene 353355 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 87 total
• MANE Select transcript: NM_001207005

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30946
Approved symbol	ZNF233
Name	zinc finger protein 233
Location	19q13.31
Locus type	gene with protein product
Status	Approved
Aliases	FLJ38032
Ensembl gene	ENSG00000159915
Ensembl biotype	protein_coding
Entrez	353355

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 8 protein_coding

ENST00000391958, ENST00000588489, ENST00000589522, ENST00000590668, ENST00000592581, ENST00000683810, ENST00000947740, ENST00000947741

RefSeq mRNA: 3 — MANE Select: NM_001207005 NM_001207005, NM_001330529, NM_181756

CCDS: CCDS33047, CCDS82363

Canonical transcript exons

ENST00000683810 — 5 exons

Exon	Start	End
ENSE00002486723	44266198	44266324
ENSE00002743744	44259886	44259938
ENSE00002770847	44272899	44275317
ENSE00003558446	44264314	44264375
ENSE00003646134	44266866	44266961

Expression profiles

Bgee: expression breadth ubiquitous, 167 present calls, max score 85.47.

FANTOM5 (CAGE): breadth broad, TPM avg 1.0189 / max 57.4145, expressed in 452 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
176259	0.9891	446
176258	0.0298	10

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.47	gold quality
left ventricle myocardium	UBERON:0006566	82.76	gold quality
cardiac muscle of right atrium	UBERON:0003379	82.46	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.39	gold quality
sperm	CL:0000019	80.51	gold quality
cortical plate	UBERON:0005343	77.06	gold quality
myocardium	UBERON:0002349	75.05	gold quality
adrenal tissue	UBERON:0018303	74.46	gold quality
testis	UBERON:0000473	74.42	gold quality
left testis	UBERON:0004533	74.01	gold quality
right testis	UBERON:0004534	72.54	gold quality
cerebellar cortex	UBERON:0002129	72.14	gold quality
cerebellar hemisphere	UBERON:0002245	72.13	gold quality
ganglionic eminence	UBERON:0004023	71.93	gold quality
prefrontal cortex	UBERON:0000451	71.71	gold quality
cerebellum	UBERON:0002037	71.53	gold quality
colonic epithelium	UBERON:0000397	71.42	gold quality
right hemisphere of cerebellum	UBERON:0014890	71.25	gold quality
heart left ventricle	UBERON:0002084	71.08	gold quality
apex of heart	UBERON:0002098	71.06	gold quality
ventricular zone	UBERON:0003053	70.77	gold quality
cardiac ventricle	UBERON:0002082	70.61	gold quality
muscle layer of sigmoid colon	UBERON:0035805	70.28	gold quality
Brodmann (1909) area 9	UBERON:0013540	70.18	gold quality
anterior cingulate cortex	UBERON:0009835	69.09	gold quality
frontal cortex	UBERON:0001870	68.52	gold quality
right frontal lobe	UBERON:0002810	68.51	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	68.47	gold quality
right uterine tube	UBERON:0001302	68.33	gold quality
neocortex	UBERON:0001950	68.31	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.79

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

38 targeting ZNF233, 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-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-12119	99.87	68.35	1653
HSA-MIR-202-5P	99.78	67.65	991
HSA-MIR-1976	99.74	65.48	1127
HSA-MIR-494-3P	99.70	71.45	2795
HSA-MIR-10393-5P	99.65	68.01	1368
HSA-MIR-3942-3P	99.57	69.03	2854
HSA-MIR-510-3P	99.54	70.06	2965
HSA-MIR-12123	99.52	71.79	2990
HSA-MIR-4452	99.50	68.45	1493
HSA-MIR-3911	99.38	66.95	1087
HSA-MIR-329-5P	99.27	68.11	1597
HSA-MIR-1264	99.25	66.81	1317
HSA-MIR-664A-3P	99.22	71.08	2696
HSA-MIR-4738-3P	98.98	67.98	1846
HSA-MIR-7157-3P	98.95	68.70	1582
HSA-MIR-6074	98.89	69.64	2187
HSA-MIR-4764-5P	98.88	65.53	894
HSA-MIR-382-3P	98.83	67.10	1074
HSA-MIR-384	98.71	67.34	1229
HSA-MIR-6834-3P	98.16	65.77	551
HSA-MIR-4303	98.01	68.13	2304
HSA-MIR-4778-5P	97.96	68.06	1634
HSA-MIR-337-3P	97.90	69.37	1052
HSA-MIR-3670	97.88	64.39	763
HSA-MIR-7113-5P	97.88	67.33	1735
HSA-MIR-676-3P	97.86	65.70	668

Literature-anchored findings (GeneRIF, showing 1)

• Study shows that manipulation of ZNF233 expression in hepatocellular carcinoma (HCC) cells affected cell growth through regulating cell cycle progression. Tumorigenicity assay further found that silencing ZNF233 suppressed HCC cell proliferation in vivo, suggesting an oncogenic role of ZNF233 in HCC development. (PMID:30179682)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp108	ENSMUSG00000030486
mus_musculus	Zfp235	ENSMUSG00000047603
mus_musculus	Zfp93	ENSMUSG00000055305
mus_musculus	Zfp114	ENSMUSG00000068962
mus_musculus	Zfp109	ENSMUSG00000074283
rattus_norvegicus	Zfp108	ENSRNOG00000032625
rattus_norvegicus	Znf235	ENSRNOG00000068100

Paralogs (51): WIZ (ENSG00000011451), ZNF416 (ENSG00000083817), MYNN (ENSG00000085274), PRDM4 (ENSG00000110851), PRDM2 (ENSG00000116731), ZBTB17 (ENSG00000116809), ZNF644 (ENSG00000122482), GZF1 (ENSG00000125812), ZNF426 (ENSG00000130818), ZNF287 (ENSG00000141040), ZNF697 (ENSG00000143067), ZNF687 (ENSG00000143373), ZNF214 (ENSG00000149050), ZNF547 (ENSG00000152433), ZNF776 (ENSG00000152443), ZNF230 (ENSG00000159882), ZNF222 (ENSG00000159885), ZNF333 (ENSG00000160961), ZNF319 (ENSG00000166188), ZNF592 (ENSG00000166716), ZNF646 (ENSG00000167395), ZNF507 (ENSG00000168813), ZNF768 (ENSG00000169957), ZNF417 (ENSG00000173480), ZNF408 (ENSG00000175213), ZBTB41 (ENSG00000177888), ZNF223 (ENSG00000178386), ZNF852 (ENSG00000178917), ZNF784 (ENSG00000179922), ZNF572 (ENSG00000180938), ZNF707 (ENSG00000181135), ZNF746 (ENSG00000181220), ZNF467 (ENSG00000181444), ZNF530 (ENSG00000183647), ZNF17 (ENSG00000186272), ZNF527 (ENSG00000189164), ZKSCAN7 (ENSG00000196345), ZNF34 (ENSG00000196378), ZNF774 (ENSG00000196391), ZNF777 (ENSG00000196453)

Protein

Protein identifiers

Zinc finger protein 233 — A6NK53 (reviewed: A6NK53)

All UniProt accessions (5): A6NK53, K7EJE5, K7EJT0, K7EN46, K7ER86

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 (3): NP_001193934, NP_001317458, NP_861421 (=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
IPR050752	C2H2-ZF_domain	Family

Pfam: PF00096, PF01352

UniProt features (17 total): zinc finger region 12, sequence variant 2, chain 1, domain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NK53-F1	52.80	0.01

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 56 (showing top): STAT5A_01, SNACANNNYSYAGA_UNKNOWN, PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_7, PEDRIOLI_MIR31_TARGETS_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, GLI4_TARGET_GENES, IRF5_TARGET_GENES, KLF7_TARGET_GENES, SNAI1_TARGET_GENES, YBX1_TARGET_GENES, ZBTB18_TARGET_GENES, ZIM3_TARGET_GENES, ZNF146_TARGET_GENES, ZNF30_TARGET_GENES, ZNF331_TARGET_GENES

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

GO Molecular Function (4): DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700), zinc ion binding (GO:0008270), 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
transcription cis-regulatory region binding	1
regulation of DNA-templated transcription	1
transcription regulator activity	1
transition metal ion binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

316 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF233	OR6S1	Q8NH40	599
ZNF233	DEPDC4	Q8N2C3	507
ZNF233	ARGFX	A6NJG6	375
ZNF233	GAGE2A	Q6NT46	367
ZNF233	GIGYF1	O75420	366
ZNF233	DENND4A	Q7Z401	329
ZNF233	UBXN11	Q5T124	322
ZNF233	PCYT1B	Q9Y5K3	322
ZNF233	TRMT2A	Q8IZ69	321
ZNF233	CDC42EP4	Q9H3Q1	311
ZNF233	DPEP2	Q9H4A9	311
ZNF233	ANO7	Q6IWH7	308
ZNF233	ELAPOR1	Q6UXG2	308
ZNF233	DCAF15	Q66K64	297
ZNF233	ART3	Q13508	293

IntAct

5 interactions, top by confidence:

A	B	Type	Score
CACNA1A	ZNF233	psi-mi:“MI:0915”(physical association)	0.370
PB2	SEC15L3	psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350
ZNF233	SCHIP1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (4): ZNF233 (Affinity Capture-MS), ZNF233 (Proximity Label-MS), ZNF233 (Affinity Capture-RNA), ZNF233 (Two-hybrid)

ESM2 similar proteins: A0JPL0, A6NK53, E7ETH6, E9Q8G5, O14628, P21506, P51508, Q09FC8, Q13360, Q2M218, Q2M3X9, Q2VY69, Q3KQV3, Q3SY52, Q4R882, Q5HY98, Q5REN4, Q5RES8, Q68DI1, Q6NX49, Q6P280, Q6PG37, Q6V9R5, Q6ZMW2, Q7Z340, Q86XU0, Q8IYI8, Q8N587, Q8N720, Q8N859, Q8NB42, Q8NDW4, Q8NEK5, Q8WXB4, Q96MR9, Q96MU6, Q96NG8, Q96NJ3, Q96SR6, Q9BR84

Diamond homologs: A0A1W2PQL4, A0JNB1, A0JPL0, A6NK53, A6QLU5, A6QPT6, A7MBI1, A8MT65, A8MUV8, A8MWA4, B2RXC5, B4DU55, B4DX44, E9PYI1, O14628, O75346, P0CH99, P0CI00, P17014, P17030, P17032, P17098, P51786, P85977, Q02386, Q06730, Q06732, Q0VAW7, Q12901, Q13360, Q14586, Q14588, Q14590, Q16587, Q2M3X9, Q2VY69, Q32M78, Q3ZCX4, Q49AA0, Q4R6J4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	79
Likely benign	6
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

775 predictions. Top by Δscore:

Variant	Effect	Δscore
19:44260029:G:GT	donor_gain	1.0000
19:44264312:A:AG	acceptor_gain	1.0000
19:44264313:G:GG	acceptor_gain	1.0000
19:44264313:GT:G	acceptor_gain	1.0000
19:44264313:GTT:G	acceptor_gain	1.0000
19:44264313:GTTC:G	acceptor_gain	1.0000
19:44264313:GTTCT:G	acceptor_gain	1.0000
19:44264375:GGT:G	donor_loss	1.0000
19:44264376:G:GG	donor_gain	1.0000
19:44266320:AGTGG:A	donor_loss	1.0000
19:44266321:GTGG:G	donor_gain	1.0000
19:44266323:GG:G	donor_gain	1.0000
19:44266324:GG:G	donor_gain	1.0000
19:44266324:GGTGA:G	donor_loss	1.0000
19:44266325:G:GG	donor_gain	1.0000
19:44266325:G:T	donor_loss	1.0000
19:44266862:ACAG:A	acceptor_gain	1.0000
19:44266863:C:G	acceptor_gain	1.0000
19:44266864:A:AG	acceptor_gain	1.0000
19:44266864:A:T	acceptor_loss	1.0000
19:44266864:AG:A	acceptor_gain	1.0000
19:44266865:G:GT	acceptor_gain	1.0000
19:44266865:GG:G	acceptor_gain	1.0000
19:44266865:GGC:G	acceptor_gain	1.0000
19:44266865:GGCT:G	acceptor_gain	1.0000
19:44266865:GGCTA:G	acceptor_gain	1.0000
19:44266958:TCAG:T	donor_loss	1.0000
19:44266959:CAG:C	donor_loss	1.0000
19:44266960:AGG:A	donor_loss	1.0000
19:44266961:GG:G	donor_loss	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000449764 (19:44261267 C>T), RS1000555991 (19:44262879 C>A,T), RS1000666203 (19:44267118 A>G), RS1000734311 (19:44271753 A>C,G,T), RS1000946777 (19:44265880 T>C), RS1001050601 (19:44259824 G>C), RS1001160867 (19:44261519 G>C), RS1001405718 (19:44259577 C>T), RS1001507574 (19:44268347 T>G), RS1001599213 (19:44268611 T>C), RS1001877895 (19:44274168 C>T), RS1002071732 (19:44262515 G>T), RS1002102375 (19:44267746 T>C), RS1002326042 (19:44261800 C>T), RS1002773355 (19:44270115 T>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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression	4
aristolochic acid I	increases expression	1
bisphenol A	decreases expression	1
titanium dioxide	decreases expression, increases methylation	1
S-(1,2-dichlorovinyl)cysteine	increases expression	1
entinostat	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
Temozolomide	decreases expression	1
Sunitinib	decreases expression	1
Vorinostat	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Lead	increases expression	1
Methotrexate	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Zinc Sulfate	increases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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