ZNF879

Summary

ZNF879 (zinc finger protein 879, HGNC:37273) is a protein-coding gene on chromosome 5q35.3, encoding Zinc finger protein 879 (B4DU55). May be involved in transcriptional regulation.

This gene encodes a kruppel-associated box-containing zinc finger protein (KRAB-ZFP). The encoded protein contains an N-terminal kruppel-associated box (KRAB) domain and thirteen C-terminal C2H2-type zinc finger domains. The KRAB-ZFPs represent the largest family of mammalian transcriptional repressors, which function through the recruitment of the nuclear co-factor KRAB-Associated Protein 1 (KAP1), to engage histone modifiers and induce heterochromatin formation.

Source: NCBI Gene 345462 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 79 total
• MANE Select transcript: NM_001136116

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:37273
Approved symbol	ZNF879
Name	zinc finger protein 879
Location	5q35.3
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp686E2433
Ensembl gene	ENSG00000234284
Ensembl biotype	protein_coding
Entrez	345462

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 11 protein_coding

ENST00000444149, ENST00000519896, ENST00000521285, ENST00000522442, ENST00000866182, ENST00000866183, ENST00000866184, ENST00000866185, ENST00000866186, ENST00000913246, ENST00000959254

RefSeq mRNA: 4 — MANE Select: NM_001136116 NM_001136116, NM_001353372, NM_001353373, NM_001353374

CCDS: CCDS47352

Canonical transcript exons

ENST00000444149 — 5 exons

Exon	Start	End
ENSE00001621331	179024970	179025037
ENSE00001767553	179032205	179035064
ENSE00002111968	179023804	179023904
ENSE00002435866	179027473	179027599
ENSE00003689725	179028032	179028127

Expression profiles

Bgee: expression breadth ubiquitous, 204 present calls, max score 87.29.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 2.7463 / max 41.2517, expressed in 1239 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
60535	2.1753	1083
60536	0.5710	322

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pancreatic ductal cell	CL:0002079	87.29	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.65	gold quality
secondary oocyte	CL:0000655	82.68	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.54	gold quality
tibialis anterior	UBERON:0001385	81.83	silver quality
epithelial cell of pancreas	CL:0000083	76.21	silver quality
deltoid	UBERON:0001476	74.79	silver quality
cortical plate	UBERON:0005343	74.65	gold quality
palpebral conjunctiva	UBERON:0001812	74.64	gold quality
oocyte	CL:0000023	74.23	gold quality
ileal mucosa	UBERON:0000331	74.22	gold quality
calcaneal tendon	UBERON:0003701	73.81	gold quality
stromal cell of endometrium	CL:0002255	73.04	gold quality
ventricular zone	UBERON:0003053	72.70	gold quality
cerebellar hemisphere	UBERON:0002245	71.95	gold quality
right hemisphere of cerebellum	UBERON:0014890	71.92	gold quality
cerebellar cortex	UBERON:0002129	71.80	gold quality
ganglionic eminence	UBERON:0004023	71.76	gold quality
granulocyte	CL:0000094	71.26	gold quality
islet of Langerhans	UBERON:0000006	71.23	gold quality
hindlimb stylopod muscle	UBERON:0004252	70.96	gold quality
apex of heart	UBERON:0002098	70.67	gold quality
leukocyte	CL:0000738	70.65	gold quality
muscle of leg	UBERON:0001383	70.65	gold quality
cerebellum	UBERON:0002037	70.57	gold quality
monocyte	CL:0000576	70.48	gold quality
smooth muscle tissue	UBERON:0001135	70.44	gold quality
gastrocnemius	UBERON:0001388	70.25	gold quality
lower esophagus muscularis layer	UBERON:0035833	68.67	gold quality
lower esophagus	UBERON:0013473	68.66	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.07

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): STAT1

miRNA regulators (miRDB)

39 targeting ZNF879, 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-3613-3P	100.00	76.36	7965
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-3934-3P	99.76	65.51	1351
HSA-MIR-5580-3P	99.70	69.41	2052
HSA-MIR-1290	99.59	69.90	2079
HSA-MIR-3120-3P	99.54	70.28	2669
HSA-MIR-3609	99.52	69.89	2587
HSA-MIR-548AH-5P	99.52	69.73	2626
HSA-MIR-486-5P	99.51	70.39	707
HSA-MIR-136-5P	99.50	67.26	1153
HSA-MIR-4687-3P	99.48	66.41	968
HSA-MIR-4728-3P	99.47	68.94	981
HSA-MIR-889-5P	99.41	68.75	1025
HSA-MIR-5697	99.39	67.74	1249
HSA-MIR-135A-5P	99.36	71.85	1601
HSA-MIR-135B-5P	99.36	71.63	1613
HSA-MIR-584-3P	99.35	67.69	1082
HSA-MIR-145-3P	99.33	67.66	764
HSA-MIR-7974	99.24	65.48	1137
HSA-MIR-593-3P	99.22	67.28	1327
HSA-MIR-6814-5P	99.03	66.68	1273
HSA-MIR-155-3P	99.03	67.99	924
HSA-MIR-3164	99.02	68.39	1071
HSA-MIR-6820-3P	99.02	68.50	1035
HSA-MIR-384	98.71	67.34	1229
HSA-MIR-34B-3P	98.70	67.40	1171

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp879	ENSMUSG00000044296
rattus_norvegicus	Zfp879	ENSRNOG00000030517

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 879 — B4DU55 (reviewed: B4DU55)

All UniProt accessions (4): B4DU55, E5RGZ8, E5RI37, E5RJY9

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.

RefSeq proteins (4): NP_001129588, NP_001340301, NP_001340302, NP_001340303 (=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 13, sequence conflict 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-B4DU55-F1	70.43	0.26

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 62 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_DN, OSMAN_BLADDER_CANCER_DN, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, MIKKELSEN_ES_ICP_WITH_H3K4ME3, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, KAT5_TARGET_GENES, RYBP_TARGET_GENES, SUPT16H_TARGET_GENES, ZBTB12_TARGET_GENES, ZNF274_TARGET_GENES, ZNF331_TARGET_GENES, ZNF407_TARGET_GENES, ZNF610_TARGET_GENES, ZNF711_TARGET_GENES

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

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
nucleic acid binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

186 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF879	ZAR1L	A6NP61	584
ZNF879	ZNF385B	Q569K4	418
ZNF879	GBX1	Q14549	392
ZNF879	NPM2	Q86SE8	370
ZNF879	KCNF1	Q9H3M0	367
ZNF879	BTG4	Q9NY30	355
ZNF879	WEE2	P0C1S8	355
ZNF879	SMC1B	Q8NDV3	321
ZNF879	TEAD3	Q99594	302
ZNF879	PM20D2	Q8IYS1	295
ZNF879	HES6	Q96HZ4	272
ZNF879	LITAF	Q99732	248
ZNF879	CELSR1	Q9NYQ6	246
ZNF879	ZFP36L1	Q07352	242
ZNF879	CPEB1	Q9BZB8	237

IntAct

3 interactions, top by confidence:

A	B	Type	Score
ZNF879	ECE1	psi-mi:“MI:0915”(physical association)	0.370
CHAF1B	ZNF879	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (4): ZNF879 (Affinity Capture-RNA), ZNF879 (Affinity Capture-MS), ZNF879 (Affinity Capture-MS), ZNF879 (Two-hybrid)

ESM2 similar proteins: A2RRD8, A6NHJ4, A6NK75, B4DU55, O75346, P0DPD5, P15621, P17030, P17039, P52737, Q0VGE8, Q14588, Q147U1, Q15928, Q2M3X9, Q3KNS6, Q494X3, Q4R6C2, Q5HYK9, Q5R5Q6, Q5R5S6, Q5REA0, Q5REK1, Q60585, Q61751, Q6ECI4, Q6P9Y7, Q6ZN19, Q6ZNA1, Q7Z3V5, Q86T29, Q86WZ6, Q8N141, Q8N7K0, Q8N9F8, Q8NA42, Q8NCK3, Q8NDQ6, Q8NEM1, Q8WV37

Diamond homologs: A0A1W2PQL4, A0JNB1, A0JPL0, A6NK53, A6QLU5, A6QPT6, A7MBI1, A8MT65, A8MUV8, A8MWA4, B2RXC5, B4DU55, B4DX44, E9PYI1, O14628, O75346, P0CH99, P0CI00, P17014, P17030, P17032, P17098, P51786, P85977, Q02386, Q06730, Q06732, Q0VAW7, Q12901, Q13360, Q14586, Q14588, Q14590, Q16587, Q2M3X9, Q2VY69, Q32M78, Q3ZCX4, Q49AA0, Q4R6J4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	68
Likely benign	7
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

900 predictions. Top by Δscore:

Variant	Effect	Δscore
5:179024965:TCCA:T	acceptor_loss	1.0000
5:179024967:CAG:C	acceptor_loss	1.0000
5:179024968:A:AG	acceptor_gain	1.0000
5:179024969:G:GA	acceptor_gain	1.0000
5:179024969:GGT:G	acceptor_gain	1.0000
5:179024969:GGTGC:G	acceptor_gain	1.0000
5:179025035:CAGG:C	donor_loss	1.0000
5:179025038:G:GG	donor_gain	1.0000
5:179027597:TGGGT:T	donor_loss	1.0000
5:179027598:GGGTA:G	donor_loss	1.0000
5:179027599:GGTAA:G	donor_loss	1.0000
5:179024963:A:AG	acceptor_gain	0.9900
5:179024968:AG:A	acceptor_gain	0.9900
5:179024968:AGGT:A	acceptor_gain	0.9900
5:179024969:GG:G	acceptor_gain	0.9900
5:179024969:GGTG:G	acceptor_gain	0.9900
5:179027472:GGA:G	acceptor_gain	0.9900
5:179027598:GG:G	donor_gain	0.9900
5:179027599:GG:G	donor_gain	0.9900
5:179027600:G:GG	donor_gain	0.9900
5:179027601:T:A	donor_loss	0.9900
5:179028027:AACAG:A	acceptor_loss	0.9900
5:179028029:CAGG:C	acceptor_loss	0.9900
5:179028030:A:AG	acceptor_gain	0.9900
5:179028030:AG:A	acceptor_gain	0.9900
5:179028030:AGG:A	acceptor_gain	0.9900
5:179028030:AGGGA:A	acceptor_loss	0.9900
5:179028031:G:GG	acceptor_gain	0.9900
5:179028031:GG:G	acceptor_gain	0.9900
5:179028031:GGG:G	acceptor_gain	0.9900

AlphaMissense

3748 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:179032753:T:C	F269L	0.998
5:179032755:C:A	F269L	0.998
5:179032755:C:G	F269L	0.998
5:179032921:T:C	F325L	0.998
5:179032923:C:A	F325L	0.998
5:179032923:C:G	F325L	0.998
5:179033005:T:C	F353L	0.998
5:179033007:C:A	F353L	0.998
5:179033007:C:G	F353L	0.998
5:179033039:G:C	R364P	0.998
5:179033173:T:C	F409L	0.998
5:179033175:C:A	F409L	0.998
5:179033175:C:G	F409L	0.998
5:179033257:T:C	F437L	0.998
5:179033259:C:A	F437L	0.998
5:179033259:C:G	F437L	0.998
5:179033425:T:C	F493L	0.998
5:179033427:C:A	F493L	0.998
5:179033427:C:G	F493L	0.998
5:179033509:T:C	F521L	0.998
5:179033511:C:A	F521L	0.998
5:179033511:C:G	F521L	0.998
5:179033593:T:C	F549L	0.998
5:179033595:T:A	F549L	0.998
5:179033595:T:G	F549L	0.998
5:179032940:T:C	L331P	0.997
5:179033011:T:C	S355P	0.997
5:179033202:T:A	H418Q	0.997
5:179033202:T:G	H418Q	0.997
5:179033452:C:G	H502D	0.997

dbSNP variants (sampled 300 via entrez): RS1000106398 (5:179034687 A>G), RS1000264654 (5:179023172 A>G), RS1000716792 (5:179024722 A>G), RS1000850498 (5:179033774 C>A,T), RS1001345262 (5:179034006 G>A), RS1001521175 (5:179030917 G>A,T), RS1001624682 (5:179025587 T>C), RS1001661844 (5:179031257 C>T), RS1001669637 (5:179026056 G>T), RS1001729018 (5:179025812 G>C), RS1001940096 (5:179032258 A>T), RS1002005789 (5:179026898 A>G), RS1002012923 (5:179031117 C>T), RS1002515646 (5:179029464 A>G), RS1002545180 (5:179032379 C>T)

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

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, affects expression	3
Air Pollutants	affects expression, increases abundance, decreases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
GSK-J4	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases methylation	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	increases methylation	1
avobenzone	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
MT19c compound	increases expression	1
Benzo(a)pyrene	decreases methylation, affects methylation	1
Methapyrilene	increases methylation	1
Ozone	affects expression, increases abundance	1
Tetrachlorodibenzodioxin	affects expression	1
Cyclosporine	increases expression	1
Aflatoxin M1	decreases expression	1
Cadmium Chloride	increases expression	1
Okadaic Acid	increases expression	1
Particulate Matter	increases abundance, decreases expression	1
Magnetite Nanoparticles	decreases expression	1

Clinical trials (associated diseases)

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