ZNF33A

Summary

ZNF33A (zinc finger protein 33A, HGNC:13096) is a protein-coding gene on chromosome 10p11.1, encoding Zinc finger protein 33A (Q06730). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus.

Source: NCBI Gene 7581 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 128 total
• MANE Select transcript: NM_006954

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13096
Approved symbol	ZNF33A
Name	zinc finger protein 33A
Location	10p11.1
Locus type	gene with protein product
Status	Approved
Aliases	KOX5, KOX31, KIAA0065, FLJ23404, ZZAPK
Ensembl gene	ENSG00000189180
Ensembl biotype	protein_coding
OMIM	194521
Entrez	7581

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 12 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000307441, ENST00000374618, ENST00000432900, ENST00000458705, ENST00000469037, ENST00000476504, ENST00000478556, ENST00000628825, ENST00000867607, ENST00000867608, ENST00000867609, ENST00000921346, ENST00000921347, ENST00000921348

RefSeq mRNA: 15 — MANE Select: NM_006954 NM_001278170, NM_001278171, NM_001278173, NM_001278174, NM_001278175, NM_001278176, NM_001278177, NM_001278178, NM_001278179, NM_001324175, NM_001324176, NM_001324177, NM_001324178, NM_006954, NM_006974

CCDS: CCDS31182, CCDS44372, CCDS60514, CCDS73088, CCDS73089

Canonical transcript exons

ENST00000432900 — 5 exons

Exon	Start	End
ENSE00001775936	38054375	38060087
ENSE00002289974	38010675	38010783
ENSE00003500666	38016871	38017015
ENSE00003553199	38012298	38012350
ENSE00003670816	38017291	38017386

Expression profiles

Bgee: expression breadth ubiquitous, 257 present calls, max score 94.65.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.1133 / max 585.7370, expressed in 1778 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
104719	16.3102	1770
104717	0.3716	58
104720	0.2769	111
104718	0.1546	60

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cerebellar vermis	UBERON:0004720	94.65	gold quality
upper arm skin	UBERON:0004263	94.13	gold quality
tendon of biceps brachii	UBERON:0008188	94.05	gold quality
cortical plate	UBERON:0005343	93.29	gold quality
palpebral conjunctiva	UBERON:0001812	92.93	gold quality
thymus	UBERON:0002370	92.80	gold quality
sural nerve	UBERON:0015488	92.79	gold quality
tendon	UBERON:0000043	92.45	gold quality
epithelium of nasopharynx	UBERON:0001951	92.19	gold quality
nasopharynx	UBERON:0001728	92.17	gold quality
urethra	UBERON:0000057	91.70	gold quality
endothelial cell	CL:0000115	91.52	gold quality
eye	UBERON:0000970	91.51	gold quality
medial globus pallidus	UBERON:0002477	91.46	gold quality
embryo	UBERON:0000922	91.41	gold quality
ganglionic eminence	UBERON:0004023	91.41	gold quality
renal medulla	UBERON:0000362	91.36	gold quality
calcaneal tendon	UBERON:0003701	91.23	gold quality
layer of synovial tissue	UBERON:0007616	91.21	gold quality
tibia	UBERON:0000979	91.17	gold quality
oviduct epithelium	UBERON:0004804	91.16	gold quality
superior surface of tongue	UBERON:0007371	91.08	gold quality
parotid gland	UBERON:0001831	91.04	gold quality
bone marrow cell	CL:0002092	90.88	gold quality
kidney epithelium	UBERON:0004819	90.85	gold quality
mucosa of paranasal sinus	UBERON:0005030	90.84	gold quality
amniotic fluid	UBERON:0000173	90.52	gold quality
globus pallidus	UBERON:0001875	90.46	gold quality
epithelial cell of pancreas	CL:0000083	90.41	silver quality
bronchial epithelial cell	CL:0002328	90.20	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.41

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

131 targeting ZNF33A, 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-8485	100.00	77.57	4731
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-101-3P	99.94	75.03	2230
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
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-10527-5P	99.91	72.28	3754
HSA-MIR-3686	99.90	70.53	2432
HSA-MIR-153-5P	99.89	73.86	6317

Literature-anchored findings (GeneRIF, showing 3)

• Results suggest that ZAK might play a role as an upstream signal to suppress the ZZaPK function and decrease E2F expression. (PMID:12535642)
• Genome-wide copy number variation-, validation- and screening study implicates a new copy number polymorphism associated with suicide attempts in major depressive disorder. (PMID:32554045)
• ZNF711 puts a spell on DNA. (PMID:35132177)

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), 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 33A — Q06730 (reviewed: Q06730)

Alternative names: Zinc finger and ZAK-associated protein with KRAB domain, Zinc finger protein 11A, Zinc finger protein KOX31

All UniProt accessions (4): A0A0A0MR11, A0A0A0MRS1, Q06730, Q9H5I4

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subunit / interactions. Interacts with MAP3K20/ZAK.

Subcellular location. Nucleus.

Similarity. Belongs to the krueppel C2H2-type zinc-finger protein family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q06730-1	1	yes
Q06730-2	2
Q06730-3	3

RefSeq proteins (15): NP_001265099, NP_001265100, NP_001265102, NP_001265103, NP_001265104, NP_001265105, NP_001265106, NP_001265107, NP_001265108, NP_001311104, NP_001311105, NP_001311106, NP_001311107, NP_008885, NP_008905 (=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 (35 total): zinc finger region 16, cross-link 8, sequence conflict 4, 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-Q06730-F1	63.52	0.08

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (8): 180, 237, 312, 456, 676, 732, 72, 92

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway
R-HSA-9843940	Regulation of endogenous retroelements by KRAB-ZFP proteins

MSigDB gene sets: 51 (showing top): NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN, WANG_CISPLATIN_RESPONSE_AND_XPC_DN, chr10p11, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOBP_NEGATIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, ZWANG_DOWN_BY_2ND_EGF_PULSE, CSR_EARLY_UP.V1_DN, REACTOME_EPIGENETIC_REGULATION_OF_GENE_EXPRESSION, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ARNT2_TARGET_GENES, HOXA7_TARGET_GENES, TEAD2_TARGET_GENES, ZFHX3_TARGET_GENES, MIR153_5P

GO Biological Process (4): regulation of DNA-templated transcription (GO:0006355), regulation of transcription by RNA polymerase II (GO:0006357), regulation of macromolecule metabolic process (GO:0060255), regulation of primary metabolic process (GO:0080090)

GO Molecular Function (5): DNA-binding transcription factor activity (GO:0003700), zinc ion binding (GO:0008270), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), metal ion binding (GO:0046872)

GO Cellular Component (1): nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
RNA Polymerase II Transcription	1
Regulation of endogenous retroelements	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of DNA-templated transcription	2
regulation of metabolic process	2
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
transcription by RNA polymerase II	1
macromolecule metabolic process	1
primary metabolic process	1
transcription cis-regulatory region binding	1
transcription regulator activity	1
transition metal ion binding	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
nucleic acid binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

11 interactions, top by confidence:

A	B	Type	Score
CBX6	IGF2BP3	psi-mi:“MI:0914”(association)	0.530
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.530
Kif1c	ABLIM1	psi-mi:“MI:0914”(association)	0.350
Edc4	C4BPA	psi-mi:“MI:0914”(association)	0.350
VPS50	PHF20L1	psi-mi:“MI:0914”(association)	0.350
SLC9A8	AP1G1	psi-mi:“MI:0914”(association)	0.350
CDK11A	PRPF40A	psi-mi:“MI:0914”(association)	0.350
FMR1	ZNF33A	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (16): ZNF33A (Affinity Capture-MS), ZNF33A (Affinity Capture-MS), ZNF33A (Affinity Capture-MS), ZNF33A (Affinity Capture-MS), ZNF33A (Affinity Capture-RNA), ZAK (Affinity Capture-Western), ZNF33A (Two-hybrid), ZNF33A (Proximity Label-MS), ZNF33A (Affinity Capture-MS), ZNF33A (Affinity Capture-MS), ZNF33A (Affinity Capture-MS), ZNF33A (Affinity Capture-MS), ZNF33A (Affinity Capture-RNA), ZNF33A (Proximity Label-MS), ZNF33A (Affinity Capture-MS)

ESM2 similar proteins: A0JPL0, A3KN36, A7MBI1, A8MT65, B2RXC5, D3ZVT0, P08042, P21506, P51508, P52738, Q02525, Q06730, Q12901, Q2KI58, Q2M218, Q2M3W8, Q2M3X9, Q2VY69, Q49AA0, Q4R6J4, Q4V8A8, Q5FWF6, Q5HY98, Q5RB33, Q5RC79, Q5REF1, Q5T5D7, Q5VIY5, Q61967, Q6P2D0, Q6ZN11, Q86XU0, Q86Y25, Q8N782, Q8N859, Q8NB42, Q8TF39, Q8TF47, Q8WXB4, Q95K49

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	115
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1316 predictions. Top by Δscore:

Variant	Effect	Δscore
10:38010776:G:GT	donor_gain	1.0000
10:38010779:GTGGG:G	donor_gain	1.0000
10:38010781:GGG:G	donor_gain	1.0000
10:38010782:GG:G	donor_gain	1.0000
10:38010782:GGG:G	donor_gain	1.0000
10:38010783:GG:G	donor_gain	1.0000
10:38010783:GGTAA:G	donor_loss	1.0000
10:38010784:G:GA	donor_loss	1.0000
10:38010784:G:GG	donor_gain	1.0000
10:38012291:A:AG	acceptor_gain	1.0000
10:38016510:T:G	donor_gain	1.0000
10:38017012:GTGG:G	donor_gain	1.0000
10:38017384:CAGGT:C	donor_loss	1.0000
10:38017385:AGGT:A	donor_loss	1.0000
10:38017386:GGT:G	donor_loss	1.0000
10:38017387:G:C	donor_loss	1.0000
10:38010780:TGGG:T	donor_gain	0.9900
10:38010781:GGGG:G	donor_gain	0.9900
10:38012292:A:G	acceptor_gain	0.9900
10:38012297:GCT:G	acceptor_gain	0.9900
10:38012349:AGGTA:A	donor_loss	0.9900
10:38012350:GGT:G	donor_loss	0.9900
10:38012351:G:GG	donor_gain	0.9900
10:38012351:GTAA:G	donor_loss	0.9900
10:38012352:T:A	donor_loss	0.9900
10:38016466:A:AG	donor_gain	0.9900
10:38016867:TCA:T	acceptor_loss	0.9900
10:38016869:A:AG	acceptor_gain	0.9900
10:38016869:AGGT:A	acceptor_loss	0.9900
10:38016870:G:GA	acceptor_loss	0.9900

AlphaMissense

5463 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:38056060:T:C	F645L	0.995
10:38056062:C:A	F645L	0.995
10:38056062:C:G	F645L	0.995
10:38055304:T:C	F393L	0.994
10:38055306:T:A	F393L	0.994
10:38055306:T:G	F393L	0.994
10:38055724:T:C	F533L	0.993
10:38055726:C:A	F533L	0.993
10:38055726:C:G	F533L	0.993
10:38055743:T:C	L539P	0.993
10:38055781:T:C	F552L	0.993
10:38055783:T:A	F552L	0.993
10:38055783:T:G	F552L	0.993
10:38055407:T:C	L427P	0.992
10:38055472:T:C	F449L	0.992
10:38055474:C:A	F449L	0.992
10:38055474:C:G	F449L	0.992
10:38055808:T:C	F561L	0.992
10:38055810:T:A	F561L	0.992
10:38055810:T:G	F561L	0.992
10:38055911:T:C	L595P	0.991
10:38056079:T:C	L651P	0.991
10:38055220:T:C	F365L	0.990
10:38055222:C:A	F365L	0.990
10:38055222:C:G	F365L	0.990
10:38055388:T:C	F421L	0.990
10:38055390:T:A	F421L	0.990
10:38055390:T:G	F421L	0.990
10:38055556:T:C	F477L	0.990
10:38055558:T:A	F477L	0.990

dbSNP variants (sampled 300 via entrez): RS1000014677 (10:38058694 C>T), RS1000028254 (10:38064871 G>A), RS1000191058 (10:38038932 T>G), RS1000236182 (10:38042274 C>T), RS1000244450 (10:38042033 T>C), RS1000274780 (10:38024570 T>A), RS1000418288 (10:38036530 T>C), RS1000449802 (10:38058503 A>G), RS1000504802 (10:38014894 T>A,G), RS1000535412 (10:38053907 G>T), RS1000664207 (10:38048477 C>T), RS1000813848 (10:38065735 G>A,C), RS1000821851 (10:38010146 G>C), RS1000875271 (10:38036318 T>C), RS1000907808 (10:38026263 C>A,G,T)

Disease associations

OMIM: gene MIM:194521 | 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

30 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression	10
sodium arsenite	decreases expression	2
aristolochic acid I	decreases expression	1
bisphenol F	affects cotreatment, increases expression	1
TAK-243	increases sumoylation	1
bisphenol A	affects cotreatment, increases expression	1
2-methyl-4-isothiazolin-3-one	decreases expression	1
beta-lapachone	decreases expression	1
resorcinol	increases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
entinostat	decreases expression	1
K 7174	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
NSC 689534	affects binding, increases expression	1
Sunitinib	increases expression	1
Acetaminophen	decreases expression	1
Caffeine	increases phosphorylation	1
Copper	affects binding, increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Dimethyl Sulfoxide	increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Tetrachlorodibenzodioxin	affects expression	1
Urethane	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Aflatoxin B1	decreases expression	1
Okadaic Acid	decreases expression	1
Particulate Matter	increases expression	1

Clinical trials (associated diseases)

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