ZNF888

Summary

ZNF888 (zinc finger protein 888, HGNC:38695) is a protein-coding gene on chromosome 19q13.41, encoding Zinc finger protein 888 (P0CJ79). May be involved in transcriptional regulation.

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 388559 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 2 total
• MANE Select transcript: NM_001393938

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:38695
Approved symbol	ZNF888
Name	zinc finger protein 888
Location	19q13.41
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000213793
Ensembl biotype	protein_coding
Entrez	388559

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 5 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000596623, ENST00000638862, ENST00000884820, ENST00000933093, ENST00000933094, ENST00000965350

RefSeq mRNA: 7 — MANE Select: NM_001393938 NM_001310127, NM_001384652, NM_001384653, NM_001384654, NM_001384655, NM_001384656, NM_001393938

CCDS: CCDS86801

Canonical transcript exons

ENST00000638862 — 5 exons

Exon	Start	End
ENSE00003607759	52915196	52915322
ENSE00003802141	52904415	52908179
ENSE00003803065	52917859	52917931
ENSE00003807138	52918819	52918937
ENSE00003807720	52923369	52923428

Expression profiles

Bgee: expression breadth ubiquitous, 137 present calls, max score 93.72.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.7375 / max 61.8116, expressed in 1312 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
182538	2.2610	1033
182539	1.4765	850

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cerebellar vermis	UBERON:0004720	93.72	gold quality
endometrium	UBERON:0001295	91.47	gold quality
thymus	UBERON:0002370	88.48	gold quality
quadriceps femoris	UBERON:0001377	87.34	gold quality
rectum	UBERON:0001052	82.14	gold quality
right uterine tube	UBERON:0001302	80.62	gold quality
prostate gland	UBERON:0002367	79.01	gold quality
metanephros cortex	UBERON:0010533	78.11	gold quality
body of pancreas	UBERON:0001150	77.97	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	77.57	gold quality
pancreas	UBERON:0001264	77.34	gold quality
islet of Langerhans	UBERON:0000006	76.92	gold quality
body of stomach	UBERON:0001161	76.70	gold quality
cortex of kidney	UBERON:0001225	76.08	gold quality
gall bladder	UBERON:0002110	76.07	gold quality
calcaneal tendon	UBERON:0003701	75.95	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	75.87	gold quality
stomach	UBERON:0000945	75.73	gold quality
fallopian tube	UBERON:0003889	75.54	gold quality
urinary bladder	UBERON:0001255	75.52	gold quality
placenta	UBERON:0001987	75.51	gold quality
fundus of stomach	UBERON:0001160	75.33	gold quality
transverse colon	UBERON:0001157	74.79	gold quality
lower esophagus mucosa	UBERON:0035834	74.71	gold quality
leukocyte	CL:0000738	74.09	gold quality
monocyte	CL:0000576	73.94	gold quality
kidney	UBERON:0002113	73.80	gold quality
minor salivary gland	UBERON:0001830	73.12	gold quality
lymph node	UBERON:0000029	72.82	gold quality
bone marrow	UBERON:0002371	72.81	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-8498	yes	12.31
E-ANND-3	yes	4.27

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

29 targeting ZNF888, 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-3925-3P	100.00	69.95	1237
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-3064-3P	100.00	70.09	1254
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-12121	99.99	66.64	255
HSA-MIR-4715-3P	99.98	66.03	670
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-8087	99.90	69.55	1351
HSA-MIR-4320	99.75	65.80	793
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-1976	99.74	65.48	1127
HSA-MIR-106A-3P	99.53	67.58	995
HSA-MIR-19A-5P	99.36	66.93	1675
HSA-MIR-19B-1-5P	99.36	67.07	1669
HSA-MIR-19B-2-5P	99.36	67.07	1669
HSA-MIR-664A-3P	99.22	71.08	2696
HSA-MIR-153-3P	98.96	72.51	1644
HSA-MIR-1294	98.91	69.26	1030
HSA-MIR-9986	98.91	69.28	1024
HSA-MIR-1178-3P	98.57	67.09	890
HSA-MIR-216B-3P	98.55	67.19	1223
HSA-MIR-1246	98.54	66.21	959
HSA-MIR-4439	98.53	67.53	793
HSA-MIR-6500-3P	97.42	67.20	867
HSA-MIR-3156-5P	96.93	67.36	800
HSA-MIR-758-5P	93.99	64.46	534

Cross-species orthologs

0 orthologs

Paralogs (11): ZNF761 (ENSG00000160336), ZNF701 (ENSG00000167562), ZNF816 (ENSG00000180257), ZNF766 (ENSG00000196214), ZNF765 (ENSG00000196417), ZNF860 (ENSG00000197385), ZNF813 (ENSG00000198346), ZNF525 (ENSG00000203326), ZNF468 (ENSG00000204604), ZNF578 (ENSG00000258405), (ENSG00000269825)

Protein

Protein identifiers

Zinc finger protein 888 — P0CJ79 (reviewed: P0CJ79)

All UniProt accessions (1): P0CJ79

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 (7): NP_001297056, NP_001371581, NP_001371582, NP_001371583, NP_001371584, NP_001371585, NP_001380867* (*=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 (21 total): zinc finger region 18, chain 1, domain 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0CJ79-F1	70.27	0.15

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 204

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 20 (showing top): GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, CHAF1B_TARGET_GENES, SALL4_TARGET_GENES, MIR6833_3P, MIR664A_3P, MIR4768_5P, MIR3925_3P, MIR3064_3P, MIR19A_5P, MIR19B_1_5P_MIR19B_2_5P, MIR1178_3P, MIR1246, MIR758_5P, GOMF_DNA_BINDING_TRANSCRIPTION_FACTOR_ACTIVITY

GO Biological Process (3): regulation of transcription by RNA polymerase II (GO:0006357), regulation of anatomical structure morphogenesis (GO:0022603), 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
anatomical structure morphogenesis	1
regulation of developmental process	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

112 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF888	C11orf21	Q9P2W6	543
ZNF888	KRTCAP3	Q53RY4	527
ZNF888	ACTRT3	Q9BYD9	510
ZNF888	MOB3A	Q96BX8	507
ZNF888	PRR15	Q8IV56	506
ZNF888	PRR15L	Q9BU68	501
ZNF888	C1orf116	Q9BW04	448
ZNF888	EVI2A	P22794	435
ZNF888	ACSM5	Q6NUN0	419
ZNF888	FMO2	Q99518	398
ZNF888	BCAM	P50895	398
ZNF888	RIPK4	P57078	364
ZNF888	HHLA2	Q9UM44	323
ZNF888	HOXB6	P09068	315
ZNF888	SSX1	Q16384	307

IntAct

11 interactions, top by confidence:

A	B	Type	Score
ZNF324B	ZNF316	psi-mi:“MI:0914”(association)	0.530
ZNF354C	IPO8	psi-mi:“MI:0914”(association)	0.530
ZNF354C	LRP4	psi-mi:“MI:0914”(association)	0.530
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.530
ZNF888	VIM	psi-mi:“MI:0915”(physical association)	0.400
M		psi-mi:“MI:0914”(association)	0.350
NOTCH2	ZNF320	psi-mi:“MI:0914”(association)	0.350
RPL11	ZNF724	psi-mi:“MI:0914”(association)	0.350
RPL23A	MPHOSPH10	psi-mi:“MI:0914”(association)	0.350
ZNF691	FPGT	psi-mi:“MI:0914”(association)	0.350

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

677 predictions. Top by Δscore:

Variant	Effect	Δscore
19:52915190:CCTCA:C	donor_loss	1.0000
19:52915191:CTCA:C	donor_loss	1.0000
19:52915192:TCA:T	donor_loss	1.0000
19:52915193:CACCC:C	donor_loss	1.0000
19:52915194:A:T	donor_loss	1.0000
19:52915194:AC:A	donor_gain	1.0000
19:52915195:C:CG	donor_loss	1.0000
19:52915195:CC:C	donor_gain	1.0000
19:52915321:CC:C	acceptor_gain	1.0000
19:52915322:CC:C	acceptor_gain	1.0000
19:52915188:AT:A	donor_gain	0.9900
19:52915194:A:AC	donor_gain	0.9900
19:52915195:C:CC	donor_gain	0.9900
19:52915318:AGACC:A	acceptor_gain	0.9900
19:52915319:GACC:G	acceptor_gain	0.9900
19:52915322:CCTGA:C	acceptor_loss	0.9900
19:52915323:C:CC	acceptor_gain	0.9900
19:52915323:C:CG	acceptor_loss	0.9900
19:52915323:C:T	acceptor_gain	0.9900
19:52917932:C:CC	acceptor_gain	0.9900
19:52917946:C:CT	acceptor_gain	0.9900
19:52915211:T:TA	donor_gain	0.9800
19:52915328:A:AC	acceptor_gain	0.9800
19:52917947:A:C	acceptor_gain	0.9800
19:52915320:ACC:A	acceptor_gain	0.9700
19:52915321:CCC:C	acceptor_gain	0.9700
19:52917934:T:C	acceptor_gain	0.9700
19:52917934:T:TC	acceptor_gain	0.9700
19:52908092:G:A	donor_gain	0.9600
19:52915171:T:TA	donor_gain	0.9600

AlphaMissense

4815 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:52906393:A:C	F643L	0.998
19:52906393:A:T	F643L	0.998
19:52906395:A:G	F643L	0.998
19:52906309:G:C	F671L	0.996
19:52906309:G:T	F671L	0.996
19:52906311:A:G	F671L	0.996
19:52906477:G:C	F615L	0.996
19:52906477:G:T	F615L	0.996
19:52906479:A:G	F615L	0.996
19:52906813:G:C	F503L	0.996
19:52906813:G:T	F503L	0.996
19:52906815:A:G	F503L	0.996
19:52906897:G:C	F475L	0.996
19:52906897:G:T	F475L	0.996
19:52906899:A:G	F475L	0.996
19:52906225:A:C	F699L	0.995
19:52906225:A:T	F699L	0.995
19:52906227:A:G	F699L	0.995
19:52906561:A:C	F587L	0.994
19:52906561:A:T	F587L	0.994
19:52906563:A:G	F587L	0.994
19:52906282:A:C	H680Q	0.991
19:52906282:A:T	H680Q	0.991
19:52906645:A:C	F559L	0.991
19:52906645:A:T	F559L	0.991
19:52906647:A:G	F559L	0.991
19:52906729:G:C	F531L	0.991
19:52906729:G:T	F531L	0.991
19:52906731:A:G	F531L	0.991
19:52907149:G:C	F391L	0.991

dbSNP variants (sampled 300 via entrez): RS1000120090 (19:52917083 T>C), RS1000335476 (19:52906884 G>A), RS1000978076 (19:52923773 A>G), RS1001116969 (19:52916159 A>C), RS1001325120 (19:52923648 T>C), RS1001377901 (19:52922860 G>A), RS1001447600 (19:52912402 C>A,T), RS1001450926 (19:52917316 G>T), RS1001458938 (19:52912624 A>C), RS1001659482 (19:52923461 C>A,G,T), RS1001985943 (19:52913062 G>A), RS1002050250 (19:52912004 G>A), RS1002715880 (19:52924942 A>G), RS1002851651 (19:52908365 A>G), RS1003051594 (19:52921098 G>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

1 associations (top):

Study	Trait	p-value
GCST90002396_45	Mean reticulocyte volume	2.000000e-10

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0010701	mean reticulocyte volume

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
Cadmium Chloride	decreases expression, increases abundance, increases expression	2
TAK-243	increases sumoylation	1
triphenyl phosphate	affects expression	1
di-n-butylphosphoric acid	affects expression	1
Cadmium	increases abundance, increases expression	1
Triclosan	decreases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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