ZNF853

Summary

ZNF853 (zinc finger protein 853, HGNC:21767) is a protein-coding gene on chromosome 7p22.1, encoding Zinc finger protein 853 (P0CG23).

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II.

Source: NCBI Gene 54753 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 121 total
• MANE Select transcript: NM_017560

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21767
Approved symbol	ZNF853
Name	zinc finger protein 853
Location	7p22.1
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp434J1015
Ensembl gene	ENSG00000236609
Ensembl biotype	protein_coding
Entrez	54753

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000457543, ENST00000854261, ENST00000963925

RefSeq mRNA: 2 — MANE Select: NM_017560 NM_001353546, NM_017560

CCDS: CCDS59048

Canonical transcript exons

ENST00000457543 — 3 exons

Exon	Start	End
ENSE00001595926	6615610	6616186
ENSE00001759400	6617190	6617307
ENSE00001763082	6621122	6624290

Expression profiles

Bgee: expression breadth ubiquitous, 194 present calls, max score 87.05.

FANTOM5 (CAGE): breadth broad, TPM avg 1.9218 / max 26.7140, expressed in 723 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
77163	1.8450	711
77162	0.0768	35

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
hypothalamus	UBERON:0001898	87.05	gold quality
amygdala	UBERON:0001876	86.94	gold quality
anterior cingulate cortex	UBERON:0009835	86.09	gold quality
gastrocnemius	UBERON:0001388	85.83	gold quality
muscle of leg	UBERON:0001383	85.51	gold quality
prefrontal cortex	UBERON:0000451	85.17	gold quality
putamen	UBERON:0001874	84.68	gold quality
right frontal lobe	UBERON:0002810	84.61	gold quality
hindlimb stylopod muscle	UBERON:0004252	84.47	gold quality
tibialis anterior	UBERON:0001385	84.29	gold quality
nucleus accumbens	UBERON:0001882	83.77	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	83.66	gold quality
substantia nigra	UBERON:0002038	83.55	gold quality
neocortex	UBERON:0001950	83.46	gold quality
Brodmann (1909) area 9	UBERON:0013540	83.41	gold quality
Ammon’s horn	UBERON:0001954	83.18	gold quality
frontal cortex	UBERON:0001870	83.07	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	83.07	gold quality
caudate nucleus	UBERON:0001873	82.96	gold quality
spinal cord	UBERON:0002240	82.93	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	82.61	silver quality
cerebral cortex	UBERON:0000956	82.55	gold quality
midbrain	UBERON:0001891	82.53	gold quality
temporal lobe	UBERON:0001871	81.88	gold quality
forebrain	UBERON:0001890	81.88	gold quality
ventricular zone	UBERON:0003053	81.69	gold quality
apex of heart	UBERON:0002098	81.66	gold quality
cortical plate	UBERON:0005343	80.97	gold quality
brain	UBERON:0000955	80.60	gold quality
muscle layer of sigmoid colon	UBERON:0035805	80.04	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.35

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA2514.1	ZNF853	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:39605530

miRNA regulators (miRDB)

45 targeting ZNF853, 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-6721-5P	99.93	68.92	2981
HSA-MIR-454-3P	99.91	74.01	1925
HSA-MIR-130A-3P	99.90	73.31	1861
HSA-MIR-130B-3P	99.90	73.27	1850
HSA-MIR-301A-3P	99.90	73.15	1839
HSA-MIR-301B-3P	99.90	73.19	1836
HSA-MIR-3666	99.90	73.24	1833
HSA-MIR-4295	99.90	73.11	1838
HSA-MIR-544A	99.84	68.66	1965
HSA-MIR-1249-5P	99.61	66.55	2049
HSA-MIR-6797-5P	99.61	66.55	2084
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-1290	99.59	69.90	2079
HSA-MIR-3682-3P	99.58	67.63	865
HSA-MIR-671-5P	99.52	67.11	1277
HSA-MIR-486-3P	99.51	66.82	1901
HSA-MIR-20A-3P	99.44	69.10	1575
HSA-MIR-6165	99.44	67.12	1389
HSA-MIR-508-5P	99.41	64.25	1248
HSA-MIR-4251	99.40	69.19	3363
HSA-MIR-1276	99.36	68.18	1642
HSA-MIR-1272	99.34	68.79	878
HSA-MIR-3978	99.24	68.39	2201
HSA-MIR-7109-5P	99.18	66.13	1057
HSA-MIR-6734-3P	99.15	66.27	1627
HSA-MIR-3152-3P	99.10	66.35	678
HSA-MIR-328-5P	99.08	64.65	1000
HSA-MIR-6885-5P	98.71	64.33	902
HSA-MIR-423-5P	98.69	67.48	1522
HSA-MIR-6887-5P	98.56	68.49	1295

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp853	ENSMUSG00000093910
rattus_norvegicus	Zfp853	ENSRNOG00000030579

Paralogs (30): ZNF263 (ENSG00000006194), ZNF213 (ENSG00000085644), 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)

Protein

Protein identifiers

Zinc finger protein 853 — P0CG23 (reviewed: P0CG23)

All UniProt accessions (1): P0CG23

RefSeq proteins (2): NP_001340475, NP_060030* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR050331	Zinc_finger_PRDM4/PRDM1/PRDM14	Family

Pfam: PF00096

UniProt features (13 total): zinc finger region 5, sequence variant 3, region of interest 2, compositionally biased region 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0CG23-F1	67.53	0.36

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 32 (showing top): chr7p22, SENESE_HDAC3_TARGETS_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, DODD_NASOPHARYNGEAL_CARCINOMA_DN, FIGUEROA_AML_METHYLATION_CLUSTER_3_DN, FIGUEROA_AML_METHYLATION_CLUSTER_4_DN, ZHOU_INFLAMMATORY_RESPONSE_FIMA_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, SQSTM1_TARGET_GENES, MIR544A, MIR20A_3P, GSE11057_NAIVE_VS_CENT_MEMORY_CD4_TCELL_UP, MIR637, MIR3682_3P, MIR3152_3P

GO Biological Process (1): regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (4): 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), metal ion binding (GO:0046872)

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

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
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
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

406 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF853	FOXL2NB	Q6ZUU3	507
ZNF853	GARIN5A	Q6IPT2	477
ZNF853	RSPH10B2	B2RC85	450
ZNF853	AAR2	Q9Y312	405
ZNF853	ZNF768	Q9H5H4	405
ZNF853	ZNF521	Q96K83	403
ZNF853	ZNF148	Q9UQR1	394
ZNF853	TULP2	O00295	392
ZNF853	ZNF790	Q6PG37	389
ZNF853	CCDC102B	Q68D86	384
ZNF853	ZMIZ2	Q8NF64	382
ZNF853	ZNF552	Q9H707	382
ZNF853	LRRC23	Q53EV4	370
ZNF853	ZNF232	Q9UNY5	369
ZNF853	GREB1L	Q9C091	358

IntAct

0 interactions, top by confidence:

BioGRID (1): ZNF853 (Affinity Capture-MS)

ESM2 similar proteins: A0A0J9YY54, A0A1B0GV03, A6NEF3, A6NEM1, A6NI86, A8MZA4, B4DH59, D3YVF0, D3YZV8, E9PXT9, F6QRE9, H0YKK7, P0C7A2, P0CG23, P0DX02, P14590, P21263, P22793, P24710, P62521, P79386, Q07283, Q0P6D6, Q28181, Q3BBV2, Q4VC44, Q6AXX0, Q6H9L7, Q6P3W6, Q6P5H2, Q6ZQX7, Q86T75, Q86X53, Q8CHD8, Q8N660, Q8N7Z2, Q8N9W4, Q95337, Q99PG2, Q9BXX3

Diamond homologs: P0CG23, Q3US17, Q569E7, Q5TEC3, Q96MX3, O88553, P17141, P21506, Q02526, Q3ZCX4, Q6ZSS3, Q8N8Y5, Q9UDV6, Q9Y2P0, Q9Y6Q3, A1YEV9, A1YG26, A1YG60, A2ANX9, A2T712, A2T736, A2T7L7, A3KN32, A7Y7X5, B0K011, E9Q6W4, O14771, O15391, O35738, O43474, O62836, O95125, P08048, P10925, P17010, P17012, P17022, P17041, P20662, P24399

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	116
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

524 predictions. Top by Δscore:

Variant	Effect	Δscore
7:6617179:TTTCA:T	acceptor_loss	1.0000
7:6617180:TTCA:T	acceptor_loss	1.0000
7:6617181:TCA:T	acceptor_loss	1.0000
7:6617182:CA:C	acceptor_loss	1.0000
7:6617183:A:AG	acceptor_gain	1.0000
7:6617183:A:T	acceptor_loss	1.0000
7:6617184:G:A	acceptor_loss	1.0000
7:6617184:G:GA	acceptor_gain	1.0000
7:6617184:GC:G	acceptor_gain	1.0000
7:6617184:GCA:G	acceptor_gain	1.0000
7:6617184:GCAC:G	acceptor_gain	1.0000
7:6617184:GCACA:G	acceptor_gain	1.0000
7:6617303:CTCAG:C	donor_loss	1.0000
7:6617304:TCAGG:T	donor_loss	1.0000
7:6617305:CAGG:C	donor_loss	1.0000
7:6617306:AG:A	donor_loss	1.0000
7:6617307:GGT:G	donor_loss	1.0000
7:6617308:GTGA:G	donor_loss	1.0000
7:6617309:T:A	donor_loss	1.0000
7:6617186:A:AG	acceptor_gain	0.9900
7:6617277:G:GT	donor_gain	0.9900
7:6616184:CAGG:C	donor_loss	0.9800
7:6616187:G:GA	donor_loss	0.9800
7:6616188:T:A	donor_loss	0.9800
7:6617187:C:G	acceptor_gain	0.9800
7:6617914:GGTGC:G	donor_gain	0.9800
7:6621117:CACA:C	acceptor_loss	0.9800
7:6621119:CA:C	acceptor_loss	0.9800
7:6616187:G:GG	donor_gain	0.9700
7:6616173:A:T	donor_gain	0.9600

AlphaMissense

4236 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:6622471:T:C	F494L	1.000
7:6622473:C:A	F494L	1.000
7:6622473:C:G	F494L	1.000
7:6622555:T:C	F522L	1.000
7:6622556:T:C	F522S	1.000
7:6622557:C:A	F522L	1.000
7:6622557:C:G	F522L	1.000
7:6622582:C:G	H531D	1.000
7:6622639:T:C	F550L	1.000
7:6622640:T:C	F550S	1.000
7:6622641:C:A	F550L	1.000
7:6622641:C:G	F550L	1.000
7:6622723:T:C	F578L	1.000
7:6622724:T:C	F578S	1.000
7:6622725:C:A	F578L	1.000
7:6622725:C:G	F578L	1.000
7:6622472:T:C	F494S	0.999
7:6622472:T:G	F494C	0.999
7:6622498:C:A	H503N	0.999
7:6622498:C:G	H503D	0.999
7:6622500:C:A	H503Q	0.999
7:6622500:C:G	H503Q	0.999
7:6622556:T:G	F522C	0.999
7:6622574:T:C	L528P	0.999
7:6622582:C:A	H531N	0.999
7:6622584:C:A	H531Q	0.999
7:6622584:C:G	H531Q	0.999
7:6622594:C:G	H535D	0.999
7:6622596:C:A	H535Q	0.999
7:6622596:C:G	H535Q	0.999

dbSNP variants (sampled 300 via entrez): RS1000020967 (7:6621237 C>T), RS1000167489 (7:6615264 G>T), RS1000197938 (7:6616040 C>A), RS1000517048 (7:6613616 G>A), RS1001184367 (7:6615874 G>A,C), RS1001234490 (7:6624532 C>A,T), RS1001300315 (7:6615619 C>A,T), RS1001890616 (7:6614366 G>A), RS1002795896 (7:6622104 G>A,C), RS1003312851 (7:6623281 C>A,T), RS1004538147 (7:6615417 A>G), RS1004590441 (7:6615569 C>T), RS1004828264 (7:6623005 A>C), RS1005181067 (7:6621630 G>A,C), RS1005233191 (7:6621958 G>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

2 associations (top):

Study	Trait	p-value
GCST005951_155	Body mass index	1.000000e-08
GCST90002391_217	Mean corpuscular hemoglobin concentration	1.000000e-09

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0004528	mean corpuscular hemoglobin concentration

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, increases methylation	6
Tretinoin	decreases expression, increases expression	2
Particulate Matter	increases abundance, increases expression	2
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
ferrous chloride	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
monomethylarsonous acid	decreases 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
licochalcone B	increases expression	1
bisphenol S	decreases expression	1
jinfukang	affects cotreatment, decreases expression	1
Sunitinib	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	increases methylation	1
Cisplatin	affects cotreatment, decreases expression	1
Estradiol	affects cotreatment, increases expression	1
Lead	affects expression	1
Niclosamide	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Antirheumatic Agents	increases expression	1

Clinical trials (associated diseases)

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