ZNF490

Summary

ZNF490 (zinc finger protein 490, HGNC:23705) is a protein-coding gene on chromosome 19p13.2-p13.13, encoding Zinc finger protein 490 (Q9ULM2). 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 57474 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 45 total
• MANE Select transcript: NM_020714

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23705
Approved symbol	ZNF490
Name	zinc finger protein 490
Location	19p13.2-p13.13
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1198
Ensembl gene	ENSG00000188033
Ensembl biotype	protein_coding
OMIM	620118
Entrez	57474

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000311437, ENST00000414906, ENST00000440366, ENST00000465656, ENST00000944721

RefSeq mRNA: 1 — MANE Select: NM_020714 NM_020714

CCDS: CCDS12272

Canonical transcript exons

ENST00000311437 — 5 exons

Exon	Start	End
ENSE00001419843	12576100	12581724
ENSE00003488187	12609158	12609202
ENSE00003576373	12582850	12582910
ENSE00003656957	12583430	12583556
ENSE00003843869	12610564	12610813

Expression profiles

Bgee: expression breadth ubiquitous, 174 present calls, max score 97.90.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.5334 / max 85.6525, expressed in 1731 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
179318	3.5445	1539
179319	2.9517	1381
179316	0.0285	10
179317	0.0086	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	97.90	gold quality
oviduct epithelium	UBERON:0004804	94.41	gold quality
tendon of biceps brachii	UBERON:0008188	89.74	gold quality
medial globus pallidus	UBERON:0002477	83.58	gold quality
sural nerve	UBERON:0015488	83.53	gold quality
tendon	UBERON:0000043	81.99	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.27	gold quality
calcaneal tendon	UBERON:0003701	78.84	gold quality
globus pallidus	UBERON:0001875	77.93	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	77.92	gold quality
ileal mucosa	UBERON:0000331	77.37	silver quality
cortical plate	UBERON:0005343	76.44	gold quality
tibialis anterior	UBERON:0001385	76.36	silver quality
bone marrow cell	CL:0002092	76.31	gold quality
leukocyte	CL:0000738	75.14	gold quality
monocyte	CL:0000576	75.09	gold quality
fallopian tube	UBERON:0003889	73.94	gold quality
islet of Langerhans	UBERON:0000006	73.88	gold quality
stromal cell of endometrium	CL:0002255	73.56	gold quality
granulocyte	CL:0000094	73.21	gold quality
ganglionic eminence	UBERON:0004023	73.17	gold quality
adrenal tissue	UBERON:0018303	72.79	gold quality
ventricular zone	UBERON:0003053	72.08	gold quality
lymph node	UBERON:0000029	72.00	gold quality
colonic epithelium	UBERON:0000397	71.84	gold quality
corpus callosum	UBERON:0002336	71.71	gold quality
blood	UBERON:0000178	70.34	gold quality
spleen	UBERON:0002106	70.20	gold quality
secondary oocyte	CL:0000655	70.00	silver quality
pancreatic ductal cell	CL:0002079	69.66	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.18

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA2495.1	ZNF490	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:39605320

Upstream regulators (CollecTRI, top): STAT1

miRNA regulators (miRDB)

134 targeting ZNF490, 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-3925-3P	100.00	69.95	1237
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-6748-5P	100.00	65.81	1057
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-3134	100.00	66.43	777
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-4487	99.96	64.58	1252
HSA-MIR-4493	99.90	66.48	977
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-605-3P	99.88	69.22	1833
HSA-MIR-221-5P	99.86	65.45	1052
HSA-MIR-8073	99.86	65.21	1118
HSA-MIR-4728-5P	99.85	69.39	4718

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 490 — Q9ULM2 (reviewed: Q9ULM2)

All UniProt accessions (3): Q9ULM2, C9JID3, F8WDW6

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_065765* (*=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
IPR050752	C2H2-ZF_domain	Family

Pfam: PF00096, PF01352, PF13465

UniProt features (16 total): zinc finger region 13, chain 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9ULM2-F1	71.91	0.14

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 91 (showing top): BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_DN, MODULE_239, chr19p13, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ALKBH3_TARGET_GENES, CBX5_TARGET_GENES, CBX7_TARGET_GENES, CIITA_TARGET_GENES, DIDO1_TARGET_GENES, ELF2_TARGET_GENES, FOXG1_TARGET_GENES, FOXN3_TARGET_GENES, HES4_TARGET_GENES, HMG20B_TARGET_GENES

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

GO Molecular Function (7): 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), protein binding (GO:0005515), metal ion binding (GO:0046872), sequence-specific double-stranded DNA binding (GO:1990837)

GO Cellular Component (1): nucleus (GO:0005634)

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
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
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
binding	1
cation binding	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

582 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF490	PRADC1	Q9BSG0	571
ZNF490	NBPF3	Q9H094	565
ZNF490	DGCR6L	Q9BY27	490
ZNF490	TTC22	Q5TAA0	475
ZNF490	LRIG2	O94898	474
ZNF490	BLOC1S3	Q6QNY0	464
ZNF490	OSBPL3	Q9H4L5	455
ZNF490	SYNE1	Q8NF91	452
ZNF490	PRSS37	A4D1T9	447
ZNF490	KRTCAP3	Q53RY4	444
ZNF490	SLC35E2A	P0CK97	435
ZNF490	CCDC18	Q5T9S5	430
ZNF490	TBC1D7	Q9P0N9	429
ZNF490	DTNA	Q9Y4J8	426
ZNF490	SLC35E2B	P0CK96	419

IntAct

122 interactions, top by confidence:

A	B	Type	Score
ZNF490	CEP70	psi-mi:“MI:0915”(physical association)	0.780
TRIM41	ZNF490	psi-mi:“MI:0915”(physical association)	0.780
MDFI	ZNF490	psi-mi:“MI:0915”(physical association)	0.780
ZNF490	ZC4H2	psi-mi:“MI:0915”(physical association)	0.780
CEP70	ZNF490	psi-mi:“MI:0915”(physical association)	0.780
ZNF490	TRIM41	psi-mi:“MI:0915”(physical association)	0.780
ZNF490	MDFI	psi-mi:“MI:0915”(physical association)	0.780
ZC4H2	ZNF490	psi-mi:“MI:0915”(physical association)	0.780
MTUS2	ZNF490	psi-mi:“MI:0915”(physical association)	0.740
ZNF490	MTUS2	psi-mi:“MI:0915”(physical association)	0.740
KRTAP10-7	ZNF490	psi-mi:“MI:0915”(physical association)	0.720
NDEL1	ZNF490	psi-mi:“MI:0915”(physical association)	0.720
ZNF490	NDEL1	psi-mi:“MI:0915”(physical association)	0.720
ZNF490	KRTAP10-7	psi-mi:“MI:0915”(physical association)	0.720

BioGRID (66): ZNF490 (Two-hybrid), ZNF490 (Two-hybrid), ZNF490 (Two-hybrid), ZNF490 (Two-hybrid), CCDC136 (Two-hybrid), CEP70 (Two-hybrid), TSGA10 (Two-hybrid), NDEL1 (Two-hybrid), LZTS2 (Two-hybrid), TRIM41 (Two-hybrid), KRT40 (Two-hybrid), KRTAP10-7 (Two-hybrid), KRTAP10-3 (Two-hybrid), ZNF490 (Two-hybrid), ZNF490 (Two-hybrid)

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: A0JPK3, A2RRD8, A2VDQ7, A3KN32, A8MUZ8, A8MWA4, C9JN71, E9QAG8, O60384, O60765, O75820, P0CH99, P0CI00, P10076, P10755, P15621, P16374, P16415, P17017, P17024, P51523, P52737, P52740, Q06730, Q06732, Q08AG5, Q0D2J5, Q13106, Q13360, Q15928, Q15935, Q15973, Q32M78, Q3KP31, Q4R4C7, Q4R6J4, Q4R882, Q5R9F0, Q5RC79, Q5REI6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 39 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Keratinization	5	12.1×	6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	34
Likely benign	2
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1407 predictions. Top by Δscore:

Variant	Effect	Δscore
19:12581720:GACTT:G	acceptor_gain	1.0000
19:12581722:CTT:C	acceptor_gain	1.0000
19:12581723:TT:T	acceptor_gain	1.0000
19:12581725:C:CC	acceptor_gain	1.0000
19:12581725:CTGT:C	acceptor_loss	1.0000
19:12582845:CTCA:C	donor_loss	1.0000
19:12582846:TCACC:T	donor_loss	1.0000
19:12582847:CA:C	donor_loss	1.0000
19:12582848:ACC:A	donor_loss	1.0000
19:12582849:C:CT	donor_loss	1.0000
19:12583555:TCCTA:T	acceptor_loss	1.0000
19:12583557:C:CA	acceptor_loss	1.0000
19:12583558:T:C	acceptor_loss	1.0000
19:12583579:T:C	acceptor_gain	1.0000
19:12583579:T:TC	acceptor_gain	1.0000
19:12609156:A:AC	donor_gain	1.0000
19:12609157:C:CC	donor_gain	1.0000
19:12610582:T:A	donor_gain	1.0000
19:12611080:ATGG:A	donor_loss	1.0000
19:12611081:TGG:T	donor_loss	1.0000
19:12611084:T:A	donor_loss	1.0000
19:12623684:ATATT:A	acceptor_gain	1.0000
19:12623685:T:G	acceptor_gain	1.0000
19:12623686:A:AG	acceptor_gain	1.0000
19:12623686:ATT:A	acceptor_gain	1.0000
19:12623686:ATTG:A	acceptor_gain	1.0000
19:12623687:T:G	acceptor_gain	1.0000
19:12623688:T:TA	acceptor_gain	1.0000
19:12623689:G:A	acceptor_gain	1.0000
19:12623692:T:A	acceptor_gain	1.0000

AlphaMissense

3540 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:12581382:G:C	F231L	0.993
19:12581382:G:T	F231L	0.993
19:12581384:A:G	F231L	0.993
19:12581298:G:C	F259L	0.991
19:12581298:G:T	F259L	0.991
19:12581300:A:G	F259L	0.991
19:12583522:A:G	F66S	0.991
19:12580542:G:C	F511L	0.987
19:12580542:G:T	F511L	0.987
19:12580544:A:G	F511L	0.987
19:12581355:A:C	H240Q	0.987
19:12581355:A:T	H240Q	0.987
19:12581214:A:C	F287L	0.986
19:12581214:A:T	F287L	0.986
19:12581216:A:G	F287L	0.986
19:12581275:C:G	R267P	0.986
19:12580626:G:C	F483L	0.985
19:12580626:G:T	F483L	0.985
19:12580628:A:G	F483L	0.985
19:12583521:G:C	F66L	0.985
19:12583521:G:T	F66L	0.985
19:12583523:A:G	F66L	0.985
19:12581130:G:C	F315L	0.984
19:12581130:G:T	F315L	0.984
19:12581132:A:G	F315L	0.984
19:12581343:A:C	H244Q	0.981
19:12581343:A:T	H244Q	0.981
19:12580710:G:C	F455L	0.980
19:12580710:G:T	F455L	0.980
19:12580712:A:G	F455L	0.980

dbSNP variants (sampled 300 via entrez): RS1000000748 (19:12579952 A>T), RS1000166965 (19:12601434 C>A,T), RS1000217519 (19:12605046 G>A,C), RS1000275387 (19:12601767 C>A,T), RS1000362989 (19:12611378 C>T), RS1000369713 (19:12605891 ATT>A,AT,ATTT), RS1000422144 (19:12605744 T>C), RS1000543427 (19:12588161 G>T), RS1000599747 (19:12578720 G>T), RS1000685868 (19:12594592 A>G,T), RS1000705726 (19:12594349 C>T), RS1000782330 (19:12583693 G>C,T), RS1000930119 (19:12577970 C>G), RS1000973502 (19:12606038 G>A), RS1001183734 (19:12580340 G>A,T)

Disease associations

OMIM: gene MIM:620118 | 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
GCST010988_15	Adult body size	1.000000e-08

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
arsenite	affects binding, increases reaction	1
ferrous chloride	decreases expression	1
abrine	decreases expression	1
licochalcone B	increases expression	1
Sunitinib	increases expression	1
Acetaminophen	increases expression	1
Air Pollutants	affects expression, increases abundance	1
Ozone	affects expression, increases abundance	1
Tetrachlorodibenzodioxin	increases expression	1
Urethane	increases expression	1
Copper Sulfate	increases expression	1
Lactic Acid	decreases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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