ZNF253

Summary

ZNF253 (zinc finger protein 253, HGNC:13497) is a protein-coding gene on chromosome 19p13.11, encoding Zinc finger protein 253 (O75346). May function as a transcription factor.

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 DNA-templated transcription. Predicted to be located in nucleus.

Source: NCBI Gene 56242 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 71 total
• MANE Select transcript: NM_021047

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13497
Approved symbol	ZNF253
Name	zinc finger protein 253
Location	19p13.11
Locus type	gene with protein product
Status	Approved
Aliases	BMZF-1, FLJ90391
Ensembl gene	ENSG00000256771
Ensembl biotype	protein_coding
OMIM	606954
Entrez	56242

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 retained_intron

ENST00000355650, ENST00000589668, ENST00000589717, ENST00000592725, ENST00000937512

RefSeq mRNA: 3 — MANE Select: NM_021047 NM_001331133, NM_001331134, NM_021047

CCDS: CCDS42532, CCDS86729

Canonical transcript exons

ENST00000589717 — 4 exons

Exon	Start	End
ENSE00001493113	19865882	19865999
ENSE00001657276	19878481	19878607
ENSE00002861280	19891474	19894674
ENSE00003502821	19880051	19880146

Expression profiles

Bgee: expression breadth ubiquitous, 224 present calls, max score 97.40.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.3793 / max 689.6874, expressed in 1561 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
174834	7.7864	1295
174833	4.2070	1255
174835	2.1547	711
174832	0.2311	84

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	97.40	silver quality
ganglionic eminence	UBERON:0004023	90.62	gold quality
cortical plate	UBERON:0005343	87.37	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.92	gold quality
ventricular zone	UBERON:0003053	85.91	gold quality
endometrium epithelium	UBERON:0004811	85.56	gold quality
endothelial cell	CL:0000115	84.07	silver quality
calcaneal tendon	UBERON:0003701	82.41	gold quality
endometrium	UBERON:0001295	81.44	gold quality
diaphragm	UBERON:0001103	80.81	gold quality
hindlimb stylopod muscle	UBERON:0004252	80.79	gold quality
adrenal tissue	UBERON:0018303	80.17	gold quality
islet of Langerhans	UBERON:0000006	80.14	gold quality
embryo	UBERON:0000922	79.92	gold quality
medial globus pallidus	UBERON:0002477	79.49	gold quality
tendon	UBERON:0000043	78.66	gold quality
colonic epithelium	UBERON:0000397	78.64	gold quality
biceps brachii	UBERON:0001507	78.45	silver quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	77.81	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.50	gold quality
lymph node	UBERON:0000029	76.14	gold quality
pigmented layer of retina	UBERON:0001782	76.00	gold quality
corpus callosum	UBERON:0002336	75.92	gold quality
rectum	UBERON:0001052	75.80	gold quality
muscle of leg	UBERON:0001383	75.58	gold quality
ovary	UBERON:0000992	75.43	gold quality
globus pallidus	UBERON:0001875	75.43	gold quality
right lobe of thyroid gland	UBERON:0001119	75.23	gold quality
thyroid gland	UBERON:0002046	75.19	gold quality
muscle organ	UBERON:0001630	75.17	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.51

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

47 targeting ZNF253, 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-3689D	100.00	66.14	1181
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-511-3P	99.99	68.85	1467
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-4645-5P	99.98	65.81	1284
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-4699-3P	99.71	70.15	3142
HSA-MIR-3059-5P	99.70	69.93	2491
HSA-MIR-12124	99.68	69.17	2700
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-4310	99.59	68.84	2527
HSA-MIR-372-5P	99.41	69.11	2299
HSA-MIR-183-3P	99.41	69.41	1598

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
danio_rerio		ENSDARG00000099025

Paralogs (18): ZNF430 (ENSG00000118620), ZNF92 (ENSG00000146757), ZNF66 (ENSG00000160229), ZNF22 (ENSG00000165512), 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), ZNF723 (ENSG00000268696)

Protein

Protein identifiers

Zinc finger protein 253 — O75346 (reviewed: O75346)

Alternative names: Bone marrow zinc finger 1, Zinc finger protein 411

All UniProt accessions (2): O75346, K7EP55

UniProt curated annotations — full annotation on UniProt →

Function. May function as a transcription factor. Seem to have a transcriptional repression activity.

Subcellular location. Nucleus.

Tissue specificity. Expressed in bone marrow and in monocytic and immature erythroid cell lines.

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

Isoforms (2)

UniProt ID	Names	Canonical?
O75346-1	1	yes
O75346-2	2

RefSeq proteins (3): NP_001318062, NP_001318063, NP_066385* (*=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

Pfam: PF00096, PF01352, PF13465

UniProt features (17 total): zinc finger region 11, sequence conflict 3, chain 1, domain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O75346-F1	71.58	0.19

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 71 (showing top): BLALOCK_ALZHEIMERS_DISEASE_UP, BASAKI_YBX1_TARGETS_DN, MORF_PTEN, chr19p13, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, VEGF_A_UP.V1_DN, BRCA1_DN.V1_DN, CTIP_DN.V1_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ASH1L_TARGET_GENES, CIITA_TARGET_GENES, ZNF350_TARGET_GENES, ZNF512B_TARGET_GENES, MIR616_5P

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

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
DNA-templated transcription	2
regulation of DNA-templated transcription	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
regulation of gene expression	1
regulation of RNA biosynthetic process	1
negative regulation of RNA biosynthetic process	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
nucleic acid binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

404 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF253	PNMA1	Q8ND90	495
ZNF253	TSPAN6	O43657	472
ZNF253	PCGF2	P35227	429
ZNF253	CCNI2	Q6ZMN8	420
ZNF253	CCR1	P32246	416
ZNF253	MORN3	Q6PF18	403
ZNF253	TP63	Q9H3D4	398
ZNF253	NDRG1	Q92597	398
ZNF253	LCP2	Q13094	395
ZNF253	CCDC148	Q8NFR7	392
ZNF253	FCER1G	P30273	386
ZNF253	ZFHX4	Q86UP3	384
ZNF253	NFATC2	Q13469	383
ZNF253	C11orf96	Q7Z7L8	379
ZNF253	SIRT1	Q96EB6	374

IntAct

11 interactions, top by confidence:

A	B	Type	Score
LDOC1	ZNF253	psi-mi:“MI:0915”(physical association)	0.530
LDOC1	ZNF253	psi-mi:“MI:0407”(direct interaction)	0.530
RPL27A	ZNF320	psi-mi:“MI:0914”(association)	0.350
FBLN5	ZNF320	psi-mi:“MI:0914”(association)	0.350
NOTCH2	ZNF320	psi-mi:“MI:0914”(association)	0.350
FAXC	METTL15	psi-mi:“MI:0914”(association)	0.350
TIMM50	ZNF320	psi-mi:“MI:0914”(association)	0.350
AKR1B1	ZNF253	psi-mi:“MI:0915”(physical association)	0.000
ZNF253		psi-mi:“MI:0915”(physical association)	0.000
	ZNF253	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (7): ZNF253 (Affinity Capture-MS), ZNF253 (Affinity Capture-MS), ZNF253 (Affinity Capture-MS), ZNF253 (Affinity Capture-MS), ZNF253 (Affinity Capture-MS), ZNF253 (Affinity Capture-MS), ZNF253 (Affinity Capture-RNA)

ESM2 similar proteins: A0A1W2PQL4, A0JPL0, A2RRD8, A6NHJ4, A6NP11, B4DX44, O75346, O95780, P0CB33, P21506, P51508, P52738, Q0D2J5, Q0VGE8, Q12901, Q13360, Q14593, Q15973, Q2M218, Q2M3X9, Q2VY69, Q3SXZ3, Q5HY98, Q5RCJ2, Q5VIY5, Q6J6I6, Q7L2R6, Q86XU0, Q86Y25, Q8IW36, Q8IYN0, Q8IYX0, Q8N782, Q8N883, Q8N9Z0, Q8NDP4, Q95K49, Q969W8, Q96H40, Q96N58

Diamond homologs: A0A1W2PQL4, A6NK75, A6NN14, A6NNF4, A6NP11, A8MQ14, A8MTY0, A8MUV8, A8MXY4, B4DX44, B4DXR9, E9PYI1, O14628, O43345, O75290, O75346, O75373, O75437, O95780, P0CB33, P0DKX0, P0DPD5, P16373, P17019, P17038, P21506, P35789, P52736, P52738, P52744, Q03923, Q03924, Q03936, Q03938, Q05481, Q14586, Q14593, Q14929, Q15928, Q3KNS6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	63
Likely benign	3
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

542 predictions. Top by Δscore:

Variant	Effect	Δscore
19:19865997:ATGGT:A	donor_loss	1.0000
19:19865999:GGTG:G	donor_loss	1.0000
19:19878568:G:T	donor_gain	1.0000
19:19891472:A:AG	acceptor_gain	1.0000
19:19891473:G:GG	acceptor_gain	1.0000
19:19891473:GTTAT:G	acceptor_gain	1.0000
19:19865998:TG:T	donor_gain	0.9900
19:19865999:GG:G	donor_gain	0.9900
19:19866000:G:GG	donor_gain	0.9900
19:19878475:TTCCA:T	acceptor_loss	0.9900
19:19878476:TCCA:T	acceptor_loss	0.9900
19:19878479:AG:A	acceptor_gain	0.9900
19:19878480:GG:G	acceptor_gain	0.9900
19:19878568:G:GT	donor_gain	0.9900
19:19880143:CCAG:C	donor_loss	0.9900
19:19880144:CAG:C	donor_loss	0.9900
19:19880145:AG:A	donor_loss	0.9900
19:19880146:GG:G	donor_loss	0.9900
19:19880148:T:G	donor_loss	0.9900
19:19891473:GTT:G	acceptor_gain	0.9900
19:19865997:ATG:A	donor_gain	0.9800
19:19878472:GTTTT:G	acceptor_loss	0.9800
19:19878473:TTTTC:T	acceptor_loss	0.9800
19:19878479:A:AG	acceptor_gain	0.9800
19:19878480:G:GG	acceptor_gain	0.9800
19:19878603:CCTTG:C	donor_loss	0.9800
19:19878607:GGT:G	donor_loss	0.9800
19:19878608:G:A	donor_loss	0.9800
19:19878609:T:G	donor_loss	0.9800
19:19878610:G:GG	donor_loss	0.9800

AlphaMissense

3311 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:19892544:T:C	F433L	0.992
19:19892546:T:A	F433L	0.992
19:19892546:T:G	F433L	0.992
19:19891872:T:C	F209L	0.989
19:19891874:T:A	F209L	0.989
19:19891874:T:G	F209L	0.989
19:19891956:T:C	F237L	0.989
19:19891958:T:A	F237L	0.989
19:19891958:T:G	F237L	0.989
19:19892040:T:C	F265L	0.988
19:19892042:C:A	F265L	0.988
19:19892042:C:G	F265L	0.988
19:19892460:T:C	F405L	0.988
19:19892462:T:A	F405L	0.988
19:19892462:T:G	F405L	0.988
19:19892628:T:C	F461L	0.986
19:19892630:T:A	F461L	0.986
19:19892630:T:G	F461L	0.986
19:19892376:T:C	F377L	0.985
19:19892378:T:A	F377L	0.985
19:19892378:T:G	F377L	0.985
19:19892292:T:C	F349L	0.984
19:19892294:T:A	F349L	0.984
19:19892294:T:G	F349L	0.984
19:19892047:G:C	R267P	0.980
19:19892208:T:C	F321L	0.978
19:19892210:T:A	F321L	0.978
19:19892210:T:G	F321L	0.978
19:19892124:T:C	F293L	0.973
19:19892126:T:A	F293L	0.973

dbSNP variants (sampled 300 via entrez): RS1000044464 (19:19875701 CTCTT>C), RS1000056028 (19:19874637 C>T), RS1000106540 (19:19874432 A>C), RS1000182983 (19:19892079 C>T), RS1000199579 (19:19882797 C>T), RS1000365170 (19:19887339 C>T), RS1000417772 (19:19887022 C>A,T), RS1000476943 (19:19889424 G>A), RS1000574501 (19:19894070 G>C,T), RS1000812541 (19:19870731 T>G), RS1000828667 (19:19868110 G>C,T), RS1000881207 (19:19868568 T>A), RS1001030450 (19:19876998 C>T), RS1001055862 (19:19875642 G>A,T), RS1001109869 (19:19875523 G>A)

Disease associations

OMIM: gene MIM:606954 | 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

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression	5
Formaldehyde	increases expression, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
triphenyl phosphate	affects expression	1
sodium arsenite	increases abundance, increases expression	1
potassium chromate(VI)	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
Fulvestrant	decreases methylation	1
Air Pollutants	increases abundance, affects expression	1
Arsenic	increases abundance, increases expression	1
Benzo(a)pyrene	increases methylation	1
Succimer	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Methyl Methanesulfonate	increases expression	1
Ozone	affects expression, increases abundance	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Vanadates	decreases expression	1
Antirheumatic Agents	increases expression	1
Copper Sulfate	increases expression	1
Vitamin K 3	affects expression	1
Magnetite Nanoparticles	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

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