ZNF213

Summary

ZNF213 (zinc finger protein 213, HGNC:13005) is a protein-coding gene on chromosome 16p13.3, encoding Zinc finger protein 213 (O14771). May be involved in transcriptional regulation.

C2H2 zinc finger proteins, such as ZNF213, have bipartite structures in which one domain binds DNA or RNA and the other modulates target gene expression.

Source: NCBI Gene 7760 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 97 total
• MANE Select transcript: NM_004220

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13005
Approved symbol	ZNF213
Name	zinc finger protein 213
Location	16p13.3
Locus type	gene with protein product
Status	Approved
Aliases	CR53, ZKSCAN21, ZSCAN53
Ensembl gene	ENSG00000085644
Ensembl biotype	protein_coding
OMIM	608387
Entrez	7760

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 6 protein_coding, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000396878, ENST00000572647, ENST00000573771, ENST00000574575, ENST00000574902, ENST00000574928, ENST00000576416, ENST00000576863

RefSeq mRNA: 2 — MANE Select: NM_004220 NM_001134655, NM_004220

CCDS: CCDS10495

Canonical transcript exons

ENST00000396878 — 6 exons

Exon	Start	End
ENSE00001778499	3135029	3135387
ENSE00002203200	3137166	3137679
ENSE00002673948	3140689	3142804
ENSE00003572651	3138745	3138818
ENSE00003646385	3138975	3139098
ENSE00003750197	3138418	3138541

Expression profiles

Bgee: expression breadth ubiquitous, 251 present calls, max score 96.46.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.0502 / max 41.6971, expressed in 1663 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
152400	2.0723	1306
152397	1.1340	643
152398	0.7539	477
152399	0.0900	23

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	96.46	gold quality
cardiac muscle of right atrium	UBERON:0003379	94.07	silver quality
left ventricle myocardium	UBERON:0006566	93.20	silver quality
parotid gland	UBERON:0001831	91.48	gold quality
myocardium	UBERON:0002349	90.59	silver quality
kidney epithelium	UBERON:0004819	90.02	silver quality
tendon of biceps brachii	UBERON:0008188	89.95	gold quality
right testis	UBERON:0004534	87.69	gold quality
cerebellar vermis	UBERON:0004720	87.58	gold quality
left testis	UBERON:0004533	87.45	gold quality
endothelial cell	CL:0000115	87.31	silver quality
nasal cavity epithelium	UBERON:0005384	86.75	silver quality
upper arm skin	UBERON:0004263	86.51	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	86.26	silver quality
ileal mucosa	UBERON:0000331	86.25	gold quality
lateral globus pallidus	UBERON:0002476	86.06	gold quality
testis	UBERON:0000473	86.00	gold quality
quadriceps femoris	UBERON:0001377	85.68	silver quality
vastus lateralis	UBERON:0001379	85.07	silver quality
gingival epithelium	UBERON:0001949	85.04	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.93	gold quality
lower lobe of lung	UBERON:0008949	84.85	gold quality
epithelial cell of pancreas	CL:0000083	84.49	gold quality
gingiva	UBERON:0001828	84.40	gold quality
substantia nigra pars reticulata	UBERON:0001966	84.01	gold quality
entorhinal cortex	UBERON:0002728	83.92	gold quality
lateral nuclear group of thalamus	UBERON:0002736	83.63	gold quality
gastrocnemius	UBERON:0001388	83.36	gold quality
cortical plate	UBERON:0005343	83.23	gold quality
superficial temporal artery	UBERON:0001614	83.17	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-MTAB-4850	no	4.44
E-ANND-3	no	2.92

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA2121.1	ZNF213	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:27852650

miRNA regulators (miRDB)

67 targeting ZNF213, 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-4481	100.00	66.42	1669
HSA-MIR-3134	100.00	66.43	777
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-371A-3P	99.99	66.77	91
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-4745-5P	99.98	65.95	1028
HSA-MIR-512-3P	99.97	67.35	1049
HSA-MIR-8075	99.97	67.20	962
HSA-MIR-4487	99.96	64.58	1252
HSA-MIR-8082	99.95	67.27	1170
HSA-MIR-6753-3P	99.93	66.57	637
HSA-MIR-7107-3P	99.93	66.73	627
HSA-MIR-4671-3P	99.88	72.46	1045
HSA-MIR-3151-5P	99.86	63.83	1069
HSA-MIR-10395-5P	99.86	67.35	676
HSA-MIR-520F-3P	99.82	71.32	1216
HSA-MIR-3934-3P	99.76	65.51	1351
HSA-MIR-6794-5P	99.76	66.38	1048
HSA-MIR-6752-3P	99.72	66.71	1587
HSA-MIR-1825	99.72	68.11	1089
HSA-MIR-1296-3P	99.72	64.04	636
HSA-MIR-4716-3P	99.69	66.73	1022
HSA-MIR-3202	99.66	67.70	2737
HSA-MIR-6848-3P	99.64	66.49	885
HSA-MIR-9851-3P	99.63	69.68	1110
HSA-MIR-6132	99.60	65.83	1554
HSA-MIR-6836-5P	99.60	65.62	1538
HSA-MIR-6081	99.48	66.07	1446

Literature-anchored findings (GeneRIF, showing 1)

• ZNF213 negatively controls triple negative breast cancer progression via Hippo/YAP signaling. (PMID:33939216)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp213	ENSMUSG00000071256
rattus_norvegicus	Zfp213	ENSRNOG00000021872

Paralogs (30): ZNF263 (ENSG00000006194), ZNF500 (ENSG00000103199), ZKSCAN1 (ENSG00000106261), ZNF205 (ENSG00000122386), ZSCAN9 (ENSG00000137185), PGBD1 (ENSG00000137338), ZNF215 (ENSG00000149054), ZSCAN12 (ENSG00000158691), ZNF394 (ENSG00000160908), ZNF75A (ENSG00000162086), ZSCAN21 (ENSG00000166529), ZNF232 (ENSG00000167840), ZNF24 (ENSG00000172466), ZNF449 (ENSG00000173275), ZSCAN4 (ENSG00000180532), ZSCAN22 (ENSG00000182318), ZNF75D (ENSG00000186376), ZNF396 (ENSG00000186496), ZNF397 (ENSG00000186812), ZSCAN30 (ENSG00000186814), ZKSCAN4 (ENSG00000187626), ZSCAN23 (ENSG00000187987), ZKSCAN3 (ENSG00000189298), ZSCAN16 (ENSG00000196812), ZSCAN25 (ENSG00000197037), ZSCAN26 (ENSG00000197062), ZNF165 (ENSG00000197279), ZKSCAN8 (ENSG00000198315), ZSCAN31 (ENSG00000235109), ZNF853 (ENSG00000236609)

Protein

Protein identifiers

Zinc finger protein 213 — O14771 (reviewed: O14771)

Alternative names: Putative transcription factor CR53, Zinc finger protein with KRAB and SCAN domains 21

All UniProt accessions (6): O14771, A0A0S2Z4L6, I3L1Z4, I3L216, I3L2V8, I3L473

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

Tissue specificity. Widely expressed with highest levels in testis.

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

Isoforms (2)

UniProt ID	Names	Canonical?
O14771-1	1	yes
O14771-2	2

RefSeq proteins (2): NP_001128127, NP_004211* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001909	KRAB	Domain
IPR003309	SCAN_dom	Domain
IPR013087	Znf_C2H2_type	Domain
IPR036051	KRAB_dom_sf	Homologous_superfamily
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR038269	SCAN_sf	Homologous_superfamily
IPR050717	C2H2-ZF_Transcription_Reg	Family

Pfam: PF00096, PF01352, PF02023, PF13465

UniProt features (12 total): zinc finger region 5, domain 2, splice variant 2, chain 1, sequence conflict 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O14771-F1	66.13	0.28

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 77 (showing top): GTGCCTT_MIR506, IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR, SANSOM_APC_MYC_TARGETS, SANSOM_APC_TARGETS_REQUIRE_MYC, NIKOLSKY_BREAST_CANCER_16P13_AMPLICON, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, KATSANOU_ELAVL1_TARGETS_DN, AKT_UP.V1_DN, MTOR_UP.V1_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, CBX7_TARGET_GENES, CEBPZ_TARGET_GENES, DLX4_TARGET_GENES, E2F2_TARGET_GENES, FEV_TARGET_GENES

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

GO Molecular Function (6): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), zinc ion binding (GO:0008270), DNA binding (GO:0003677), 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
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
regulation of transcription by RNA polymerase II	1
transition metal ion binding	1
nucleic acid binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

492 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF213	OR1F1	O43749	447
ZNF213	PSPC1	Q8WXF1	441
ZNF213	NONO	P30807	432
ZNF213	THUMPD3	Q9BV44	431
ZNF213	TIGD7	Q6NT04	419
ZNF213	SFPQ	P23246	396
ZNF213	GABPA	Q06546	395
ZNF213	PAGR1	Q9BTK6	379
ZNF213	PKIB	Q9C010	352
ZNF213	TRNAU1AP	Q9NX07	337
ZNF213	RNF187	Q5TA31	325
ZNF213	RNF181	Q9P0P0	321
ZNF213	GDE1	Q9NZC3	319
ZNF213	PDZK1	Q5T2W1	309
ZNF213	RNF31	Q96EP0	301

IntAct

44 interactions, top by confidence:

A	B	Type	Score
ZNF213	ZSCAN21	psi-mi:“MI:0915”(physical association)	0.670
ZNF213	SCAND1	psi-mi:“MI:0915”(physical association)	0.670
ZNF397	ZNF213	psi-mi:“MI:0914”(association)	0.640
ZNF213	LNX1	psi-mi:“MI:0915”(physical association)	0.560
ZNF213	FBXO17	psi-mi:“MI:0915”(physical association)	0.560
ZNF213	EEF2KMT	psi-mi:“MI:0915”(physical association)	0.560
ZNF213	LMO4	psi-mi:“MI:0915”(physical association)	0.560
ZNF213	PPL	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN32	ZNF197	psi-mi:“MI:0914”(association)	0.530
ZNF397	ZNF197	psi-mi:“MI:0914”(association)	0.530
ZKSCAN4	ZNF213	psi-mi:“MI:0914”(association)	0.530
PGBD1	ZNF213	psi-mi:“MI:0914”(association)	0.530
ZNF213	ZNF24	psi-mi:“MI:0914”(association)	0.530
ZNF213	CFTR	psi-mi:“MI:0915”(physical association)	0.370
ZSCAN20	ZNF197	psi-mi:“MI:0914”(association)	0.350
ZNF232	ZNF197	psi-mi:“MI:0914”(association)	0.350
ZSCAN1	ZNF213	psi-mi:“MI:0914”(association)	0.350
ZNF213	DDX3X	psi-mi:“MI:0914”(association)	0.350
ZKSCAN8	ZNF320	psi-mi:“MI:0914”(association)	0.350
MZF1	ZNF213	psi-mi:“MI:0914”(association)	0.350
ZNF213	BMP1	psi-mi:“MI:0914”(association)	0.350
TGIF2	ZNF213	psi-mi:“MI:0914”(association)	0.350
LNX1	ZNF213	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (42): ZNF213 (Affinity Capture-MS), ZNF213 (Affinity Capture-MS), ZNF213 (Affinity Capture-MS), ZNF213 (Affinity Capture-MS), ZNF213 (Affinity Capture-MS), ZNF213 (Affinity Capture-MS), ZNF213 (Affinity Capture-MS), ZNF213 (Affinity Capture-MS), ZNF213 (Affinity Capture-MS), ZNF213 (Affinity Capture-MS), ZNF213 (Affinity Capture-MS), ZNF213 (Two-hybrid), EEF2KMT (Two-hybrid), PPL (Two-hybrid), LMO4 (Two-hybrid)

ESM2 similar proteins: A0A087WVF3, A0A087WXS9, A0A087X179, A0A087X1G2, A6NDS4, A6NER0, A6QPT6, B9A6J9, M3WHG5, O14771, O15482, O15553, O19110, O76081, P0C7X1, P0C7X3, P0C7X4, P35125, P48778, P48967, P79209, Q13670, Q15697, Q2TBC4, Q3T191, Q3UZD7, Q4R2Z8, Q5DRQ5, Q5SSQ6, Q5XFX8, Q69ZB3, Q6DHY5, Q6IPX1, Q6ZMN8, Q8BLR5, Q8BWA8, Q8IYF1, Q8IZP1, Q8JZW5, Q8N7G0

Diamond homologs: A1YEP8, A1YEQ3, A1YEV9, A1YFW2, A1YFW6, A1YG26, A1YG48, A1YG60, A1YGJ4, A1YGK6, A2T6E3, A2T6V8, A2T6W2, A2T712, A2T736, A2T7D2, A2T7D7, A2T7F2, A2T7F4, A2T7L7, A2T812, A6QNZ0, A6QPT6, B2KFW1, O14709, O14771, O14978, O15535, O43309, O60304, O95125, P10073, P17022, P17028, P17029, P17040, P28698, P49910, P51815, P59923

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	72
Likely benign	10
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1300 predictions. Top by Δscore:

Variant	Effect	Δscore
16:3135059:G:GT	donor_gain	1.0000
16:3137676:ACAGG:A	donor_loss	1.0000
16:3137678:AGGT:A	donor_loss	1.0000
16:3137680:G:GC	donor_loss	1.0000
16:3137681:T:G	donor_loss	1.0000
16:3138412:GCACA:G	acceptor_loss	1.0000
16:3138413:CACA:C	acceptor_loss	1.0000
16:3138414:ACAG:A	acceptor_gain	1.0000
16:3138415:CA:C	acceptor_loss	1.0000
16:3138416:A:AG	acceptor_gain	1.0000
16:3138416:AG:A	acceptor_gain	1.0000
16:3138417:G:GC	acceptor_loss	1.0000
16:3138417:G:GG	acceptor_gain	1.0000
16:3138417:GG:G	acceptor_gain	1.0000
16:3138417:GGAT:G	acceptor_gain	1.0000
16:3138537:TAGCG:T	donor_gain	1.0000
16:3138538:AGCG:A	donor_gain	1.0000
16:3138539:GCG:G	donor_gain	1.0000
16:3138539:GCGG:G	donor_gain	1.0000
16:3138540:CG:C	donor_gain	1.0000
16:3138540:CGGTG:C	donor_loss	1.0000
16:3138541:GG:G	donor_gain	1.0000
16:3138541:GGT:G	donor_loss	1.0000
16:3138542:G:GA	donor_loss	1.0000
16:3138542:G:GG	donor_gain	1.0000
16:3138546:G:GG	donor_gain	1.0000
16:3138743:A:AG	acceptor_gain	1.0000
16:3138744:G:GG	acceptor_gain	1.0000
16:3138744:GCCC:G	acceptor_gain	1.0000
16:3138744:GCCCA:G	acceptor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000267260 (16:3139962 C>T), RS1000445393 (16:3133235 G>C,T), RS1000476568 (16:3133054 G>A), RS1000486670 (16:3134851 C>T), RS1000570780 (16:3134575 T>C), RS1000773259 (16:3143024 C>T), RS1001381950 (16:3140600 G>A,T), RS1001605999 (16:3142989 C>T), RS1001663519 (16:3135138 G>C), RS1001733177 (16:3134889 A>G), RS1001945149 (16:3136475 T>C), RS1002958448 (16:3136310 T>C), RS1003151959 (16:3141792 C>G), RS1003281531 (16:3142083 G>GC), RS1003384265 (16:3142725 G>A,T)

Disease associations

OMIM: gene MIM:608387 | 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
GCST002119_1	Metabolite levels (X-11787)	9.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0005276	hydroxy-leucine measurement

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
sodium arsenite	increases expression	2
aristolochic acid I	increases expression	1
GSK-J4	decreases expression	1
dicrotophos	increases expression	1
ferrous chloride	decreases expression	1
4-aminophenylarsenoxide	affects binding, decreases reaction	1
di-n-butylphosphoric acid	affects expression	1
2-palmitoylglycerol	increases expression	1
ICG 001	increases expression	1
abrine	increases expression	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Arsenic Trioxide	affects binding, decreases reaction	1
Acetaminophen	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	increases methylation	1
Tobacco Smoke Pollution	increases expression	1
Urethane	increases expression	1
Particulate Matter	increases abundance, increases 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_XW19	HEK293 eGFP-ZNF213	Transformed cell line	Female

Clinical trials (associated diseases)

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