ZNF256

Summary

ZNF256 (zinc finger protein 256, HGNC:13049) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger protein 256 (Q9Y2P7). Transcriptional repressor that plays a role in cell proliferation.

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in negative regulation of DNA-templated transcription. Located in nucleoplasm.

Source: NCBI Gene 10172 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 82 total
• MANE Select transcript: NM_005773

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13049
Approved symbol	ZNF256
Name	zinc finger protein 256
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Aliases	BMZF-3
Ensembl gene	ENSG00000152454
Ensembl biotype	protein_coding
OMIM	606956
Entrez	10172

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000282308, ENST00000598928

RefSeq mRNA: 2 — MANE Select: NM_005773 NM_001375403, NM_005773

CCDS: CCDS12966

Canonical transcript exons

ENST00000282308 — 3 exons

Exon	Start	End
ENSE00001005300	57940833	57942647
ENSE00002479482	57943934	57944060
ENSE00003062874	57947442	57947706

Expression profiles

Bgee: expression breadth ubiquitous, 187 present calls, max score 90.24.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.1731 / max 73.3363, expressed in 1490 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
182923	4.9601	1479
182922	0.2130	87

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	90.24	gold quality
secondary oocyte	CL:0000655	89.28	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.32	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.07	gold quality
ventricular zone	UBERON:0003053	78.26	gold quality
apex of heart	UBERON:0002098	77.46	gold quality
ganglionic eminence	UBERON:0004023	76.38	gold quality
heart left ventricle	UBERON:0002084	76.13	gold quality
skin of abdomen	UBERON:0001416	75.84	gold quality
cardiac ventricle	UBERON:0002082	75.82	gold quality
right atrium auricular region	UBERON:0006631	74.88	gold quality
skin of leg	UBERON:0001511	74.43	gold quality
heart	UBERON:0000948	74.42	gold quality
cardiac atrium	UBERON:0002081	74.41	gold quality
cortical plate	UBERON:0005343	73.99	gold quality
islet of Langerhans	UBERON:0000006	73.69	gold quality
stromal cell of endometrium	CL:0002255	73.63	gold quality
zone of skin	UBERON:0000014	73.59	gold quality
smooth muscle tissue	UBERON:0001135	73.55	gold quality
colonic epithelium	UBERON:0000397	73.22	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	72.58	gold quality
amniotic fluid	UBERON:0000173	72.51	gold quality
left ovary	UBERON:0002119	72.40	gold quality
hindlimb stylopod muscle	UBERON:0004252	72.30	gold quality
right lung	UBERON:0002167	72.24	gold quality
ovary	UBERON:0000992	72.17	gold quality
lower esophagus muscularis layer	UBERON:0035833	72.06	gold quality
lower esophagus	UBERON:0013473	72.04	gold quality
granulocyte	CL:0000094	71.95	gold quality
muscle of leg	UBERON:0001383	71.84	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.77

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

2 targets.

Target	Regulation
GDNF
TRIM28

Literature-anchored findings (GeneRIF, showing 1)

• These findings suggest that BMZF3 is a transcriptional repressor induced by GDNF that plays a role in cell proliferation. (PMID:18060868)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	zfx	ENSDARG00000074453
danio_rerio		ENSDARG00000098424
mus_musculus	Zfy2	ENSMUSG00000000103
mus_musculus	Zfy1	ENSMUSG00000053211
rattus_norvegicus	Zfy1	ENSRNOG00000053042

Paralogs (38): ZFX (ENSG00000005889), ZBTB11 (ENSG00000066422), ZFAT (ENSG00000066827), ZFY (ENSG00000067646), ZNF586 (ENSG00000083828), IKZF5 (ENSG00000095574), ZNF419 (ENSG00000105136), ZNF549 (ENSG00000121406), ZSCAN20 (ENSG00000121903), ZNF304 (ENSG00000131845), PRDM15 (ENSG00000141956), ZNF660 (ENSG00000144792), ZNF711 (ENSG00000147180), ZNF773 (ENSG00000152439), ZNF837 (ENSG00000152475), ZNF691 (ENSG00000164011), ZNF610 (ENSG00000167554), E4F1 (ENSG00000167967), ZNF562 (ENSG00000171466), ZNF561 (ENSG00000171469), ZNF584 (ENSG00000171574), ZIK1 (ENSG00000171649), ZNF570 (ENSG00000171827), ZSCAN2 (ENSG00000176371), ZNF552 (ENSG00000178935), ZNF154 (ENSG00000179909), ZNF792 (ENSG00000180884), ZNF793 (ENSG00000188227), ZNF548 (ENSG00000188785), ZNF79 (ENSG00000196152), ZNF418 (ENSG00000196724), ZNF772 (ENSG00000197128), ZNF583 (ENSG00000198440), ZNF480 (ENSG00000198464), ZNF551 (ENSG00000204519), ZNF134 (ENSG00000213762), ZNF587B (ENSG00000269343), ZNF8 (ENSG00000278129)

Protein

Protein identifiers

Zinc finger protein 256 — Q9Y2P7 (reviewed: Q9Y2P7)

Alternative names: Bone marrow zinc finger 3

All UniProt accessions (2): Q9Y2P7, M0R2X0

UniProt curated annotations — full annotation on UniProt →

Function. Transcriptional repressor that plays a role in cell proliferation. Requires TRIM28 for its activity.

Subunit / interactions. Interacts with TRIM28.

Subcellular location. Nucleus.

Domain organisation. The KRAB domain mediates interaction with TRIM28 and is required for transcriptional repressor activity.

Induction. By GDNF/glial cell line-derived neurotrophic factor.

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

Isoforms (2)

UniProt ID	Names	Canonical?
Q9Y2P7-1	1	yes
Q9Y2P7-2	2

RefSeq proteins (2): NP_001362332, NP_005764* (*=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
IPR056436	Znf-C2H2_ZIC1-5/GLI1-3-like	Domain

Pfam: PF00096, PF01352, PF23561

UniProt features (24 total): zinc finger region 15, sequence conflict 3, chain 1, domain 1, region of interest 1, compositionally biased region 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y2P7-F1	69.05	0.25

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 30 (showing top): KONDO_PROSTATE_CANCER_HCP_WITH_H3K27ME3, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, MODULE_49, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, CSHL1_TARGET_GENES, SALL4_TARGET_GENES, ZFP91_TARGET_GENES, ZNF22_TARGET_GENES, ZNF561_TARGET_GENES, HDGF_TARGET_GENES, NOTCH3_TARGET_GENES, OSMAN_BLOOD_CHAD63_KH_AGE_18_50YO_HIGH_DOSE_SUBJECTS_24HR_DN, GSE17974_0H_VS_6H_IN_VITRO_ACT_CD4_TCELL_UP, GSE17974_0H_VS_12H_IN_VITRO_ACT_CD4_TCELL_UP

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

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
binding	1
cation binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1

Protein interactions and networks

STRING

480 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF256	J3KPS3	J3KPS3	655
ZNF256	ALDOA	P04075	651
ZNF256	RTBDN	Q9BSG5	541
ZNF256	KIAA1958	Q8N8K9	407
ZNF256	RSPRY1	Q96DX4	377
ZNF256	PGCKA1	Q8IY42	356
ZNF256	K7EJK4	K7EJK4	348
ZNF256	TMEM248	Q9NWD8	326
ZNF256	GRAMD1C	Q8IYS0	322
ZNF256	DCAF4	Q8WV16	320
ZNF256	SDR42E1	Q8WUS8	319
ZNF256	TTC38	Q5R3I4	305
ZNF256	SCAND3	Q6R2W3	305
ZNF256	ERVMER34-1	Q9H9K5	305
ZNF256	ABTB3	A6QL63	299

IntAct

5 interactions, top by confidence:

A	B	Type	Score
KRTAP10-7	ZNF256	psi-mi:“MI:0915”(physical association)	0.560
ZNF256	TRIM28	psi-mi:“MI:0915”(physical association)	0.400
C9orf72	CHD2	psi-mi:“MI:0914”(association)	0.350
ZNF256	KRTAP10-7	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (4): KRTAP10-7 (Two-hybrid), ZNF256 (Affinity Capture-RNA), ZNF256 (Positive Genetic), TRIM28 (Affinity Capture-Western)

ESM2 similar proteins: A0JNB1, A1YF12, A1YG88, A2T759, B2RUI1, O43296, O75123, P10072, P17020, P17021, P17097, P51814, P52740, P52741, 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, Q8TAU3

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	71
Likely benign	9
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

269 predictions. Top by Δscore:

Variant	Effect	Δscore
19:57947437:CATA:C	donor_loss	1.0000
19:57947438:ATAC:A	donor_loss	1.0000
19:57947439:TA:T	donor_loss	1.0000
19:57947440:A:AC	donor_gain	1.0000
19:57947441:C:CC	donor_gain	1.0000
19:57947441:C:G	donor_loss	1.0000
19:57942644:CCAC:C	acceptor_gain	0.9900
19:57942645:CAC:C	acceptor_gain	0.9900
19:57942645:CACC:C	acceptor_gain	0.9900
19:57942647:CCTGA:C	acceptor_loss	0.9900
19:57942648:C:CG	acceptor_loss	0.9900
19:57942649:T:A	acceptor_loss	0.9900
19:57943927:ACCTT:A	donor_loss	0.9900
19:57943928:CCTT:C	donor_loss	0.9900
19:57943929:CTT:C	donor_loss	0.9900
19:57943930:TTAC:T	donor_loss	0.9900
19:57943931:TA:T	donor_loss	0.9900
19:57943932:ACCCA:A	donor_loss	0.9900
19:57943932:A:AC	donor_gain	0.9800
19:57943933:C:CC	donor_gain	0.9800
19:57947440:AC:A	donor_gain	0.9800
19:57947441:CC:C	donor_gain	0.9800
19:57942648:C:CC	acceptor_gain	0.9700
19:57943932:AC:A	donor_gain	0.9700
19:57943933:CC:C	donor_gain	0.9700
19:57944057:TGCC:T	acceptor_gain	0.9700
19:57944079:A:C	acceptor_gain	0.9700
19:57944059:CC:C	acceptor_gain	0.9600
19:57944060:CC:C	acceptor_gain	0.9600
19:57944059:CCCT:C	acceptor_loss	0.9500

AlphaMissense

4210 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:57941308:A:C	F500L	0.996
19:57941308:A:T	F500L	0.996
19:57941310:A:G	F500L	0.996
19:57941644:A:C	F388L	0.996
19:57941644:A:T	F388L	0.996
19:57941646:A:G	F388L	0.996
19:57941056:A:C	F584L	0.995
19:57941056:A:T	F584L	0.995
19:57941058:A:G	F584L	0.995
19:57941140:A:C	F556L	0.995
19:57941140:A:T	F556L	0.995
19:57941142:A:G	F556L	0.995
19:57941812:A:C	F332L	0.993
19:57941812:A:T	F332L	0.993
19:57941814:A:G	F332L	0.993
19:57941728:A:C	F360L	0.992
19:57941728:A:T	F360L	0.992
19:57941730:A:G	F360L	0.992
19:57941392:A:C	F472L	0.991
19:57941392:A:T	F472L	0.991
19:57941394:A:G	F472L	0.991
19:57941627:A:G	L394P	0.991
19:57941039:A:G	L590P	0.990
19:57941224:A:C	F528L	0.988
19:57941224:A:T	F528L	0.988
19:57941226:A:G	F528L	0.988
19:57941783:T:G	Q342P	0.988
19:57941896:A:C	F304L	0.988
19:57941896:A:T	F304L	0.988
19:57941898:A:G	F304L	0.988

dbSNP variants (sampled 300 via entrez): RS1000137206 (19:57945863 C>A), RS1000330065 (19:57949339 C>A,T), RS1000412719 (19:57943325 G>A), RS1000694413 (19:57943845 T>C,G), RS1000725051 (19:57943579 T>C), RS1000795712 (19:57942731 C>A), RS1001088617 (19:57948328 T>A,C), RS1001208286 (19:57946873 T>C), RS1001355942 (19:57940660 T>C,G), RS1001804093 (19:57948450 A>G), RS1001848820 (19:57943754 A>C), RS1002141961 (19:57948143 A>G,T), RS1002236222 (19:57947777 C>G), RS1002493543 (19:57941047 G>A,C), RS1002611607 (19:57948164 C>A,T)

Disease associations

OMIM: gene MIM:606956 | 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

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
TAK-243	increases sumoylation	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases expression, increases abundance	1
propionaldehyde	increases expression	1
sodium arsenite	decreases expression	1
butyraldehyde	increases expression	1
cupric oxide	increases expression	1
methacrylaldehyde	increases expression, increases abundance, affects cotreatment	1
di-n-butylphosphoric acid	affects 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	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Temozolomide	increases expression	1
Acrolein	affects cotreatment, increases expression, increases abundance	1
Air Pollutants	affects cotreatment, increases abundance, increases expression	1
Atrazine	decreases expression	1
Benzo(a)pyrene	decreases methylation	1
Cadmium	decreases expression	1
Ozone	affects cotreatment, increases expression, increases abundance	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Valproic Acid	decreases expression	1
Zinc	decreases expression	1
Aflatoxin B1	increases methylation	1
Fluorescein-5-isothiocyanate	affects binding	1
Copper Sulfate	increases expression	1
Volatile Organic Compounds	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

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