ZNF485

Summary

ZNF485 (zinc finger protein 485, HGNC:23440) is a protein-coding gene on chromosome 10q11.21, encoding Zinc finger protein 485 (Q8NCK3). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription activator 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 220992 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 75 total
• MANE Select transcript: NM_145312

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23440
Approved symbol	ZNF485
Name	zinc finger protein 485
Location	10q11.21
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000198298
Ensembl biotype	protein_coding
Entrez	220992

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 7 protein_coding, 1 retained_intron

ENST00000361807, ENST00000374435, ENST00000430885, ENST00000480678, ENST00000896014, ENST00000938411, ENST00000938412, ENST00000954239

RefSeq mRNA: 5 — MANE Select: NM_145312 NM_001318140, NM_001318141, NM_001318142, NM_001318143, NM_145312

CCDS: CCDS7205

Canonical transcript exons

ENST00000361807 — 5 exons

Exon	Start	End
ENSE00001309597	43609255	43609350
ENSE00001412909	43606438	43606546
ENSE00002483094	43608614	43608740
ENSE00003688472	43606997	43607074
ENSE00003847663	43616291	43617904

Expression profiles

Bgee: expression breadth ubiquitous, 182 present calls, max score 88.26.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.5368 / max 86.1217, expressed in 1477 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
104758	2.9608	1294
104759	1.5759	870

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.26	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.89	gold quality
body of pancreas	UBERON:0001150	75.35	gold quality
gastrocnemius	UBERON:0001388	73.39	gold quality
pancreas	UBERON:0001264	73.09	gold quality
muscle of leg	UBERON:0001383	72.95	gold quality
cortical plate	UBERON:0005343	72.37	gold quality
hindlimb stylopod muscle	UBERON:0004252	72.26	gold quality
granulocyte	CL:0000094	71.78	gold quality
islet of Langerhans	UBERON:0000006	70.86	gold quality
stromal cell of endometrium	CL:0002255	69.55	gold quality
ventricular zone	UBERON:0003053	69.53	gold quality
ganglionic eminence	UBERON:0004023	69.22	gold quality
lower esophagus mucosa	UBERON:0035834	69.12	gold quality
smooth muscle tissue	UBERON:0001135	69.00	gold quality
calcaneal tendon	UBERON:0003701	68.50	gold quality
vermiform appendix	UBERON:0001154	68.46	gold quality
left ovary	UBERON:0002119	68.37	gold quality
apex of heart	UBERON:0002098	68.04	gold quality
right ovary	UBERON:0002118	68.01	gold quality
rectum	UBERON:0001052	67.96	gold quality
right adrenal gland	UBERON:0001233	67.70	gold quality
esophagus mucosa	UBERON:0002469	67.69	gold quality
left adrenal gland cortex	UBERON:0035825	67.48	gold quality
lymph node	UBERON:0000029	67.32	gold quality
left adrenal gland	UBERON:0001234	67.20	gold quality
right lobe of liver	UBERON:0001114	66.66	gold quality
body of stomach	UBERON:0001161	66.66	gold quality
right adrenal gland cortex	UBERON:0035827	66.65	gold quality
mucosa of transverse colon	UBERON:0004991	66.53	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.96

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

34 targeting ZNF485, 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-656-3P	100.00	72.15	2788
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-3671	99.90	73.04	3897
HSA-LET-7A-2-3P	99.87	70.53	1921
HSA-LET-7G-3P	99.85	70.43	1929
HSA-MIR-448	99.79	72.37	2103
HSA-MIR-10393-3P	99.72	66.56	961
HSA-MIR-6801-5P	99.72	66.50	981
HSA-MIR-5700	99.64	69.88	2280
HSA-MIR-4743-3P	99.62	68.12	2095
HSA-MIR-888-3P	99.53	69.77	1057
HSA-MIR-302B-5P	99.50	69.49	1857
HSA-MIR-302D-5P	99.50	69.34	1863
HSA-MIR-103A-1-5P	99.39	67.78	1545
HSA-MIR-103A-2-5P	99.39	67.72	1577
HSA-MIR-4797-5P	99.39	68.01	1354
HSA-MIR-4652-3P	99.33	70.02	2742
HSA-MIR-504-3P	99.30	67.18	1745
HSA-MIR-6719-3P	99.29	67.78	1387
HSA-MIR-4279	99.19	66.70	2437
HSA-MIR-939-3P	98.97	65.07	2347
HSA-MIR-606	98.72	67.34	960
HSA-MIR-496	98.66	69.80	931
HSA-MIR-2117	98.48	67.97	1307
HSA-MIR-9903	98.47	66.70	748
HSA-MIR-2681-3P	98.18	65.28	577
HSA-MIR-5585-5P	97.95	68.80	1024

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
drosophila_melanogaster	CG18476	FBGN0037931
drosophila_melanogaster	CG10669	FBGN0039329

Paralogs (5): ZNF664 (ENSG00000179195), ZNF648 (ENSG00000179930), ZNF721 (ENSG00000182903), ZFP62 (ENSG00000196670), ZNF808 (ENSG00000198482)

Protein

Protein identifiers

Zinc finger protein 485 — Q8NCK3 (reviewed: Q8NCK3)

All UniProt accessions (2): C9JV60, Q8NCK3

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.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8NCK3-1	1	yes
Q8NCK3-2	2

RefSeq proteins (5): NP_001305069, NP_001305070, NP_001305071, NP_001305072, NP_660355* (*=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
IPR050758	Znf_C2H2-type	Family

Pfam: PF00096, PF01352

UniProt features (15 total): zinc finger region 11, chain 1, domain 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NCK3-F1	79.02	0.38

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 66 (showing top): YAATNRNNNYNATT_UNKNOWN, GAANYNYGACNY_UNKNOWN, COUP_01, SRF_Q5_01, TGACATY_UNKNOWN, PPAR_DR1_Q2, GATA1_03, IK2_01, TAL1BETAE47_01, TGGAAA_NFAT_Q4_01, OSF2_Q6, WGTTNNNNNAAA_UNKNOWN, COUP_DR1_Q6, HNF4ALPHA_Q6, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING

GO Biological Process (4): regulation of transcription by RNA polymerase II (GO:0006357), negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of DNA-templated transcription (GO:0006355), positive regulation of transcription by RNA polymerase II (GO:0045944)

GO Molecular Function (8): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), zinc ion binding (GO:0008270), DNA binding (GO:0003677), protein binding (GO:0005515), sequence-specific DNA binding (GO:0043565), metal ion binding (GO:0046872)

GO Cellular Component (2): nucleus (GO:0005634), nucleoplasm (GO:0005654)

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
transcription by RNA polymerase II	3
RNA polymerase II transcription regulatory region sequence-specific DNA binding	3
regulation of transcription by RNA polymerase II	2
DNA-binding transcription factor activity, RNA polymerase II-specific	2
regulation of DNA-templated transcription	1
negative regulation of DNA-templated transcription	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
positive regulation of DNA-templated transcription	1
cis-regulatory region sequence-specific DNA binding	1
negative regulation of transcription by RNA polymerase II	1
DNA-binding transcription repressor activity	1
DNA-binding transcription activator activity	1
positive regulation of transcription by RNA polymerase II	1
transition metal ion binding	1
nucleic acid binding	1
binding	1
DNA binding	1
cation binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1

Protein interactions and networks

STRING

370 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF485	PLEKHG7	Q6ZR37	475
ZNF485	RASGEF1A	Q8N9B8	475
ZNF485	EHF	Q9NZC4	383
ZNF485	VSIG8	P0DPA2	354
ZNF485	LYPD6B	Q8NI32	325
ZNF485	FBXL16	Q8N461	314
ZNF485	A0A087WUC5	A0A087WUC5	312
ZNF485	USP43	Q70EL4	300
ZNF485	GREB1	Q4ZG55	276
ZNF485	RET	P07949	269
ZNF485	LRP12	Q9Y561	265
ZNF485	KCNS3	Q9BQ31	242
ZNF485	MBOAT2	Q6ZWT7	228
ZNF485	NCOA4	Q13772	220
ZNF485	TIAM2	Q8IVF5	220

IntAct

13 interactions, top by confidence:

A	B	Type	Score
ZFP41	ZNF485	psi-mi:“MI:0915”(physical association)	0.560
SDCBP	ZNF485	psi-mi:“MI:0915”(physical association)	0.560
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.530
KLF8		psi-mi:“MI:0914”(association)	0.350
RPS19	ZNF320	psi-mi:“MI:0914”(association)	0.350
PURG	ZNF320	psi-mi:“MI:0914”(association)	0.350
ZNF485	DAP3	psi-mi:“MI:0914”(association)	0.350
ZNF485	RPL13	psi-mi:“MI:0914”(association)	0.350
ZFP41	ZNF485	psi-mi:“MI:0915”(physical association)	0.000
SDCBP	ZNF485	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (31): ZNF485 (Affinity Capture-MS), ZNF485 (Two-hybrid), ZNF485 (Two-hybrid), ZFP41 (Two-hybrid), MRPL32 (Affinity Capture-MS), GADD45GIP1 (Affinity Capture-MS), ZNF512 (Affinity Capture-MS), ZNF485 (Affinity Capture-MS), ZNF485 (Affinity Capture-MS), MRPS5 (Affinity Capture-MS), MRPS9 (Affinity Capture-MS), KRI1 (Affinity Capture-MS), RPS27A (Affinity Capture-MS), LARP7 (Affinity Capture-MS), MRPL44 (Affinity Capture-MS)

ESM2 similar proteins: A2RRD8, A6NHJ4, B4DX44, O75346, P10077, P10755, P15621, P16372, P16373, P51786, P52737, P85977, Q0VGE8, Q14588, Q147U1, Q15928, Q15973, Q2M3X9, Q3KNS6, Q3MIS6, Q494X3, Q5HY98, Q5RBQ3, Q5REK1, Q5VIY5, Q60585, Q61751, Q6GQR8, Q7L2R6, Q7TSH9, Q8IYX0, Q8N782, Q8N823, Q8N988, Q8N9F8, Q8NA42, Q8NCK3, Q8NDP4, Q8NEP9, Q8TC21

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	62
Likely benign	8
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

750 predictions. Top by Δscore:

Variant	Effect	Δscore
10:43608701:G:T	donor_gain	1.0000
10:43606547:GTTC:G	donor_gain	0.9900
10:43606551:G:GG	donor_gain	0.9900
10:43606569:GC:G	donor_gain	0.9900
10:43606869:GC:G	donor_gain	0.9900
10:43606995:A:AG	acceptor_gain	0.9900
10:43606995:AGATT:A	acceptor_gain	0.9900
10:43606996:G:GG	acceptor_gain	0.9900
10:43606996:GATT:G	acceptor_gain	0.9900
10:43606996:GATTG:G	acceptor_gain	0.9900
10:43608612:AG:A	acceptor_gain	0.9900
10:43608613:GG:G	acceptor_gain	0.9900
10:43608701:G:GT	donor_gain	0.9900
10:43608737:GTGG:G	donor_gain	0.9900
10:43608739:GG:G	donor_gain	0.9900
10:43608740:GG:G	donor_gain	0.9900
10:43608746:G:GT	donor_gain	0.9900
10:43616289:A:AG	acceptor_gain	0.9900
10:43616290:G:GA	acceptor_gain	0.9900
10:43616290:GTC:G	acceptor_gain	0.9900
10:43606512:G:GT	donor_gain	0.9800
10:43606622:G:T	donor_gain	0.9800
10:43606992:CCCA:C	acceptor_loss	0.9800
10:43606993:CCA:C	acceptor_loss	0.9800
10:43606994:CA:C	acceptor_loss	0.9800
10:43606996:GAT:G	acceptor_gain	0.9800
10:43608609:TGCA:T	acceptor_loss	0.9800
10:43608610:GCA:G	acceptor_loss	0.9800
10:43608611:CAGG:C	acceptor_loss	0.9800
10:43608612:A:AT	acceptor_loss	0.9800

AlphaMissense

2940 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:43616794:T:C	F251L	0.998
10:43616796:C:A	F251L	0.998
10:43616796:C:G	F251L	0.998
10:43617130:T:C	F363L	0.996
10:43617132:T:A	F363L	0.996
10:43617132:T:G	F363L	0.996
10:43616710:T:C	F223L	0.995
10:43616712:C:A	F223L	0.995
10:43616712:C:G	F223L	0.995
10:43617214:T:C	F391L	0.995
10:43617216:T:A	F391L	0.995
10:43617216:T:G	F391L	0.995
10:43616878:T:C	F279L	0.994
10:43616880:C:A	F279L	0.994
10:43616880:C:G	F279L	0.994
10:43616962:T:C	F307L	0.994
10:43616964:T:A	F307L	0.994
10:43616964:T:G	F307L	0.994
10:43616819:G:C	R259P	0.993
10:43616835:T:A	H264Q	0.992
10:43616835:T:G	H264Q	0.992
10:43617298:T:C	F419L	0.992
10:43617300:T:A	F419L	0.992
10:43617300:T:G	F419L	0.992
10:43608648:T:C	F20S	0.991
10:43616739:T:A	H232Q	0.991
10:43616739:T:G	H232Q	0.991
10:43617046:T:C	F335L	0.991
10:43617048:C:A	F335L	0.991
10:43617048:C:G	F335L	0.991

dbSNP variants (sampled 300 via entrez): RS1000095131 (10:43615564 G>A,C,T), RS1000117163 (10:43608571 C>A,T), RS1000182789 (10:43610126 A>G,T), RS1000279872 (10:43612433 T>C), RS1000628163 (10:43606938 A>G), RS1000812139 (10:43618385 C>T), RS1001223450 (10:43610552 C>T), RS1001284039 (10:43610840 C>G), RS1001778805 (10:43615061 T>G), RS1002238891 (10:43608470 CCCCTGAG>C), RS1002270223 (10:43608186 G>C), RS1003454626 (10:43611508 A>T), RS1003526884 (10:43613438 G>A), RS1003568141 (10:43609175 C>T), RS1003758322 (10:43615724 T>C)

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

2 associations (top):

Study	Trait	p-value
GCST005518_1	Premature menopause in childhood cancer survivors	2.000000e-06
GCST009391_256	Metabolite levels	3.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0010426	triacylglycerol 54:8 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression	2
(+)-JQ1 compound	decreases expression	2
Benzo(a)pyrene	affects methylation, increases methylation	2
Estradiol	increases expression	2
aristolochic acid I	decreases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
GSK-J4	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	increases expression	1
benzo(e)pyrene	increases methylation	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
aflatoxin B2	increases methylation	1
nickel sulfate	decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
Temozolomide	increases expression	1
Sunitinib	decreases expression	1
Zoledronic Acid	decreases expression	1
Vorinostat	affects cotreatment, increases expression	1
Formaldehyde	decreases expression	1
Methapyrilene	increases methylation	1
Oxygen	decreases expression	1
Silicon Dioxide	increases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Urethane	decreases expression	1
Zearalenone	increases expression	1
Aflatoxin B1	increases expression	1

Clinical trials (associated diseases)

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