ZNF878

Summary

ZNF878 (zinc finger protein 878, HGNC:37246) is a protein-coding gene on chromosome 19p13.2, encoding Zinc finger protein 878 (C9JN71). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription 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 729747 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 7 total
• MANE Select transcript: NM_001080404

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:37246
Approved symbol	ZNF878
Name	zinc finger protein 878
Location	19p13.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000257446
Ensembl biotype	protein_coding
Entrez	729747

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000547628, ENST00000929191

RefSeq mRNA: 1 — MANE Select: NM_001080404 NM_001080404

CCDS: CCDS45984

Canonical transcript exons

ENST00000547628 — 4 exons

Exon	Start	End
ENSE00002351857	12052799	12052961
ENSE00003476818	12046368	12046428
ENSE00003499367	12046634	12046760
ENSE00003544954	12043805	12045209

Expression profiles

Bgee: expression breadth ubiquitous, 122 present calls, max score 75.80.

FANTOM5 (CAGE): breadth broad, TPM avg 1.5280 / max 58.7241, expressed in 479 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
179285	1.5280	479

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	75.80	gold quality
placenta	UBERON:0001987	60.10	gold quality
endometrium	UBERON:0001295	57.58	gold quality
metanephros cortex	UBERON:0010533	56.84	gold quality
ventricular zone	UBERON:0003053	56.69	gold quality
ganglionic eminence	UBERON:0004023	56.23	gold quality
right ovary	UBERON:0002118	55.61	gold quality
islet of Langerhans	UBERON:0000006	55.44	gold quality
tonsil	UBERON:0002372	55.30	gold quality
bone marrow	UBERON:0002371	55.23	gold quality
right adrenal gland	UBERON:0001233	55.07	gold quality
stromal cell of endometrium	CL:0002255	55.03	silver quality
adult mammalian kidney	UBERON:0000082	54.93	gold quality
right adrenal gland cortex	UBERON:0035827	54.61	gold quality
pancreas	UBERON:0001264	54.58	gold quality
body of pancreas	UBERON:0001150	54.52	gold quality
cortex of kidney	UBERON:0001225	54.46	gold quality
kidney	UBERON:0002113	54.44	gold quality
left adrenal gland	UBERON:0001234	54.35	gold quality
left ovary	UBERON:0002119	54.28	gold quality
ovary	UBERON:0000992	53.84	gold quality
myometrium	UBERON:0001296	53.04	gold quality
cerebellar cortex	UBERON:0002129	52.80	gold quality
left adrenal gland cortex	UBERON:0035825	52.78	gold quality
cerebellum	UBERON:0002037	52.72	gold quality
cerebellar hemisphere	UBERON:0002245	52.65	gold quality
smooth muscle tissue	UBERON:0001135	52.26	gold quality
colonic epithelium	UBERON:0000397	52.19	gold quality
adrenal gland	UBERON:0002369	52.17	gold quality
lower esophagus	UBERON:0013473	52.12	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.26

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA2574.1	ZNF878	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:39605320

Upstream regulators (CollecTRI, top): STAT1

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp867	ENSMUSG00000054519
rattus_norvegicus	Zfp867	ENSRNOG00000022431

Paralogs (15): ZNF14 (ENSG00000105708), ZNF57 (ENSG00000171970), ZNF791 (ENSG00000173875), ZNF443 (ENSG00000180855), ZNF101 (ENSG00000181896), ZNF563 (ENSG00000188868), ZNF799 (ENSG00000196466), ZNF700 (ENSG00000196757), ZNF441 (ENSG00000197044), ZNF433 (ENSG00000197647), ZNF44 (ENSG00000197857), ZNF823 (ENSG00000197933), ZNF442 (ENSG00000198342), ZNF844 (ENSG00000223547), ZNF709 (ENSG00000242852)

Protein

Protein identifiers

Zinc finger protein 878 — C9JN71 (reviewed: C9JN71)

All UniProt accessions (1): C9JN71

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 (1): NP_001073873* (*=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 (17 total): zinc finger region 15, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-C9JN71-F1	78.93	0.44

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 27 (showing top): FOSTER_TOLERANT_MACROPHAGE_DN, BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_CIS, TSENG_IRS1_TARGETS_DN, ZHANG_BREAST_CANCER_PROGENITORS_UP, chr19p13, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, MIKKELSEN_ES_ICP_WITH_H3K4ME3, BAKKER_FOXO3_TARGETS_DN, TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, GSE7568_CTRL_VS_24H_TGFB_TREATED_MACROPHAGES_WITH_IL4_AND_DEXAMETHASONE_UP, MANNO_MIDBRAIN_NEUROTYPES_HPROGBP, MANNO_MIDBRAIN_NEUROTYPES_HNBM, MANNO_MIDBRAIN_NEUROTYPES_HNBML1, GOMF_DNA_BINDING_TRANSCRIPTION_FACTOR_ACTIVITY

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 transcription regulatory region sequence-specific DNA binding (GO:0000977), 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
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
transcription cis-regulatory region binding	1
chromatin	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	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

142 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF878	C8orf48	Q96LL4	578
ZNF878	FHIP2A	Q5W0V3	419
ZNF878	ZNF704	Q6ZNC4	358
ZNF878	DNAAF3	Q8N9W5	305
ZNF878	ADAP1	O75689	304
ZNF878	DMRTA2	Q96SC8	302
ZNF878	CREB3L4	Q8TEY5	296
ZNF878	PAFAH1B3	Q15102	276
ZNF878	ZNF451	Q9Y4E5	272
ZNF878	IVD	P26440	272
ZNF878	CYTL1	Q9NRR1	257
ZNF878	THOP1	P52888	251
ZNF878	RABAC1	Q9UI14	250
ZNF878	SAMSN1	Q9NSI8	248
ZNF878	NIPA1	Q7RTP0	243

IntAct

4 interactions, top by confidence:

A	B	Type	Score
ZNF878	H2BC9	psi-mi:“MI:0915”(physical association)	0.400
ZNF878	ECE1	psi-mi:“MI:0915”(physical association)	0.370
INSR	RIMOC1	psi-mi:“MI:0914”(association)	0.350

BioGRID (6): HIST1H2BH (Proximity Label-MS), ZNF878 (Protein-peptide), ZNF878 (Affinity Capture-MS), KIF5B (Cross-Linking-MS (XL-MS)), ZNF878 (Proximity Label-MS), ZNF878 (Proximity Label-MS)

ESM2 similar proteins: A6NDX5, A6NK75, A6NNF4, A6NP11, B4DXR9, B7Z6K7, C9JN71, O43361, O75290, O75373, P0CJ79, P0DKX0, P17019, P17021, P17035, P17039, P35789, Q02386, Q03938, Q08AN1, Q13106, Q15928, Q3ZCX4, Q5R9F0, Q5SXM1, Q68EA5, Q6P9A1, Q6PDB4, Q6ZN06, Q6ZN08, Q6ZNG1, Q76KX8, Q86V71, Q86XN6, Q8IYB9, Q8N4W9, Q8NEP9, Q8TBZ8, Q8TC21, Q8TF32

Diamond homologs: A0JPK3, A8MT65, C9JN71, E9QAG8, G3X9G7, O75820, P16373, P16374, P16415, P17017, P17024, P17025, P51815, P52737, Q08AG5, Q08ER8, Q0D2J5, Q15973, Q2M218, Q3KP31, Q3V080, Q494X3, Q4R4C7, Q5MYW4, Q5R9F0, Q5R9S5, Q5REI6, Q5REK1, Q68EA5, Q6P560, Q6P5C7, Q6ZQV5, Q7L945, Q86T29, Q8BGV5, Q8C6P8, Q8IYI8, Q8IZC7, Q8N7K0, Q8N972

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

666 predictions. Top by Δscore:

Variant	Effect	Δscore
19:12046628:TCTTA:T	donor_loss	1.0000
19:12046629:CTTA:C	donor_loss	1.0000
19:12046630:TTA:T	donor_loss	1.0000
19:12046632:A:AC	donor_gain	1.0000
19:12046633:C:CC	donor_gain	1.0000
19:12046771:CCACA:C	acceptor_gain	1.0000
19:12046772:CACA:C	acceptor_gain	1.0000
19:12046775:A:C	acceptor_gain	1.0000
19:12052794:CTCA:C	donor_loss	1.0000
19:12052795:TCA:T	donor_loss	1.0000
19:12052796:CACCA:C	donor_loss	1.0000
19:12052798:C:CT	donor_loss	1.0000
19:12045207:CTT:C	acceptor_gain	0.9900
19:12045208:TT:T	acceptor_gain	0.9900
19:12045210:C:CC	acceptor_gain	0.9900
19:12046443:C:T	acceptor_gain	0.9900
19:12046672:T:TA	donor_gain	0.9900
19:12046673:C:A	donor_gain	0.9900
19:12046759:TC:T	acceptor_gain	0.9900
19:12046759:TCCTG:T	acceptor_loss	0.9900
19:12046760:CC:C	acceptor_gain	0.9900
19:12046760:CCTG:C	acceptor_loss	0.9900
19:12046760:CCTGA:C	acceptor_loss	0.9900
19:12046772:C:T	acceptor_gain	0.9900
19:12046774:CA:C	acceptor_gain	0.9900
19:12046775:A:AC	acceptor_gain	0.9900
19:12052129:CA:C	donor_gain	0.9900
19:12052797:A:AC	donor_gain	0.9900
19:12052797:AC:A	donor_gain	0.9900
19:12052798:C:CC	donor_gain	0.9900

AlphaMissense

3538 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:12044357:G:C	F348L	0.992
19:12044357:G:T	F348L	0.992
19:12044359:A:G	F348L	0.992
19:12043853:A:C	F516L	0.986
19:12043853:A:T	F516L	0.986
19:12043855:A:G	F516L	0.986
19:12044189:G:C	F404L	0.986
19:12044189:G:T	F404L	0.986
19:12044191:A:G	F404L	0.986
19:12043937:G:C	F488L	0.984
19:12043937:G:T	F488L	0.984
19:12043939:A:G	F488L	0.984
19:12044021:G:C	F460L	0.984
19:12044021:G:T	F460L	0.984
19:12044023:A:G	F460L	0.984
19:12044525:G:C	F292L	0.983
19:12044525:G:T	F292L	0.983
19:12044527:A:G	F292L	0.983
19:12044162:G:C	H413Q	0.982
19:12044162:G:T	H413Q	0.982
19:12044105:A:C	F432L	0.981
19:12044105:A:T	F432L	0.981
19:12044107:A:G	F432L	0.981
19:12044441:A:C	F320L	0.981
19:12044441:A:T	F320L	0.981
19:12044443:A:G	F320L	0.981
19:12044269:A:G	S378P	0.978
19:12044437:A:G	S322P	0.977
19:12044861:G:C	F180L	0.977
19:12044861:G:T	F180L	0.977

dbSNP variants (sampled 300 via entrez): RS1000060186 (19:12047996 A>G), RS1000189957 (19:12047779 G>A), RS1000196831 (19:12051498 G>A), RS1000270526 (19:12051832 G>A), RS1000529517 (19:12050142 T>C), RS1000603150 (19:12050341 C>T), RS1000791658 (19:12043175 A>G), RS1000999203 (19:12052269 A>G), RS1001201470 (19:12052938 A>C,G), RS1001462058 (19:12046038 T>A), RS1001600155 (19:12047053 A>C,G), RS1001829695 (19:12045852 A>G), RS1001886312 (19:12045477 C>A,G,T), RS1002497854 (19:12051888 A>G), RS1002763096 (19:12050203 C>A,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

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
methyleugenol	increases expression	1
2-methyl-4-isothiazolin-3-one	increases expression	1
Benzo(a)pyrene	increases methylation	1
Oxygen	decreases expression	1
Smoke	decreases expression	1
Urethane	increases expression	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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