ZNF486

Summary

ZNF486 (zinc finger protein 486, HGNC:20807) is a protein-coding gene on chromosome 19p12, encoding Zinc finger protein 486 (Q96H40). 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 DNA-templated transcription. Located in extracellular exosome.

Source: NCBI Gene 90649 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 126 total
• MANE Select transcript: NM_052852

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20807
Approved symbol	ZNF486
Name	zinc finger protein 486
Location	19p12
Locus type	gene with protein product
Status	Approved
Aliases	MGC2396
Ensembl gene	ENSG00000256229
Ensembl biotype	protein_coding
Entrez	90649

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000335117, ENST00000597083

RefSeq mRNA: 1 — MANE Select: NM_052852 NM_052852

CCDS: CCDS46029

Canonical transcript exons

ENST00000335117 — 4 exons

Exon	Start	End
ENSE00001629453	20167214	20167360
ENSE00002454012	20184356	20184482
ENSE00002472967	20185987	20186082
ENSE00003102934	20196964	20200488

Expression profiles

Bgee: expression breadth ubiquitous, 238 present calls, max score 93.40.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.5911 / max 476.4337, expressed in 1504 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
174851	10.0793	1499
174852	0.5118	187

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	93.40	gold quality
sperm	CL:0000019	86.49	gold quality
right lobe of thyroid gland	UBERON:0001119	85.32	gold quality
left lobe of thyroid gland	UBERON:0001120	83.41	gold quality
thyroid gland	UBERON:0002046	82.98	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.11	gold quality
ganglionic eminence	UBERON:0004023	79.11	gold quality
ventricular zone	UBERON:0003053	78.45	gold quality
islet of Langerhans	UBERON:0000006	77.07	gold quality
endometrium	UBERON:0001295	76.71	gold quality
lymph node	UBERON:0000029	75.43	gold quality
calcaneal tendon	UBERON:0003701	75.32	gold quality
mucosa of paranasal sinus	UBERON:0005030	75.21	silver quality
gall bladder	UBERON:0002110	75.00	gold quality
cortical plate	UBERON:0005343	74.59	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	73.95	gold quality
stromal cell of endometrium	CL:0002255	73.15	gold quality
vermiform appendix	UBERON:0001154	72.76	gold quality
pancreas	UBERON:0001264	72.52	gold quality
smooth muscle tissue	UBERON:0001135	72.34	gold quality
left ovary	UBERON:0002119	72.31	gold quality
metanephros cortex	UBERON:0010533	72.24	gold quality
uterus	UBERON:0000995	72.14	gold quality
adrenal tissue	UBERON:0018303	71.36	gold quality
caecum	UBERON:0001153	71.27	gold quality
ovary	UBERON:0000992	71.24	gold quality
cortex of kidney	UBERON:0001225	71.24	gold quality
superficial temporal artery	UBERON:0001614	71.06	silver quality
right ovary	UBERON:0002118	71.05	gold quality
body of pancreas	UBERON:0001150	70.89	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.51

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

140 targeting ZNF486, 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-5692A	100.00	74.40	6850
HSA-MIR-4425	100.00	67.59	1049
HSA-MIR-3064-3P	100.00	70.09	1254
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-4715-3P	99.98	66.03	670
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192

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 486 — Q96H40 (reviewed: Q96H40)

Alternative names: KRAB domain only protein 2

All UniProt accessions (2): Q96H40, M0QXQ0

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_443084* (*=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 (12 total): zinc finger region 10, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96H40-F1	68.03	0.12

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 59 (showing top): chr19p12, PARK_HSC_AND_MULTIPOTENT_PROGENITORS, HAMAI_APOPTOSIS_VIA_TRAIL_UP, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN, WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_36HR, WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_8D, NFE2L2.V2, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, GSE14415_NATURAL_TREG_VS_TCONV_UP, HDAC4_TARGET_GENES, HSD17B8_TARGET_GENES, PRKDC_TARGET_GENES, ZNF10_TARGET_GENES, ZNF350_TARGET_GENES

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

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 (2): nucleus (GO:0005634), extracellular exosome (GO:0070062)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
RNA Polymerase II Transcription	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	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
extracellular vesicle	1

Protein interactions and networks

STRING

354 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF486	PCDHGB5	Q9Y5G0	418
ZNF486	LGALS16	A8MUM7	393
ZNF486	MYEOV	Q96EZ4	388
ZNF486	ANKRD18A	Q8IVF6	371
ZNF486	THUMPD3	Q9BV44	370
ZNF486	TMED6	Q8WW62	348
ZNF486	BEND6	Q5SZJ8	348
ZNF486	C1QTNF2	Q9BXJ5	311
ZNF486	PHYHD1	Q5SRE7	306
ZNF486	PCDHGA1	Q9Y5H4	304
ZNF486	TM9SF1	O15321	299
ZNF486	CLC	Q05315	292
ZNF486	PCDHB2	Q9Y5E7	290
ZNF486	ACY3	Q96HD9	290
ZNF486	GPR15LG	Q6UWK7	290
ZNF486	ARHGAP28	Q9P2N2	290

IntAct

0 interactions, top by confidence:

BioGRID (34): ZNF486 (Reconstituted Complex), ZNF486 (Negative Genetic), ZNF486 (Affinity Capture-MS), ZNF486 (Affinity Capture-RNA), ZNF486 (Proximity Label-MS), ZNF486 (Proximity Label-MS), ZNF486 (Proximity Label-MS), ZNF486 (Proximity Label-MS), ZNF486 (Proximity Label-MS), ZNF486 (Proximity Label-MS), ZNF486 (Proximity Label-MS), ZNF486 (Proximity Label-MS), ZNF486 (Proximity Label-MS), ZNF486 (Proximity Label-MS), ZNF486 (Proximity Label-MS)

ESM2 similar proteins: A0A1W2PQL4, A0JPL0, A2RRD8, A6NHJ4, A6NP11, B4DX44, O75346, O95780, P0CB33, P21506, P51508, P52738, Q0D2J5, Q0VGE8, Q12901, Q13360, Q14593, Q15973, Q2M218, Q2M3X9, Q2VY69, Q3SXZ3, Q5HY98, Q5RCJ2, Q5VIY5, Q6J6I6, Q7L2R6, Q86XU0, Q86Y25, Q8IW36, Q8IYN0, Q8IYX0, Q8N782, Q8N883, Q8N9Z0, Q8NDP4, Q95K49, Q969W8, Q96H40, Q96N58

Diamond homologs: A0A1W2PQL4, A6NK75, A6NN14, A6NNF4, A6NP11, A8MQ14, A8MTY0, A8MUV8, A8MXY4, B4DX44, B4DXR9, E9PYI1, O14628, O43345, O75290, O75346, O75373, O75437, O95780, P0CB33, P0DKX0, P0DPD5, P16373, P17019, P17038, P21506, P35789, P52736, P52738, P52744, Q03923, Q03924, Q03936, Q03938, Q05481, Q14586, Q14593, Q14929, Q15928, Q3KNS6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	111
Likely benign	6
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1346 predictions. Top by Δscore:

Variant	Effect	Δscore
19:20185983:ACAG:A	acceptor_loss	1.0000
19:20185986:GGT:G	acceptor_gain	1.0000
19:20186080:CAG:C	donor_loss	1.0000
19:20186081:AG:A	donor_loss	1.0000
19:20186082:GG:G	donor_loss	1.0000
19:20186083:G:A	donor_loss	1.0000
19:20186084:T:G	donor_loss	1.0000
19:20196962:A:AG	acceptor_gain	1.0000
19:20196962:AGTT:A	acceptor_gain	1.0000
19:20196963:G:GA	acceptor_gain	1.0000
19:20196963:GTT:G	acceptor_gain	1.0000
19:20196963:GTTG:G	acceptor_gain	1.0000
19:20196963:GTTGT:G	acceptor_gain	1.0000
19:20184347:GTTTT:G	acceptor_loss	0.9900
19:20184348:TTTTT:T	acceptor_loss	0.9900
19:20184349:TTTTC:T	acceptor_loss	0.9900
19:20184350:TTTCA:T	acceptor_loss	0.9900
19:20184351:TTCAG:T	acceptor_loss	0.9900
19:20184352:TCAG:T	acceptor_loss	0.9900
19:20184353:CAGGA:C	acceptor_loss	0.9900
19:20184354:A:AC	acceptor_loss	0.9900
19:20184355:G:T	acceptor_loss	0.9900
19:20184443:G:T	donor_gain	0.9900
19:20184478:CCTTG:C	donor_loss	0.9900
19:20184479:CTTGG:C	donor_loss	0.9900
19:20184480:TTGGT:T	donor_loss	0.9900
19:20184481:TGGTG:T	donor_loss	0.9900
19:20184483:G:GC	donor_loss	0.9900
19:20184484:T:G	donor_loss	0.9900
19:20184485:GAGGA:G	donor_loss	0.9900

AlphaMissense

3085 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:20197785:T:C	F359L	0.994
19:20197787:C:A	F359L	0.994
19:20197787:C:G	F359L	0.994
19:20197869:T:C	F387L	0.994
19:20197871:T:A	F387L	0.994
19:20197871:T:G	F387L	0.994
19:20197617:T:C	F303L	0.988
19:20197619:T:A	F303L	0.988
19:20197619:T:G	F303L	0.988
19:20197701:T:C	F331L	0.984
19:20197703:T:A	F331L	0.984
19:20197703:T:G	F331L	0.984
19:20198037:T:C	F443L	0.984
19:20198039:T:A	F443L	0.984
19:20198039:T:G	F443L	0.984
19:20197533:T:C	F275L	0.983
19:20197535:T:A	F275L	0.983
19:20197535:T:G	F275L	0.983
19:20197792:G:C	R361P	0.983
19:20197910:T:A	H400Q	0.976
19:20197910:T:G	H400Q	0.976
19:20197826:T:A	H372Q	0.971
19:20197826:T:G	H372Q	0.971
19:20197870:T:C	F387S	0.971
19:20197804:T:C	L365P	0.970
19:20197898:T:A	H396Q	0.970
19:20197898:T:G	H396Q	0.970
19:20197786:T:C	F359S	0.968
19:20197953:T:G	Y415D	0.968
19:20197972:T:C	L421P	0.967

dbSNP variants (sampled 300 via entrez): RS1000191478 (19:20191637 G>A,C), RS1000222800 (19:20191835 A>G), RS1000286265 (19:20191399 G>A), RS1000343812 (19:20167435 C>T), RS1000423214 (19:20171761 G>A,T), RS1000492350 (19:20200312 A>G), RS1000582968 (19:20175870 G>T), RS1000718499 (19:20175747 G>A,T), RS1000817571 (19:20179197 A>G), RS1000921210 (19:20171574 A>G), RS1001141106 (19:20187851 C>T), RS1001342909 (19:20182559 C>A,T), RS1001442549 (19:20182318 A>G), RS1001508095 (19:20187463 T>C), RS1001686655 (19:20192080 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

3 associations (top):

Study	Trait	p-value
GCST003542_169	Night sleep phenotypes	7.000000e-06
GCST010244_89	Triglyceride levels	3.000000e-09
GCST010245_99	LDL cholesterol levels	3.000000e-08

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004530	triglyceride measurement
EFO:0004611	low density lipoprotein cholesterol measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases abundance, increases expression, affects cotreatment	2
chloropicrin	increases expression	2
Arsenic	increases abundance, increases expression, affects methylation, affects cotreatment	2
Benzo(a)pyrene	affects methylation, increases expression	2
triphenyl phosphate	affects expression	1
arsenite	decreases expression	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
fipronil	decreases expression	1
2-palmitoylglycerol	increases expression	1
erucylphospho-N,N,N-trimethylpropylammonium	increases expression	1
ICG 001	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Cadmium	increases abundance, increases expression	1
Doxorubicin	decreases expression	1
Estradiol	affects cotreatment, decreases reaction, increases expression	1
Manganese	increases abundance, increases expression, affects cotreatment	1
Progesterone	affects cotreatment, decreases reaction, increases expression	1
Silicon Dioxide	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	increases expression	1
Zinc	increases expression	1
8-Bromo Cyclic Adenosine Monophosphate	affects cotreatment, decreases reaction, increases expression	1
Asbestos, Crocidolite	decreases expression	1
Cadmium Chloride	increases abundance, increases expression	1
Copper Sulfate	increases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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