ZNF211

Summary

ZNF211 (zinc finger protein 211, HGNC:13003) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger protein 211 (Q13398). May be involved in transcriptional regulation.

This gene encodes a protein containing a Kruppel-associated box domain and multiple zinc finger domains. This protein may play a role in developmental processes. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 10520 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 75 total
• MANE Select transcript: NM_006385

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13003
Approved symbol	ZNF211
Name	zinc finger protein 211
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Aliases	ZNF-25, CH2H2-25
Ensembl gene	ENSG00000121417
Ensembl biotype	protein_coding
OMIM	601856
Entrez	10520

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 13 protein_coding, 3 retained_intron, 2 nonsense_mediated_decay

ENST00000240731, ENST00000254182, ENST00000299871, ENST00000347302, ENST00000391703, ENST00000407202, ENST00000535785, ENST00000540556, ENST00000540780, ENST00000541072, ENST00000541801, ENST00000542008, ENST00000859800, ENST00000859801, ENST00000948851, ENST00000948852, ENST00000948853, ENST00000948854

RefSeq mRNA: 7 — MANE Select: NM_006385 NM_001265597, NM_001265598, NM_001265599, NM_001265600, NM_001322306, NM_006385, NM_198855

CCDS: CCDS12956, CCDS12957, CCDS58686, CCDS58687, CCDS58688, CCDS74468

Canonical transcript exons

ENST00000240731 — 4 exons

Exon	Start	End
ENSE00002227809	57640704	57644041
ENSE00003477965	57633168	57633436
ENSE00003582318	57634023	57634061
ENSE00003669779	57634629	57634755

Expression profiles

Bgee: expression breadth ubiquitous, 235 present calls, max score 92.59.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.7225 / max 74.3740, expressed in 1684 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177786	6.1163	1647
177787	0.6062	347

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	92.59	gold quality
oocyte	CL:0000023	91.60	gold quality
apex of heart	UBERON:0002098	91.14	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.67	gold quality
right hemisphere of cerebellum	UBERON:0014890	88.27	gold quality
cerebellar hemisphere	UBERON:0002245	88.04	gold quality
granulocyte	CL:0000094	87.91	gold quality
cerebellar cortex	UBERON:0002129	87.87	gold quality
right uterine tube	UBERON:0001302	87.49	gold quality
adenohypophysis	UBERON:0002196	87.21	gold quality
left lobe of thyroid gland	UBERON:0001120	87.18	gold quality
right lobe of thyroid gland	UBERON:0001119	87.15	gold quality
pituitary gland	UBERON:0000007	86.89	gold quality
thyroid gland	UBERON:0002046	86.49	gold quality
cortical plate	UBERON:0005343	86.36	gold quality
right adrenal gland cortex	UBERON:0035827	86.12	gold quality
cerebellum	UBERON:0002037	86.08	gold quality
right adrenal gland	UBERON:0001233	85.80	gold quality
spleen	UBERON:0002106	85.36	gold quality
right atrium auricular region	UBERON:0006631	85.12	gold quality
heart left ventricle	UBERON:0002084	84.89	gold quality
muscle layer of sigmoid colon	UBERON:0035805	84.62	gold quality
lower esophagus muscularis layer	UBERON:0035833	84.53	gold quality
lower esophagus	UBERON:0013473	84.52	gold quality
cardiac ventricle	UBERON:0002082	84.39	gold quality
left adrenal gland	UBERON:0001234	84.28	gold quality
left adrenal gland cortex	UBERON:0035825	84.23	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	84.10	gold quality
cardiac atrium	UBERON:0002081	83.99	gold quality
small intestine Peyer’s patch	UBERON:0003454	83.97	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-CURD-10	no	279.13
E-ANND-3	no	3.43

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA1974.1	ZNF211	Factors with multiple dispersed zinc fingers
MA1974.2	ZNF211	Factors with multiple dispersed zinc fingers

JASPAR matrix evidence (PMIDs): PMID:29146583

miRNA regulators (miRDB)

73 targeting ZNF211, 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-656-3P	100.00	72.15	2788
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-4760-3P	99.93	70.50	2385
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-4697-3P	99.89	67.09	1123
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-448	99.79	72.37	2103
HSA-MIR-4694-3P	99.79	69.53	2640
HSA-MIR-577	99.78	69.13	2479
HSA-MIR-320A-3P	99.77	69.73	2107
HSA-MIR-320B	99.77	69.73	2107
HSA-MIR-320C	99.77	69.73	2107
HSA-MIR-320D	99.77	69.73	2107
HSA-MIR-4429	99.77	69.62	2111
HSA-MIR-3150A-3P	99.76	64.44	1640
HSA-MIR-6763-5P	99.76	64.68	1767
HSA-MIR-187-5P	99.74	70.26	1404

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	prdm2a	ENSDARG00000090721
drosophila_melanogaster	CG12769	FBGN0033252
caenorhabditis_elegans		WBGENE00001223
caenorhabditis_elegans		WBGENE00017406
caenorhabditis_elegans		WBGENE00019960

Paralogs (7): ZNF423 (ENSG00000102935), ZNF462 (ENSG00000148143), ZBTB39 (ENSG00000166860), ZNF597 (ENSG00000167981), ZNF445 (ENSG00000185219), ZNF786 (ENSG00000197362), ZNF521 (ENSG00000198795)

Protein

Protein identifiers

Zinc finger protein 211 — Q13398 (reviewed: Q13398)

Alternative names: Zinc finger protein C2H2-25

All UniProt accessions (5): A0A0A0MTK1, Q13398, F5GY70, F5H771, H0Y3T8

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 (8)

UniProt ID	Names	Canonical?
Q13398-1	1	yes
Q13398-2	2
Q13398-3	3
Q13398-4	4
Q13398-5	5
Q13398-6	6
Q13398-7	7
Q13398-8	8

RefSeq proteins (7): NP_001252526, NP_001252527, NP_001252528, NP_001252529, NP_001309235, NP_006376, NP_942152 (=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 (26 total): zinc finger region 12, splice variant 7, sequence variant 2, sequence conflict 2, chain 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q13398-F1	64.24	0.35

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 80 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_UP, ENK_UV_RESPONSE_KERATINOCYTE_UP, BLALOCK_ALZHEIMERS_DISEASE_UP, MODULE_123, MODULE_98, MODULE_48, MODULE_95, JAZAERI_BREAST_CANCER_BRCA1_VS_BRCA2_DN, KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, VERHAAK_GLIOBLASTOMA_CLASSICAL, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, MODULE_163, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, CEBPZ_TARGET_GENES

GO Biological Process (3): regulation of transcription by RNA polymerase II (GO:0006357), negative regulation of DNA-templated transcription (GO:0045892), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (5): 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), 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
DNA-templated transcription	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
transcription by RNA polymerase II	1
negative regulation of RNA biosynthetic process	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
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

564 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF211	HK2	P52789	578
ZNF211	CCNYL1	Q8N7R7	464
ZNF211	CLRN3	Q8NCR9	461
ZNF211	TUBG2	Q9NRH3	445
ZNF211	LPXN	O60711	410
ZNF211	CYB5R2	Q6BCY4	397
ZNF211	CEP164	Q9UPV0	392
ZNF211	CD300LB	A8K4G0	377
ZNF211	PKM	P14618	377
ZNF211	RCVRN	P35243	374
ZNF211	TNFRSF13B	O14836	369
ZNF211	LDHA	P00338	367
ZNF211	NFKBIE	O00221	366
ZNF211	GPD1L	Q8N335	341
ZNF211	MTRNR2L7	P0CJ74	325
ZNF211	SLC2A1	P11166	325

IntAct

8 interactions, top by confidence:

A	B	Type	Score
ZNF416	PGK2	psi-mi:“MI:0914”(association)	0.530
ZNF211	IPO8	psi-mi:“MI:0914”(association)	0.350
ZNF467	ZNF320	psi-mi:“MI:0914”(association)	0.350
ZNF211	NT5DC3	psi-mi:“MI:0914”(association)	0.350
ZNF211	ZNF316	psi-mi:“MI:0914”(association)	0.350
ZNF211	NDEL1	psi-mi:“MI:0915”(physical association)	0.000
NDEL1	ZNF211	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (24): SMARCAD1 (Affinity Capture-MS), TRIM37 (Affinity Capture-MS), NT5DC3 (Affinity Capture-MS), USP34 (Affinity Capture-MS), ZNF211 (Affinity Capture-MS), STRN4 (Affinity Capture-MS), EHMT2 (Affinity Capture-MS), AKAP8L (Affinity Capture-MS), DNAJB6 (Affinity Capture-MS), MLF2 (Affinity Capture-MS), RPL39 (Affinity Capture-MS), TUBA1C (Affinity Capture-MS), TRIM28 (Affinity Capture-MS), ZNF316 (Affinity Capture-MS), ZNF460 (Affinity Capture-MS)

ESM2 similar proteins: A0JNB1, A1YF12, A1YG88, A2T759, A3KN32, B2RUI1, O43296, O75123, P10072, P17020, P17097, P51814, P52736, P52740, Q07230, Q08ER8, Q13398, Q14590, Q32KN0, Q3KQV3, Q3MIS6, Q4V8A8, Q5CZA5, Q5RBQ3, Q5RBX0, Q5RCD9, Q5RCX4, Q6GQR8, Q6NX45, Q6P9A3, Q6PK81, Q7TSH9, Q7TSI0, Q7Z7L9, Q86UD4, Q8BFS8, Q8BLB0, Q8IVP9, Q8IZ26, Q8N9F8

Diamond homologs: A2RRD8, A6NFI3, A6NM28, A8MUZ8, A8MWA4, B2RUI1, B4DU55, E9Q8G5, O43296, O43361, O75467, O75820, P0CH99, P0CI00, P10078, P16373, P16374, P17021, P17023, P17032, P17097, P17098, P21506, P51786, P52740, Q06732, Q08ER8, Q13106, Q13360, Q13398, Q14592, Q147U1, Q32M78, Q3KQV3, Q3MIS6, Q3SY52, Q571J5, Q5CZA5, Q5HY98, Q5R7I8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	62
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1262 predictions. Top by Δscore:

Variant	Effect	Δscore
19:57634628:GGGAA:G	acceptor_gain	1.0000
19:57635707:A:G	donor_gain	1.0000
19:57640700:TTAG:T	acceptor_loss	1.0000
19:57633482:TCCC:T	donor_gain	0.9900
19:57633488:G:GG	donor_gain	0.9900
19:57634619:ATTAT:A	acceptor_gain	0.9900
19:57634754:GG:G	donor_gain	0.9900
19:57634754:GGGT:G	donor_loss	0.9900
19:57634755:GG:G	donor_gain	0.9900
19:57634755:GGTAA:G	donor_loss	0.9900
19:57634756:G:C	donor_loss	0.9900
19:57634757:T:TT	donor_loss	0.9900
19:57635617:GTTT:G	acceptor_gain	0.9900
19:57640696:A:AG	acceptor_gain	0.9900
19:57640697:C:G	acceptor_gain	0.9900
19:57640702:A:AG	acceptor_gain	0.9900
19:57640702:AG:A	acceptor_gain	0.9900
19:57640703:G:GG	acceptor_gain	0.9900
19:57640703:GG:G	acceptor_gain	0.9900
19:57640703:GGTT:G	acceptor_gain	0.9900
19:57634626:TA:T	acceptor_loss	0.9800
19:57634627:A:AC	acceptor_loss	0.9800
19:57634627:AG:A	acceptor_gain	0.9800
19:57634628:G:GT	acceptor_loss	0.9800
19:57634628:GG:G	acceptor_gain	0.9800
19:57634756:G:GG	donor_gain	0.9800
19:57634758:AAG:A	donor_loss	0.9800
19:57635616:A:AG	acceptor_gain	0.9800
19:57635617:G:GG	acceptor_gain	0.9800
19:57640702:AGGTT:A	acceptor_gain	0.9800

AlphaMissense

3882 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:57641534:T:C	F350L	0.996
19:57641536:T:A	F350L	0.996
19:57641536:T:G	F350L	0.996
19:57641618:T:C	F378L	0.996
19:57641620:T:A	F378L	0.996
19:57641620:T:G	F378L	0.996
19:57641702:T:C	F406L	0.996
19:57641704:T:A	F406L	0.996
19:57641704:T:G	F406L	0.996
19:57641450:T:C	F322L	0.995
19:57641452:T:A	F322L	0.995
19:57641452:T:G	F322L	0.995
19:57641870:T:C	F462L	0.994
19:57641872:T:A	F462L	0.994
19:57641872:T:G	F462L	0.994
19:57642038:T:C	F518L	0.993
19:57642040:T:A	F518L	0.993
19:57642040:T:G	F518L	0.993
19:57641645:C:G	H387D	0.989
19:57641637:T:C	L384P	0.988
19:57642122:T:C	F546L	0.988
19:57642124:T:A	F546L	0.988
19:57642124:T:G	F546L	0.988
19:57641647:C:A	H387Q	0.987
19:57641647:C:G	H387Q	0.987
19:57641786:T:C	F434L	0.987
19:57641788:T:A	F434L	0.987
19:57641788:T:G	F434L	0.987
19:57641954:T:C	F490L	0.987
19:57641956:T:A	F490L	0.987

dbSNP variants (sampled 300 via entrez): RS1000082868 (19:57638804 G>A), RS1000117549 (19:57635062 A>G), RS1000152828 (19:57631777 C>T), RS1000261229 (19:57632752 T>C), RS1000702944 (19:57640432 C>G,T), RS1000732532 (19:57633408 T>C), RS1000801999 (19:57632586 T>G), RS1001211775 (19:57644427 A>AAG), RS1001725725 (19:57636931 T>C), RS1002057273 (19:57639802 C>T), RS1002122291 (19:57638061 G>A,C), RS1002155225 (19:57637241 T>A,C), RS1002645646 (19:57643672 C>G), RS1003423628 (19:57635744 A>G), RS1003440619 (19:57632507 T>A,C)

Disease associations

OMIM: gene MIM:601856 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST004621_170	Red cell distribution width	3.000000e-12
GCST006804_69	Red cell distribution width	3.000000e-11
GCST90002396_47	Mean reticulocyte volume	1.000000e-14
GCST90002401_302	Platelet distribution width	5.000000e-19
GCST90002404_543	Red cell distribution width	2.000000e-20

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0009188	Red cell distribution width
EFO:0010701	mean reticulocyte volume
EFO:0007984	platelet component distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB clinical annotations

1 annotations.

Variant	Type	Level	Drugs	Phenotypes
rs10420097	Efficacy	3	methylphenidate	Attention Deficit Disorder with Hyperactivity

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs10420097	ZNF211	3	0.00	1	methylphenidate

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects cotreatment, increases abundance, increases expression, decreases expression	4
bisphenol A	affects cotreatment, increases methylation, decreases expression	2
methacrylaldehyde	increases abundance, affects cotreatment, increases expression	2
Acrolein	increases expression, increases abundance, affects cotreatment	2
Arsenic	affects methylation, affects cotreatment, increases abundance, increases expression	2
Benzo(a)pyrene	increases expression	2
Ozone	affects cotreatment, increases expression, increases abundance	2
aristolochic acid I	increases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases expression, increases abundance	1
geraniol	increases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
cupric oxide	increases expression	1
di-n-butylphosphoric acid	affects expression	1
abrine	increases expression	1
jinfukang	decreases expression	1
Temozolomide	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Air Pollutants	affects cotreatment, increases abundance, increases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Gallic Acid	increases expression	1
Hydralazine	affects cotreatment, increases expression	1
Manganese	affects cotreatment, increases abundance, increases expression	1
Methyl Methanesulfonate	increases expression	1
Quercetin	increases expression	1
Selenium	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Valproic Acid	affects cotreatment, 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_XW18	HEK293 eGFP-ZNF211	Transformed cell line	Female

Clinical trials (associated diseases)

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