ZNF22

Summary

ZNF22 (zinc finger protein 22, HGNC:13012) is a protein-coding gene on chromosome 10q11.21, encoding Zinc finger protein 22 (P17026). Binds DNA through the consensus sequence 5’-CAATG-3'.

Predicted to enable DNA binding activity. Predicted to be involved in regulation of gene expression. Located in nucleoplasm.

Source: NCBI Gene 7570 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 28 total
• MANE Select transcript: NM_006963

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13012
Approved symbol	ZNF22
Name	zinc finger protein 22
Location	10q11.21
Locus type	gene with protein product
Status	Approved
Aliases	KOX15, HKR-T1, ZNF422, Zfp422
Ensembl gene	ENSG00000165512
Ensembl biotype	protein_coding
OMIM	194529
Entrez	7570

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000298299, ENST00000870780, ENST00000870781, ENST00000913002, ENST00000913003

RefSeq mRNA: 1 — MANE Select: NM_006963 NM_006963

CCDS: CCDS7211

Canonical transcript exons

ENST00000298299 — 2 exons

Exon	Start	End
ENSE00001093710	45000923	45000978
ENSE00001194399	45003280	45005326

Expression profiles

Bgee: expression breadth ubiquitous, 289 present calls, max score 96.67.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.0975 / max 168.1057, expressed in 1680 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
104782	14.3271	1668
104780	0.4038	199
104781	0.3050	121
104778	0.0378	15
104779	0.0237	7

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	96.67	gold quality
ganglionic eminence	UBERON:0004023	96.54	gold quality
embryo	UBERON:0000922	95.45	gold quality
secondary oocyte	CL:0000655	94.95	gold quality
islet of Langerhans	UBERON:0000006	93.35	gold quality
cortical plate	UBERON:0005343	93.31	gold quality
body of pancreas	UBERON:0001150	93.11	gold quality
oocyte	CL:0000023	93.10	gold quality
pancreas	UBERON:0001264	92.60	gold quality
endometrium	UBERON:0001295	92.22	gold quality
lymph node	UBERON:0000029	91.32	gold quality
calcaneal tendon	UBERON:0003701	91.12	gold quality
trabecular bone tissue	UBERON:0002483	90.44	gold quality
tibia	UBERON:0000979	90.22	gold quality
peritoneum	UBERON:0002358	90.00	gold quality
omental fat pad	UBERON:0010414	90.00	gold quality
pigmented layer of retina	UBERON:0001782	89.85	gold quality
adipose tissue of abdominal region	UBERON:0007808	89.85	gold quality
retina	UBERON:0000966	89.83	gold quality
medial globus pallidus	UBERON:0002477	89.69	gold quality
subcutaneous adipose tissue	UBERON:0002190	89.63	gold quality
rectum	UBERON:0001052	89.53	gold quality
placenta	UBERON:0001987	89.50	gold quality
thoracic mammary gland	UBERON:0005200	89.42	gold quality
mammary gland	UBERON:0001911	89.37	gold quality
adipose tissue	UBERON:0001013	89.26	gold quality
connective tissue	UBERON:0002384	89.24	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	89.23	gold quality
renal glomerulus	UBERON:0000074	88.98	gold quality
pleura	UBERON:0000977	88.90	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-HCAD-4	yes	47.33
E-CURD-112	yes	40.14
E-ANND-3	yes	9.40

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

107 targeting ZNF22, 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-340-5P	100.00	72.50	4437
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-381-3P	99.93	71.87	2854
HSA-MIR-300	99.92	71.76	2856
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-4503	99.85	71.45	1869
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-1323	99.83	69.89	2471
HSA-MIR-6875-3P	99.82	70.26	2983
HSA-MIR-548AZ-3P	99.82	70.56	3549

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:dkey-210j14.3	ENSDARG00000089883
danio_rerio	si:dkey-210j14.4	ENSDARG00000090871
danio_rerio	si:ch211-284e13.5	ENSDARG00000094725
danio_rerio	si:ch1073-224n8.1	ENSDARG00000104485
danio_rerio	znf16l	ENSDARG00000105532
mus_musculus	Zfp422	ENSMUSG00000059878
rattus_norvegicus	Zfp422	ENSRNOG00000013379

Paralogs (18): ZNF430 (ENSG00000118620), ZNF92 (ENSG00000146757), ZNF66 (ENSG00000160229), ZNF680 (ENSG00000173041), ZNF114 (ENSG00000178150), ZFP41 (ENSG00000181638), ZNF730 (ENSG00000183850), ZNF479 (ENSG00000185177), ZNF626 (ENSG00000188171), ZNF431 (ENSG00000196705), ZNF100 (ENSG00000197020), ZNF257 (ENSG00000197134), ZNF98 (ENSG00000197360), ZNF675 (ENSG00000197372), ZNF273 (ENSG00000198039), ZNF737 (ENSG00000237440), ZNF253 (ENSG00000256771), ZNF723 (ENSG00000268696)

Protein

Protein identifiers

Zinc finger protein 22 — P17026 (reviewed: P17026)

Alternative names: Zinc finger protein KOX15, Zinc finger protein Krox-26

All UniProt accessions (1): P17026

UniProt curated annotations — full annotation on UniProt →

Function. Binds DNA through the consensus sequence 5’-CAATG-3’. May be involved in transcriptional regulation and may play a role in tooth formation.

Subcellular location. Nucleus.

Tissue specificity. In the embryo, expressed in developing craniofacial structures including dental epithelium of maxillary molar tooth organs, tongue epithelium and muscle, and craniofacial bone osteoblasts. In the adult, expressed in mesoderm-derived tissues such as skeletal muscle, heart, kidney and liver. Intermediate expression in spleen, thymus and brain. Low levels in endoderm-derived tissues such as intestine and colon.

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

RefSeq proteins (1): NP_008894* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF00096

UniProt features (14 total): zinc finger region 5, modified residue 3, sequence variant 2, sequence conflict 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P17026-F1	71.70	0.45

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 (3): 18, 23, 49

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 170 (showing top): BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, TSENG_IRS1_TARGETS_UP, GRUETZMANN_PANCREATIC_CANCER_DN, KAAB_FAILED_HEART_ATRIUM_DN, TTTGTAG_MIR520D, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_UP, MITSIADES_RESPONSE_TO_APLIDIN_DN, HNF1_Q6, PUJANA_CHEK2_PCC_NETWORK, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX3, ONDER_CDH1_TARGETS_2_UP

GO Biological Process (3): regulation of DNA-templated transcription (GO:0006355), regulation of gene expression (GO:0010468), odontogenesis (GO:0042476)

GO Molecular Function (5): DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700), zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (2): nucleus (GO:0005634), nucleoplasm (GO:0005654)

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
gene expression	1
regulation of macromolecule biosynthetic process	1
animal organ morphogenesis	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
binding	1
cation binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1

Protein interactions and networks

STRING

672 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF22	LPCAT2	Q7L5N7	533
ZNF22	FAM43A	Q8N2R8	441
ZNF22	SDHA	P31040	438
ZNF22	ZNF608	Q9ULD9	373
ZNF22	ZBTB21	Q9ULJ3	373
ZNF22	ZZZ3	Q8IYH5	365
ZNF22	UQCC5	Q8WVI0	361
ZNF22	NGRN	Q9NPE2	356
ZNF22	CMTR2	Q8IYT2	335
ZNF22	SFT2D3	Q587I9	323
ZNF22	SZRD1	Q7Z422	307
ZNF22	ZNF532	Q9HCE3	301
ZNF22	RUNX1T1	Q06455	298
ZNF22	MEOX2	P50222	290
ZNF22	MIER2	Q8N344	290

IntAct

87 interactions, top by confidence:

A	B	Type	Score
H2AX	PPM1G	psi-mi:“MI:0914”(association)	0.730
RPL14	RRP8	psi-mi:“MI:0914”(association)	0.640
H1-1	RRP8	psi-mi:“MI:0914”(association)	0.640
NPM1	MPHOSPH10	psi-mi:“MI:0914”(association)	0.610
RPL28	MAGEB2	psi-mi:“MI:0914”(association)	0.560
RPL37A	MPHOSPH10	psi-mi:“MI:0914”(association)	0.530
ZNF2	MPHOSPH10	psi-mi:“MI:0914”(association)	0.530
RPL18	NOP56	psi-mi:“MI:0914”(association)	0.530
ZNF71	NVL	psi-mi:“MI:0914”(association)	0.530
N	NOP56	psi-mi:“MI:0914”(association)	0.530
MAGEB2	POLRMT	psi-mi:“MI:0914”(association)	0.530
MACROH2A2	PPM1G	psi-mi:“MI:0914”(association)	0.530
PPAN	PPM1G	psi-mi:“MI:0914”(association)	0.530
MAGEB2	GTPBP10	psi-mi:“MI:0914”(association)	0.530
ABT1	ZNF316	psi-mi:“MI:0914”(association)	0.530
RPL7A	NVL	psi-mi:“MI:0914”(association)	0.530
H1-1	SURF6	psi-mi:“MI:0914”(association)	0.530
RPL6	YBX3	psi-mi:“MI:0914”(association)	0.530
ZNF22	CFTR	psi-mi:“MI:0915”(physical association)	0.510
CFTR	ZNF22	psi-mi:“MI:0915”(physical association)	0.510
ZNF22	BDKRB1	psi-mi:“MI:0915”(physical association)	0.370
PPAN	IGF2BP3	psi-mi:“MI:0914”(association)	0.350
DGCR8	MPHOSPH10	psi-mi:“MI:0914”(association)	0.350
C6orf11	RRP8	psi-mi:“MI:0914”(association)	0.350
ZNF22	NPM1	psi-mi:“MI:0914”(association)	0.350
Pik3r2	EDIL3	psi-mi:“MI:0914”(association)	0.350

BioGRID (168): ZNF22 (Affinity Capture-MS), ZNF22 (Affinity Capture-MS), RPL26L1 (Affinity Capture-MS), SRRM1 (Affinity Capture-MS), ZNF808 (Affinity Capture-MS), ZNF624 (Affinity Capture-MS), DDX52 (Affinity Capture-MS), HIST1H1C (Affinity Capture-MS), RPS3A (Affinity Capture-MS), NPM1 (Affinity Capture-MS), RPL36AL (Affinity Capture-MS), MRPL27 (Affinity Capture-MS), MRPL9 (Affinity Capture-MS), MRPL30 (Affinity Capture-MS), MRPL20 (Affinity Capture-MS)

ESM2 similar proteins: A2RRD8, A6NHJ4, B4DU55, O60765, O75346, O88553, P15621, P17026, P17036, P17141, Q02975, Q0VGE8, Q13398, Q15928, Q1LZC0, Q2M3X9, Q3KNS6, Q3SY52, Q5HY98, Q5HYK9, Q5R4X5, Q61751, Q6GQR8, Q6J6I6, Q6JLC9, Q6P9A1, Q6PK81, Q6ZMS4, Q86WZ6, Q8IZ26, Q8N9F8, Q8N9Z0, Q8NCK3, Q8NEP9, Q8NHY6, Q8WV37, Q969W8, Q96H40, Q96HQ0, Q96K75

Diamond homologs: B1H2Q6, G5EGB2, O15535, O75290, P17026, P18724, P18741, P18747, P52742, Q15937, Q17895, Q1LZC0, Q3MJ62, Q4R7X8, Q5R4X5, Q6A085, Q7Z3I7, Q8BGV5, Q8TBZ5, Q91VW9, Q969J2, Q9BRR0, Q9ERU2, Q9ERU3, Q9UEG4, Q9Z1D9, Q9Z2K3, P18715, P18719, P18725, P18729, P18731, P18735, P18737, Q3TDE8, Q966L8, P17023, P18722, P18736, P18738

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 95 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Peptide chain elongation	15	34.0×	6e-18
Viral mRNA Translation	15	34.0×	6e-18
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA	15	33.6×	6e-18
Selenocysteine synthesis	15	32.2×	7e-18
Eukaryotic Translation Termination	15	32.2×	7e-18
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	15	31.5×	8e-18
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA	15	31.5×	8e-18
Formation of a pool of free 40S subunits	15	30.0×	2e-17

GO biological processes:

GO term	Partners	Fold	FDR
cytoplasmic translation	16	34.1×	5e-18
translation	16	18.9×	4e-14
ribosomal small subunit biogenesis	7	18.3×	9e-06
rRNA processing	10	16.3×	8e-08
nucleosome assembly	9	14.5×	1e-06
RNA processing	5	12.6×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	23
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

250 predictions. Top by Δscore:

Variant	Effect	Δscore
10:45003274:A:AG	acceptor_gain	1.0000
10:45003278:A:AG	acceptor_gain	1.0000
10:45003279:G:GG	acceptor_gain	1.0000
10:45003272:A:AG	acceptor_gain	0.9900
10:45003273:C:G	acceptor_gain	0.9900
10:45003275:C:G	acceptor_gain	0.9900
10:45003277:CA:C	acceptor_loss	0.9900
10:45003279:GA:G	acceptor_gain	0.9900
10:45003279:GAA:G	acceptor_gain	0.9900
10:45003279:GAAA:G	acceptor_gain	0.9900
10:45003279:GAAAA:G	acceptor_gain	0.9900
10:45000974:GCGCG:G	donor_gain	0.9800
10:45003277:C:G	acceptor_gain	0.9800
10:45003276:A:AG	acceptor_gain	0.9700
10:45000976:GCG:G	donor_gain	0.9600
10:45003064:A:AG	acceptor_gain	0.9600
10:45003367:CCATG:C	acceptor_gain	0.9600
10:45000623:A:AG	donor_gain	0.9500
10:45000980:T:A	donor_loss	0.9500
10:45000981:GA:G	donor_loss	0.9500
10:45000584:G:GT	donor_gain	0.9400
10:45000979:G:GG	donor_gain	0.9400
10:45000982:AG:A	donor_loss	0.9000
10:45003244:T:A	acceptor_gain	0.9000
10:45003370:TG:T	acceptor_gain	0.9000
10:45003371:G:GC	acceptor_gain	0.9000
10:45000961:G:GA	donor_gain	0.8900
10:45003256:A:G	acceptor_gain	0.8800
10:45001607:GA:G	donor_gain	0.8700
10:45000977:CG:C	donor_gain	0.8600

AlphaMissense

1503 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:45003810:T:C	F148L	0.997
10:45003812:C:A	F148L	0.997
10:45003812:C:G	F148L	0.997
10:45003894:T:C	F176L	0.997
10:45003896:C:A	F176L	0.997
10:45003896:C:G	F176L	0.997
10:45003726:T:C	F120L	0.996
10:45003728:C:A	F120L	0.996
10:45003728:C:G	F120L	0.996
10:45003829:T:C	L154P	0.996
10:45003676:G:C	R103P	0.995
10:45003745:T:C	L126P	0.995
10:45003558:T:C	F64L	0.993
10:45003560:C:A	F64L	0.993
10:45003560:C:G	F64L	0.993
10:45003757:A:C	Q130P	0.993
10:45003839:T:A	H157Q	0.993
10:45003839:T:G	H157Q	0.993
10:45003841:A:C	Q158P	0.993
10:45003913:T:C	L182P	0.992
10:45003837:C:G	H157D	0.991
10:45003851:C:A	H161Q	0.991
10:45003851:C:G	H161Q	0.991
10:45003671:T:A	H101Q	0.990
10:45003671:T:G	H101Q	0.990
10:45003673:G:C	R102P	0.990
10:45003661:T:C	L98P	0.989
10:45003783:T:G	Y139D	0.989
10:45003811:T:C	F148S	0.988
10:45003867:T:G	Y167D	0.988

dbSNP variants (sampled 300 via entrez): RS1000231261 (10:45002882 T>C), RS1000242437 (10:45000756 C>T), RS1000523991 (10:44999087 G>T), RS1000629693 (10:45003292 T>C), RS1000790005 (10:45005489 A>G), RS1001906686 (10:45002387 TGCA>T), RS1002437486 (10:45004381 T>G), RS1002573003 (10:45003134 T>C,G), RS1002878600 (10:45004135 T>A,C), RS1003179358 (10:45002730 T>A), RS1003290729 (10:45005611 A>G), RS1004072125 (10:45003829 T>G), RS1004364390 (10:45004433 G>A,C), RS1004666033 (10:45003187 G>T), RS1005079384 (10:45002346 C>T)

Disease associations

OMIM: gene MIM:194529 | 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

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, decreases methylation	4
trichostatin A	decreases expression, affects cotreatment	2
Tretinoin	decreases expression	2
Cadmium Chloride	decreases expression, increases abundance	2
Particulate Matter	decreases expression, increases abundance, affects cotreatment	2
aristolochic acid I	decreases expression	1
FR900359	decreases phosphorylation	1
triphenyl phosphate	affects expression	1
sodium arsenite	decreases expression	1
tobacco tar	decreases expression, decreases reaction	1
manganese chloride	increases abundance, increases expression	1
nickel sulfate	decreases expression	1
beta-methylcholine	affects expression	1
di-n-butylphosphoric acid	affects expression	1
perfluoro-n-nonanoic acid	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
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol S	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Decitabine	decreases reaction, decreases expression	1
Sunitinib	decreases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Ethanol	affects cotreatment, decreases expression, increases abundance	1
Benzo(a)pyrene	increases methylation	1
Cadmium	decreases expression, increases abundance	1
Cisplatin	decreases expression	1
Dimethyl Sulfoxide	increases expression	1
Doxorubicin	decreases expression	1
Estradiol	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

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