ZNF880

Summary

ZNF880 (zinc finger protein 880, HGNC:37249) is a protein-coding gene on chromosome 19q13.41, encoding Zinc finger protein 880 (Q6PDB4).

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. Predicted to be active in nucleus.

Source: NCBI Gene 400713 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 101 total
• MANE Select transcript: NM_001145434

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:37249
Approved symbol	ZNF880
Name	zinc finger protein 880
Location	19q13.41
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000221923
Ensembl biotype	protein_coding
Entrez	400713

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 7 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000344085, ENST00000422689, ENST00000424032, ENST00000595099, ENST00000597976, ENST00000600321, ENST00000906539, ENST00000945824

RefSeq mRNA: 1 — MANE Select: NM_001145434 NM_001145434

CCDS: CCDS46164

Canonical transcript exons

ENST00000422689 — 4 exons

Exon	Start	End
ENSE00001603012	52383849	52385795
ENSE00002262616	52369923	52369977
ENSE00002440969	52373111	52373237
ENSE00002513520	52374299	52374427

Expression profiles

Bgee: expression breadth ubiquitous, 235 present calls, max score 96.20.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.4742 / max 221.5980, expressed in 1562 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177302	12.4742	1562

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	96.20	gold quality
calcaneal tendon	UBERON:0003701	91.76	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.14	gold quality
tendon	UBERON:0000043	86.32	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	86.14	gold quality
tendon of biceps brachii	UBERON:0008188	85.05	gold quality
sural nerve	UBERON:0015488	84.71	gold quality
apex of heart	UBERON:0002098	84.55	gold quality
islet of Langerhans	UBERON:0000006	84.53	gold quality
left ovary	UBERON:0002119	84.36	gold quality
ganglionic eminence	UBERON:0004023	84.08	gold quality
lower esophagus muscularis layer	UBERON:0035833	84.05	gold quality
cortical plate	UBERON:0005343	84.04	gold quality
lower esophagus	UBERON:0013473	83.97	gold quality
smooth muscle tissue	UBERON:0001135	83.93	gold quality
popliteal artery	UBERON:0002250	83.79	gold quality
tibial artery	UBERON:0007610	83.79	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.74	gold quality
right atrium auricular region	UBERON:0006631	83.59	gold quality
right uterine tube	UBERON:0001302	83.50	gold quality
left lobe of thyroid gland	UBERON:0001120	83.47	gold quality
thyroid gland	UBERON:0002046	83.38	gold quality
right adrenal gland	UBERON:0001233	83.05	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	83.03	gold quality
right ovary	UBERON:0002118	82.89	gold quality
heart left ventricle	UBERON:0002084	82.84	gold quality
aorta	UBERON:0000947	82.72	gold quality
right lobe of thyroid gland	UBERON:0001119	82.71	gold quality
ventricular zone	UBERON:0003053	82.59	gold quality
muscle layer of sigmoid colon	UBERON:0035805	82.56	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.60

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

34 targeting ZNF880, 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-7110-3P	100.00	73.18	2486
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-544A	99.84	68.66	1965
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-2052	99.79	69.37	2031
HSA-MIR-567	99.63	68.57	1219
HSA-MIR-4499	99.62	67.29	1470
HSA-MIR-12131	99.48	68.72	1673
HSA-MIR-183-3P	99.41	69.41	1598
HSA-MIR-297	99.40	69.58	1418
HSA-MIR-155-5P	99.35	70.16	1509
HSA-MIR-329-5P	99.27	68.11	1597
HSA-MIR-3164	99.02	68.39	1071
HSA-MIR-6820-3P	99.02	68.50	1035
HSA-MIR-3146	98.85	66.77	601
HSA-MIR-5590-5P	98.81	68.78	969
HSA-MIR-8060	98.61	66.93	1187
HSA-MIR-374C-3P	98.47	67.93	451
HSA-MIR-6771-3P	98.20	66.53	971
HSA-MIR-4659B-5P	98.03	66.84	979
HSA-MIR-4659A-5P	98.03	66.42	819
HSA-MIR-6514-3P	97.52	66.50	808
HSA-MIR-4535	97.27	65.17	469
HSA-MIR-3156-5P	96.93	67.36	800

Literature-anchored findings (GeneRIF, showing 1)

• Promoter hypermethylation and comprehensive regulation of ncRNA lead to the down-regulation of ZNF880, providing a new insight for the therapeutics and research of colorectal cancer. (PMID:37370088)

Cross-species orthologs

0 orthologs

Paralogs (176): ZNF195 (ENSG00000005801), ZNF112 (ENSG00000062370), ZNF275 (ENSG00000063587), ZNF37A (ENSG00000075407), ZNF510 (ENSG00000081386), ZNF506 (ENSG00000081665), ZNF268 (ENSG00000090612), MZF1 (ENSG00000099326), ZNF629 (ENSG00000102870), ZNF175 (ENSG00000105497), ZNF85 (ENSG00000105750), ZFP30 (ENSG00000120784), ZNF45 (ENSG00000124459), ZNF391 (ENSG00000124613), ZNF436 (ENSG00000125945), ZNF484 (ENSG00000127081), ZNF835 (ENSG00000127903), ZNF780B (ENSG00000128000), ZSCAN10 (ENSG00000130182), ZNF317 (ENSG00000130803), ZNF331 (ENSG00000130844), ZNF227 (ENSG00000131115), ZNF141 (ENSG00000131127), ZNF132 (ENSG00000131849), ZNF189 (ENSG00000136870), ZIM3 (ENSG00000141946), ZFP14 (ENSG00000142065), ZNF514 (ENSG00000144026), ZNF300 (ENSG00000145908), RBAK (ENSG00000146587), ZNF157 (ENSG00000147117), ZNF182 (ENSG00000147118), ZNF41 (ENSG00000147124), ZNF7 (ENSG00000147789), ZNF117 (ENSG00000152926), ZNF221 (ENSG00000159905), ZNF235 (ENSG00000159917), ZNF714 (ENSG00000160352), ZNF577 (ENSG00000161551), ZNF12 (ENSG00000164631)

Protein

Protein identifiers

Zinc finger protein 880 — Q6PDB4 (reviewed: Q6PDB4)

All UniProt accessions (3): Q6PDB4, F5H026, M0R0M5

Isoforms (2)

UniProt ID	Names	Canonical?
Q6PDB4-1	1	yes
Q6PDB4-2	2

RefSeq proteins (1): NP_001138906* (*=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

UniProt features (18 total): zinc finger region 14, splice variant 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6PDB4-F1	69.76	0.13

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 34 (showing top): SCHMAHL_PDGF_SIGNALING, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN, BOCHKIS_FOXA2_TARGETS, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, DODD_NASOPHARYNGEAL_CARCINOMA_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, HMGA1_TARGET_GENES, MIR7110_3P, MIR1184, MIR4776_3P, MIR5590_5P, MIR6771_3P, JINESH_BLEBBISHIELD_VS_LIVE_CONTROL_UP, JINESH_BLEBBISHIELD_TRANSFORMED_STEM_CELL_SPHERES_DN, DESCARTES_FETAL_LUNG_CSH1_CSH2_POSITIVE_CELLS

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

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 (2): nucleus (GO:0005634), nuclear lumen (GO:0031981)

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
cation binding	1
intracellular membrane-bounded organelle	1
nucleus	1
intracellular organelle lumen	1

Protein interactions and networks

STRING

306 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF880	OR2T12	Q8NG77	507
ZNF880	CLLU1-AS1	Q5K130	477
ZNF880	OR2D3	Q8NGH3	471
ZNF880	PLIN4	Q96Q06	437
ZNF880	SAMD10	Q9BYL1	418
ZNF880	SLFN5	Q08AF3	410
ZNF880	CCDC144NL	Q6NUI1	400
ZNF880	CFAP276	Q5T5A4	392
ZNF880	METTL27	Q8N6F8	374
ZNF880	CCDC126	Q96EE4	373
ZNF880	MOB3C	Q70IA8	349
ZNF880	XRRA1	Q6P2D8	349
ZNF880	GRAMD1C	Q8IYS0	349
ZNF880	FAM53A	Q6NSI3	348
ZNF880	CNBD1	Q8NA66	348

IntAct

0 interactions, top by confidence:

BioGRID (3): ZNF880 (Affinity Capture-MS), ZNF880 (Proximity Label-MS), ZNF880 (Affinity Capture-RNA)

ESM2 similar proteins: A2VDP4, A6NHJ4, O94892, P0CJ79, P17014, P17021, P17025, P17032, P17035, P18733, P51508, P51814, Q06730, Q06732, Q09FC8, Q0VGE8, Q14586, Q32M78, Q3MIS6, Q5JVG2, Q5R4K8, Q5R9S5, Q5RBQ3, Q5RCJ2, Q5RER9, Q5TYW1, Q5VIY5, Q6P560, Q6PDB4, Q6ZMW2, Q6ZN06, Q6ZNA1, Q76KX8, Q7L2R6, Q86Y25, Q8N184, Q8N823, Q8N883, Q8N8J6, Q8NEP9

Diamond homologs: A0A1W2PQL4, A2RRD8, A2VDQ7, A6NHJ4, A6NK75, A6NN14, A6NNF4, A6NP11, B4DX44, B4DXR9, E9PW05, O14628, O43345, O75290, O75346, O75373, O75820, P0CB33, P0CJ79, P0DKX0, P10755, P17032, P17035, P52738, Q02386, Q03923, Q03936, Q05481, Q08AN1, Q09FC8, Q0VGE8, Q14586, Q14593, Q147U1, Q15928, Q3MIS6, Q3SXZ3, Q494X3, Q4R6C2, Q5HY98

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	89
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

607 predictions. Top by Δscore:

Variant	Effect	Δscore
19:52373198:G:GT	donor_gain	1.0000
19:52374402:G:GT	donor_gain	1.0000
19:52369978:G:GG	donor_gain	0.9900
19:52373107:TTAG:T	acceptor_loss	0.9900
19:52373108:TAGG:T	acceptor_loss	0.9900
19:52373109:A:AG	acceptor_gain	0.9900
19:52373109:A:T	acceptor_loss	0.9900
19:52373109:AG:A	acceptor_gain	0.9900
19:52373110:G:C	acceptor_loss	0.9900
19:52373110:G:GG	acceptor_gain	0.9900
19:52373110:GG:G	acceptor_gain	0.9900
19:52373110:GGGAC:G	acceptor_gain	0.9900
19:52373198:G:T	donor_gain	0.9900
19:52373221:G:GT	donor_gain	0.9900
19:52373236:GG:G	donor_gain	0.9900
19:52373237:GG:G	donor_gain	0.9900
19:52373237:GGT:G	donor_loss	0.9900
19:52373238:G:C	donor_loss	0.9900
19:52373239:T:A	donor_loss	0.9900
19:52373240:G:GG	donor_loss	0.9900
19:52373243:GA:G	donor_gain	0.9900
19:52374296:TA:T	acceptor_loss	0.9900
19:52374298:G:GA	acceptor_loss	0.9900
19:52374298:GGA:G	acceptor_gain	0.9900
19:52374397:G:GA	donor_gain	0.9900
19:52374425:CAGG:C	donor_loss	0.9900
19:52374426:AGG:A	donor_loss	0.9900
19:52374427:GG:G	donor_loss	0.9900
19:52374428:GT:G	donor_loss	0.9900
19:52374429:T:A	donor_loss	0.9900

AlphaMissense

3859 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:52385249:T:C	F557L	0.994
19:52385251:C:A	F557L	0.994
19:52385251:C:G	F557L	0.994
19:52384409:T:C	F277L	0.993
19:52384411:C:A	F277L	0.993
19:52384411:C:G	F277L	0.993
19:52384997:T:C	F473L	0.993
19:52384999:C:A	F473L	0.993
19:52384999:C:G	F473L	0.993
19:52385081:T:C	F501L	0.993
19:52385083:T:A	F501L	0.993
19:52385083:T:G	F501L	0.993
19:52384493:T:C	F305L	0.991
19:52384495:C:A	F305L	0.991
19:52384495:C:G	F305L	0.991
19:52384325:T:C	F249L	0.986
19:52384327:C:A	F249L	0.986
19:52384327:C:G	F249L	0.986
19:52384577:T:C	F333L	0.985
19:52384579:T:A	F333L	0.985
19:52384579:T:G	F333L	0.985
19:52384829:T:C	F417L	0.985
19:52384831:T:A	F417L	0.985
19:52384831:T:G	F417L	0.985
19:52384332:G:C	R251P	0.984
19:52385004:G:C	R475P	0.984
19:52385026:T:A	H482Q	0.984
19:52385026:T:G	H482Q	0.984
19:52385165:T:C	F529L	0.984
19:52385167:C:A	F529L	0.984

dbSNP variants (sampled 300 via entrez): RS1000137941 (19:52397623 A>G), RS1000162342 (19:52373851 A>T), RS1000406233 (19:52384939 T>C), RS1000441307 (19:52392186 T>A), RS1000499454 (19:52375156 T>C), RS1000626841 (19:52386685 C>G), RS1000634391 (19:52378402 T>C), RS1000635204 (19:52374822 G>C), RS1000715596 (19:52388487 G>A), RS1000882355 (19:52397389 C>A), RS1000984949 (19:52368413 G>A), RS1001004205 (19:52369567 G>C), RS1001146987 (19:52381259 A>G), RS1001166058 (19:52369754 C>G), RS1001285244 (19:52375170 T>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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Valproic Acid	affects expression, decreases expression	2
GSK-J4	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
propionaldehyde	increases expression	1
butyraldehyde	increases expression	1
pentanal	increases expression	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
dorsomorphin	affects cotreatment, decreases expression	1
Sunitinib	increases expression	1
Aldehydes	increases expression	1
Benzo(a)pyrene	decreases methylation	1
Cadmium	increases abundance, increases expression	1
Camptothecin	increases expression	1
Estradiol	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Cadmium Chloride	increases expression, increases abundance	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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