ZNF488

Summary

ZNF488 (zinc finger protein 488, HGNC:23535) is a protein-coding gene on chromosome 10q11.22, encoding Zinc finger protein 488 (Q96MN9). Transcriptional repressor.

Predicted to enable DNA binding activity and zinc ion binding activity. Predicted to be involved in oligodendrocyte development and regulation of DNA-templated transcription. Predicted to act upstream of or within negative regulation of DNA-templated transcription and positive regulation of oligodendrocyte differentiation. Predicted to be active in nucleus.

Source: NCBI Gene 118738 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 69 total
• MANE Select transcript: NM_153034

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23535
Approved symbol	ZNF488
Name	zinc finger protein 488
Location	10q11.22
Locus type	gene with protein product
Status	Approved
Aliases	FLJ32104
Ensembl gene	ENSG00000265763
Ensembl biotype	protein_coding
Entrez	118738

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 12 protein_coding

ENST00000585316, ENST00000591025, ENST00000884605, ENST00000884606, ENST00000884607, ENST00000884608, ENST00000884609, ENST00000884610, ENST00000884611, ENST00000884612, ENST00000884613, ENST00000919271

RefSeq mRNA: 6 — MANE Select: NM_153034 NM_001346932, NM_001346933, NM_001346934, NM_001346935, NM_001346936, NM_153034

CCDS: CCDS73120

Canonical transcript exons

ENST00000585316 — 2 exons

Exon	Start	End
ENSE00002692582	47365496	47368937
ENSE00002715047	47384220	47384293

Expression profiles

Bgee: expression breadth ubiquitous, 142 present calls, max score 94.12.

FANTOM5 (CAGE): breadth broad, TPM avg 4.9399 / max 508.2662, expressed in 620 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
109282	4.9399	620

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
C1 segment of cervical spinal cord	UBERON:0006469	94.12	gold quality
spinal cord	UBERON:0002240	93.47	gold quality
ileal mucosa	UBERON:0000331	90.06	gold quality
inferior vagus X ganglion	UBERON:0005363	89.63	gold quality
substantia nigra	UBERON:0002038	85.25	gold quality
midbrain	UBERON:0001891	84.63	gold quality
jejunal mucosa	UBERON:0000399	84.52	gold quality
Ammon’s horn	UBERON:0001954	83.10	gold quality
duodenum	UBERON:0002114	82.96	gold quality
prefrontal cortex	UBERON:0000451	81.79	gold quality
medulla oblongata	UBERON:0001896	81.55	gold quality
subthalamic nucleus	UBERON:0001906	81.14	gold quality
pons	UBERON:0000988	80.57	gold quality
Brodmann (1909) area 9	UBERON:0013540	79.58	gold quality
corpus callosum	UBERON:0002336	79.21	gold quality
frontal cortex	UBERON:0001870	78.35	gold quality
putamen	UBERON:0001874	78.22	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.14	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	78.10	gold quality
right frontal lobe	UBERON:0002810	78.09	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	77.42	gold quality
cerebral cortex	UBERON:0000956	77.33	gold quality
neocortex	UBERON:0001950	77.11	gold quality
superior vestibular nucleus	UBERON:0007227	77.01	gold quality
hypothalamus	UBERON:0001898	76.84	gold quality
caudate nucleus	UBERON:0001873	76.66	gold quality
substantia nigra pars reticulata	UBERON:0001966	76.63	silver quality
Brodmann (1909) area 46	UBERON:0006483	76.34	gold quality
ventral tegmental area	UBERON:0002691	76.28	gold quality
amygdala	UBERON:0001876	76.26	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.22

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

74 targeting ZNF488, 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-6867-5P	100.00	82.21	3464
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-636	99.80	69.58	1500
HSA-MIR-1825	99.72	68.11	1089
HSA-MIR-10393-3P	99.72	66.56	961
HSA-MIR-6801-5P	99.72	66.50	981
HSA-MIR-7154-5P	99.69	70.52	1900
HSA-MIR-3660	99.68	67.33	1149
HSA-MIR-4526	99.68	67.07	1136
HSA-MIR-6762-3P	99.66	66.94	1188
HSA-MIR-1205	99.65	66.76	1826
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-6757-3P	99.63	66.88	1089
HSA-MIR-6134	99.63	65.68	1537
HSA-MIR-1249-5P	99.61	66.55	2049
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-2053	99.57	69.15	1635
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-6727-3P	99.49	65.92	1333
HSA-MIR-6081	99.48	66.07	1446
HSA-MIR-940	99.37	66.14	2064
HSA-MIR-4722-3P	99.35	65.22	1099
HSA-MIR-501-3P	99.33	66.12	651
HSA-MIR-502-3P	99.33	66.12	651

Literature-anchored findings (GeneRIF, showing 1)

• Transcription factor ZNF488 accelerates cervical cancer progression through regulating the MEK/ERK signaling pathway. (PMID:36537752)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	znf488	ENSDARG00000025017
mus_musculus	Zfp488	ENSMUSG00000044519
rattus_norvegicus	Zfp488	ENSRNOG00000057542
drosophila_melanogaster	CG13287	FBGN0035643

Paralogs (1): PRDM8 (ENSG00000152784)

Protein

Protein identifiers

Zinc finger protein 488 — Q96MN9 (reviewed: Q96MN9)

All UniProt accessions (1): Q96MN9

UniProt curated annotations — full annotation on UniProt →

Function. Transcriptional repressor. Plays a role in oligodendrocyte differentiation, together with OLIG2. Mediates Notch signaling-activated formation of oligodendrocyte precursors. Promotes differentiation of adult neural stem progenitor cells (NSPCs) into mature oligodendrocytes and contributes to remyelination following nerve injury.

Subunit / interactions. Interacts with OLIG2.

Subcellular location. Nucleus.

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

Isoforms (2)

UniProt ID	Names	Canonical?
Q96MN9-1	1	yes
Q96MN9-2	2

RefSeq proteins (6): NP_001333861, NP_001333862, NP_001333863, NP_001333864, NP_001333865, NP_694579* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR052296	TR-Histone_Methyltrans	Family

UniProt features (12 total): sequence variant 3, zinc finger region 2, region of interest 2, compositionally biased region 2, chain 1, short sequence motif 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96MN9-F1	56.63	0.14

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 64 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_UP, GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_DN, GOBP_POSITIVE_REGULATION_OF_GLIAL_CELL_DIFFERENTIATION, GOBP_GLIAL_CELL_DEVELOPMENT, GOBP_NEUROGENESIS, GOBP_REGULATION_OF_MYELINATION, GOBP_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, GOBP_POSITIVE_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, GOBP_POSITIVE_REGULATION_OF_OLIGODENDROCYTE_DIFFERENTIATION, GOBP_POSITIVE_REGULATION_OF_CELL_DIFFERENTIATION, GOBP_ENSHEATHMENT_OF_NEURONS, GOBP_REGULATION_OF_OLIGODENDROCYTE_DIFFERENTIATION, GOBP_POSITIVE_REGULATION_OF_NERVOUS_SYSTEM_PROCESS, GOBP_REGULATION_OF_NERVOUS_SYSTEM_PROCESS, GOBP_REGULATION_OF_SYSTEM_PROCESS

GO Biological Process (6): regulation of DNA-templated transcription (GO:0006355), oligodendrocyte development (GO:0014003), positive regulation of myelination (GO:0031643), negative regulation of DNA-templated transcription (GO:0045892), positive regulation of oligodendrocyte differentiation (GO:0048714), nervous system development (GO:0007399)

GO Molecular Function (4): DNA binding (GO:0003677), zinc ion binding (GO:0008270), protein binding (GO:0005515), 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
DNA-templated transcription	2
oligodendrocyte differentiation	2
regulation of gene expression	1
regulation of RNA biosynthetic process	1
glial cell development	1
regulation of myelination	1
positive regulation of nervous system process	1
myelination	1
positive regulation of cellular process	1
regulation of DNA-templated transcription	1
negative regulation of RNA biosynthetic process	1
positive regulation of glial cell differentiation	1
regulation of oligodendrocyte differentiation	1
system development	1
nucleic acid binding	1
transition metal ion binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

622 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF488	OLIG2	Q13516	572
ZNF488	SNAPC3	Q92966	548
ZNF488	ASXL1	Q8IXJ9	481
ZNF488	ANTXRL	A6NF34	476
ZNF488	WDR64	B1ANS9	418
ZNF488	KMT2D	O14686	409
ZNF488	ZNF487	B1APH4	377
ZNF488	A0A1B0GU03	A0A1B0GU03	375
ZNF488	AGAP6	Q5VW22	371
ZNF488	OLIG1	Q8TAK6	354
ZNF488	MAP7D2	Q96T17	348
ZNF488	ASAH2B	P0C7U1	348
ZNF488	GLTPD2	A6NH11	342
ZNF488	DIPK1B	Q5VUD6	322
ZNF488	UGT8	Q16880	321
ZNF488	FAM25A	B3EWG3	321

IntAct

42 interactions, top by confidence:

A	B	Type	Score
ATXN1	ZNF488	psi-mi:“MI:0915”(physical association)	0.780
GOLGA2	ZNF488	psi-mi:“MI:0915”(physical association)	0.670
ZNF488	RBPMS	psi-mi:“MI:0915”(physical association)	0.670
ZNF488	GOLGA2	psi-mi:“MI:0915”(physical association)	0.670
RBPMS	ZNF488	psi-mi:“MI:0915”(physical association)	0.670
DAB1	ZNF488	psi-mi:“MI:0915”(physical association)	0.560
ZNF488	PRR20C	psi-mi:“MI:0915”(physical association)	0.560
TRAF2	ZNF488	psi-mi:“MI:0915”(physical association)	0.560
ZNF488	KRT40	psi-mi:“MI:0915”(physical association)	0.560
BANP	ZNF488	psi-mi:“MI:0915”(physical association)	0.560
ZNF488	RIMBP3	psi-mi:“MI:0915”(physical association)	0.560
MAGED1	ZNF488	psi-mi:“MI:0915”(physical association)	0.560
PRR20C	ZNF488	psi-mi:“MI:0915”(physical association)	0.560
KRT40	ZNF488	psi-mi:“MI:0915”(physical association)	0.560
ZNF488	BANP	psi-mi:“MI:0915”(physical association)	0.560
RIMBP3	ZNF488	psi-mi:“MI:0915”(physical association)	0.560
ZNF488	TRAF2	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (25): ZNF488 (Two-hybrid), ZNF488 (Two-hybrid), ZNF488 (Two-hybrid), ZNF488 (Two-hybrid), ZNF488 (Two-hybrid), ZNF488 (Two-hybrid), ZNF488 (Two-hybrid), PRR20A (Two-hybrid), KRT40 (Two-hybrid), USO1 (Affinity Capture-MS), CTH (Affinity Capture-MS), GOPC (Affinity Capture-MS), HSPA8 (Affinity Capture-MS), CAMK2G (Affinity Capture-MS), ZNF488 (Two-hybrid)

ESM2 similar proteins: A0A5F9ZHS7, A1YGK1, A2T7E6, A8MZG2, O08574, O43593, O60393, O75593, O88621, O95231, P0C1T1, P0CG20, P20428, P97609, Q04667, Q17QR5, Q2KIS6, Q2M1V0, Q2T9Q7, Q32LE6, Q497V6, Q5JUK2, Q5M844, Q5RJB0, Q5TGS1, Q61645, Q61657, Q6ZMY3, Q6ZN32, Q6ZNG2, Q7RTU1, Q8BZW2, Q8CGW9, Q8IWN7, Q8IXT2, Q8IZ20, Q8N1L9, Q8N7G0, Q8N944, Q8N9Y4

Diamond homologs: A0A163UT06, A2AGX3, B8A5Y1, E9PZZ1, Q5HZG9, Q8BZ97, Q96MN9, Q9H4Q3, Q9NQV5, Q9NQV7, Q9NQV8, A2AJ77, E9Q3T6, P0C6Y7, Q96EQ9, Q9GZV8, Q9H4Q4, Q9NQW5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	60
Likely benign	9
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

610 predictions. Top by Δscore:

Variant	Effect	Δscore
10:47357098:T:G	acceptor_loss	0.9900
10:47357099:C:CC	acceptor_gain	0.9900
10:47357099:CT:C	acceptor_loss	0.9900
10:47357100:CCTGG:C	acceptor_loss	0.9900
10:47357101:ACCTG:A	acceptor_loss	0.9900
10:47357102:CAC:C	acceptor_gain	0.9900
10:47384216:T:G	donor_loss	0.9900
10:47384217:G:A	donor_loss	0.9900
10:47384219:AGG:A	donor_loss	0.9900
10:47384220:CAGG:C	donor_loss	0.9900
10:47357102:CACC:C	acceptor_gain	0.9800
10:47357103:TCAC:T	acceptor_gain	0.9800
10:47384217:G:GG	donor_gain	0.9800
10:47357104:TTCAC:T	acceptor_gain	0.9700
10:47370661:T:G	donor_gain	0.9700
10:47357096:GAAGA:G	acceptor_loss	0.9600
10:47357097:GGAAG:G	acceptor_loss	0.9500
10:47357100:CC:C	acceptor_gain	0.9500
10:47357101:AC:A	acceptor_gain	0.9500
10:47368936:GG:G	acceptor_gain	0.9000
10:47368937:AG:A	acceptor_gain	0.9000
10:47380866:A:AG	acceptor_gain	0.9000
10:47368936:G:GA	acceptor_loss	0.8700
10:47368937:A:T	acceptor_loss	0.8700
10:47368938:CA:C	acceptor_loss	0.8700
10:47368939:GCA:G	acceptor_loss	0.8700
10:47368940:TGCA:T	acceptor_loss	0.8700
10:47368941:CTGCA:C	acceptor_loss	0.8700
10:47380865:A:G	acceptor_gain	0.8700
10:47356767:T:TA	donor_gain	0.8600

AlphaMissense

2167 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:47367978:A:C	F284L	0.996
10:47367978:A:T	F284L	0.996
10:47367980:A:G	F284L	0.996
10:47367852:G:C	F326L	0.995
10:47367852:G:T	F326L	0.995
10:47367854:A:G	F326L	0.995
10:47367948:C:A	M294I	0.995
10:47367948:C:G	M294I	0.995
10:47367948:C:T	M294I	0.995
10:47367953:G:C	H293D	0.995
10:47367949:A:G	M294T	0.994
10:47367979:A:G	F284S	0.993
10:47367813:G:C	H339Q	0.992
10:47367813:G:T	H339Q	0.992
10:47367825:G:C	H335Q	0.992
10:47367825:G:T	H335Q	0.992
10:47367953:G:T	H293N	0.992
10:47367951:G:C	H293Q	0.991
10:47367951:G:T	H293Q	0.991
10:47368341:A:C	F163L	0.990
10:47368341:A:T	F163L	0.990
10:47368343:A:G	F163L	0.990
10:47367827:G:C	H335D	0.989
10:47367827:G:T	H335N	0.989
10:47367837:G:C	H331Q	0.989
10:47367837:G:T	H331Q	0.989
10:47367853:A:C	F326C	0.989
10:47367853:A:G	F326S	0.988
10:47367961:A:G	L290P	0.988
10:47367991:C:G	C280S	0.986

dbSNP variants (sampled 300 via entrez): RS1000011649 (10:47384820 C>G,T), RS1000205387 (10:47367803 C>A,T), RS1000253876 (10:47367543 C>T), RS1000351922 (10:47373293 C>T), RS1000902817 (10:47377610 A>T), RS1000960432 (10:47384316 C>A), RS1001012636 (10:47384025 C>G), RS1001362805 (10:47371941 C>G,T), RS1001372619 (10:47371673 C>T), RS1001613456 (10:47366507 G>A), RS1002308761 (10:47376285 C>G), RS1002375468 (10:47370124 C>T), RS1002479804 (10:47376558 C>T), RS1002964041 (10:47381016 A>T), RS1003372500 (10:47369110 C>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

4 associations (top):

Study	Trait	p-value
GCST005362_10	Attention deficit hyperactivity disorder	7.000000e-07
GCST005559_6	Virologic severity in Herpes simplex virus type 2 infection	3.000000e-06
GCST006976_33	Macular thickness	2.000000e-18
GCST010002_287	Refractive error	2.000000e-49

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0009010	HSV2 virologic severity measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

34 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects expression, decreases expression, increases methylation	2
sodium arsenite	decreases expression	2
Benzo(a)pyrene	decreases methylation, increases expression, increases methylation, affects methylation	2
Estradiol	affects cotreatment, decreases expression, increases expression	2
ethyl-p-hydroxybenzoate	increases expression	1
beta-lapachone	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
manganese chloride	increases abundance, increases expression	1
perfluorooctane sulfonic acid	decreases expression	1
pentabromodiphenyl ether	decreases expression	1
pterostilbene	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
jinfukang	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Troglitazone	decreases expression	1
Air Pollutants	increases abundance, decreases expression	1
Calcitriol	decreases expression	1
Cannabidiol	decreases expression	1
Cisplatin	increases expression, affects cotreatment	1
Manganese	increases abundance, increases expression	1
Phenylmercuric Acetate	affects cotreatment, increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Silicon Dioxide	increases expression	1
Triclosan	increases expression	1
Valproic Acid	decreases expression	1
Aflatoxin B1	increases expression	1
Antirheumatic Agents	increases expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_HD26	HEK293 eGFP-ZNF488	Transformed cell line	Female

Clinical trials (associated diseases)

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