ZNF470

Summary

ZNF470 (zinc finger protein 470, HGNC:22220) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger protein 470 (Q6ECI4). 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. Located in nuclear body.

Source: NCBI Gene 388566 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 134 total
• MANE Select transcript: NM_001001668

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:22220
Approved symbol	ZNF470
Name	zinc finger protein 470
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Aliases	CZF-1, FLJ26175
Ensembl gene	ENSG00000197016
Ensembl biotype	protein_coding
OMIM	620441
Entrez	388566

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 5 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000330619, ENST00000391709, ENST00000594953, ENST00000601059, ENST00000601579, ENST00000601902, ENST00000954844

RefSeq mRNA: 1 — MANE Select: NM_001001668 NM_001001668

CCDS: CCDS33122

Canonical transcript exons

ENST00000330619 — 6 exons

Exon	Start	End
ENSE00001419165	56576713	56582894
ENSE00001551348	56568758	56568883
ENSE00002527133	56574394	56574520
ENSE00003173072	56567468	56568038
ENSE00003459801	56570280	56570371
ENSE00003664201	56574638	56574733

Expression profiles

Bgee: expression breadth ubiquitous, 172 present calls, max score 82.46.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 2.6390 / max 71.7681, expressed in 1188 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177727	0.9223	544
177728	0.6828	407
177726	0.5243	265
177725	0.5096	285

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.46	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	79.24	gold quality
cortical plate	UBERON:0005343	78.87	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	78.87	gold quality
cerebellar hemisphere	UBERON:0002245	77.39	gold quality
cerebellar cortex	UBERON:0002129	77.31	gold quality
anterior cingulate cortex	UBERON:0009835	77.31	gold quality
Brodmann (1909) area 9	UBERON:0013540	77.27	gold quality
right hemisphere of cerebellum	UBERON:0014890	77.09	gold quality
ganglionic eminence	UBERON:0004023	76.95	gold quality
right frontal lobe	UBERON:0002810	76.74	gold quality
hypothalamus	UBERON:0001898	76.45	gold quality
ventricular zone	UBERON:0003053	75.90	gold quality
spinal cord	UBERON:0002240	75.35	gold quality
cerebellum	UBERON:0002037	75.32	gold quality
amygdala	UBERON:0001876	74.97	gold quality
prefrontal cortex	UBERON:0000451	73.99	gold quality
putamen	UBERON:0001874	73.99	gold quality
nucleus accumbens	UBERON:0001882	73.28	gold quality
stromal cell of endometrium	CL:0002255	73.21	gold quality
caudate nucleus	UBERON:0001873	72.93	gold quality
lower esophagus muscularis layer	UBERON:0035833	72.80	gold quality
lower esophagus	UBERON:0013473	72.76	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	72.62	gold quality
calcaneal tendon	UBERON:0003701	72.07	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	71.83	gold quality
popliteal artery	UBERON:0002250	71.81	gold quality
tibial artery	UBERON:0007610	71.81	gold quality
adenohypophysis	UBERON:0002196	71.47	gold quality
islet of Langerhans	UBERON:0000006	71.40	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	5.02

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA2689.1	ZNF470	Other factors with up to three adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:39605530

miRNA regulators (miRDB)

143 targeting ZNF470, 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-1277-5P	100.00	73.95	5056
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-3134	100.00	66.43	777
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-9983-3P	99.94	71.48	3631

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
rattus_norvegicus	Zfp939	ENSRNOG00000064970

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 470 — Q6ECI4 (reviewed: Q6ECI4)

Alternative names: Chondrogenesis zinc finger protein 1

All UniProt accessions (3): Q6ECI4, M0R0Q6, M0R2Y9

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

Tissue specificity. Highly expressed in testis. Very low expression in thymus. No expression in other tissues tested. Expressed in a differentiation stage-specific manner in mesenchymal chondrogenic progenitor cells.

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

Isoforms (2)

UniProt ID	Names	Canonical?
Q6ECI4-1	1	yes
Q6ECI4-2	2

RefSeq proteins (1): NP_001001668* (*=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 (29 total): zinc finger region 17, sequence variant 4, short sequence motif 2, splice variant 2, sequence conflict 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ECI4-F1	71.60	0.14

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 50 (showing top): LIU_BREAST_CANCER, GOCC_NUCLEAR_BODY, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, ZWANG_DOWN_BY_2ND_EGF_PULSE, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ZNF528_TARGET_GENES, MIR1277_5P, MIR335_3P, MIR9983_3P, MIR4803, MIR129_5P, MIR7159_5P, MIR548L, MIR520F_5P, MIR6739_3P

GO Biological Process (2): regulation of transcription by RNA polymerase II (GO:0006357), 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 (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), nuclear body (GO:0016604)

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
cation binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1
nucleoplasm	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

324 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF470	GFM1	Q96RP9	607
ZNF470	POLM	Q9NP87	423
ZNF470	OLIG3	Q7RTU3	374
ZNF470	WNK1	P54963	366
ZNF470	SPRY1	O43609	353
ZNF470	NFIC	P08651	353
ZNF470	SLC6A1	P30531	353
ZNF470	PDGFC	Q9NRA1	353
ZNF470	TCF12	Q99081	352
ZNF470	SUGCT	Q9HAC7	348
ZNF470	NSD1	Q96L73	340
ZNF470	GRB2	P29354	306
ZNF470	SLC25A45	Q8N413	297
ZNF470	CYP20A1	Q6UW02	290
ZNF470	HIRA	P54198	277

IntAct

0 interactions, top by confidence:

BioGRID (4): ZNF470 (Affinity Capture-MS), ZNF470 (Affinity Capture-RNA), GAPDH (Cross-Linking-MS (XL-MS)), ZNF470 (Affinity Capture-RNA)

ESM2 similar proteins: A2VDQ7, A6NNF4, A8MQ14, A8MTY0, E9QAG8, O75290, O75373, P08043, P0CJ79, P10751, P17017, P17027, P17039, P35789, P51522, P51523, Q08AN1, Q14585, Q14587, Q3SYV7, Q3ZCX4, Q4R4C7, Q52M93, Q5MCW4, Q5R5U3, Q5R8X1, Q5R9F0, Q5SXM1, Q6ECI4, Q6JLC9, Q6P3V2, Q6P5C7, Q6ZN57, Q86UE3, Q86XN6, Q86YE8, Q8C827, Q8IYB9, Q8N4W9, Q8N7M2

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	125
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

876 predictions. Top by Δscore:

Variant	Effect	Δscore
19:56568755:CA:C	acceptor_loss	1.0000
19:56568756:A:AG	acceptor_gain	1.0000
19:56568756:AGA:A	acceptor_loss	1.0000
19:56568757:G:GA	acceptor_gain	1.0000
19:56568757:G:GT	acceptor_loss	1.0000
19:56568757:GAT:G	acceptor_gain	1.0000
19:56568880:TCAGG:T	donor_loss	1.0000
19:56568882:AGGTA:A	donor_loss	1.0000
19:56568883:GGT:G	donor_loss	1.0000
19:56568884:GTAG:G	donor_loss	1.0000
19:56568885:T:A	donor_loss	1.0000
19:56570278:A:AG	acceptor_gain	1.0000
19:56570279:G:GG	acceptor_gain	1.0000
19:56574517:GTGG:G	donor_gain	1.0000
19:56574730:CCAGG:C	donor_loss	1.0000
19:56574731:CAGG:C	donor_loss	1.0000
19:56574732:AGG:A	donor_loss	1.0000
19:56574735:T:G	donor_loss	1.0000
19:56568023:GGGAC:G	donor_gain	0.9900
19:56568025:GAC:G	donor_gain	0.9900
19:56568036:CAGG:C	donor_loss	0.9900
19:56568037:AGGT:A	donor_loss	0.9900
19:56568038:GGTA:G	donor_loss	0.9900
19:56568039:G:GA	donor_loss	0.9900
19:56568040:T:A	donor_loss	0.9900
19:56568752:TTACA:T	acceptor_loss	0.9900
19:56568757:GATGA:G	acceptor_gain	0.9900
19:56568884:G:GG	donor_gain	0.9900
19:56570277:CA:C	acceptor_loss	0.9900
19:56570278:AGCTC:A	acceptor_loss	0.9900

AlphaMissense

4797 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:56578233:T:C	F602L	0.997
19:56578235:C:A	F602L	0.997
19:56578235:C:G	F602L	0.997
19:56578317:T:C	F630L	0.997
19:56578319:T:A	F630L	0.997
19:56578319:T:G	F630L	0.997
19:56578401:T:C	F658L	0.997
19:56578403:C:A	F658L	0.997
19:56578403:C:G	F658L	0.997
19:56577729:T:C	F434L	0.996
19:56577731:T:A	F434L	0.996
19:56577731:T:G	F434L	0.996
19:56577390:T:C	F321L	0.995
19:56577392:C:A	F321L	0.995
19:56577392:C:G	F321L	0.995
19:56578149:T:C	F574L	0.995
19:56578151:T:A	F574L	0.995
19:56578151:T:G	F574L	0.995
19:56577897:T:C	F490L	0.994
19:56577899:C:A	F490L	0.994
19:56577899:C:G	F490L	0.994
19:56578485:T:C	F686L	0.994
19:56578487:C:A	F686L	0.994
19:56578487:C:G	F686L	0.994
19:56577306:T:C	F293L	0.993
19:56577308:C:A	F293L	0.993
19:56577308:C:G	F293L	0.993
19:56577474:T:C	F349L	0.993
19:56577476:T:A	F349L	0.993
19:56577476:T:G	F349L	0.993

dbSNP variants (sampled 300 via entrez): RS1000327266 (19:56570497 C>T), RS1000377712 (19:56582453 A>C,G), RS1000951101 (19:56574895 C>T), RS1000986246 (19:56581143 C>T), RS1001202032 (19:56583342 G>A), RS1001299671 (19:56570832 C>T), RS1001416911 (19:56571003 C>A,G,T), RS1001542445 (19:56569897 G>A), RS1001890933 (19:56581964 A>C,G), RS1001950811 (19:56570134 G>C), RS1002114480 (19:56581808 C>A,T), RS1002175614 (19:56575321 A>G), RS1002286416 (19:56575582 C>T), RS1002387323 (19:56582127 CTT>C), RS1002555193 (19:56579231 G>A)

Disease associations

OMIM: gene MIM:620441 | 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
GCST001762_373	Obesity-related traits	9.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004344	birth weight

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression	3
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
GSK-J4	decreases expression	1
TAK-243	increases sumoylation	1
methylmercuric chloride	decreases expression	1
methyleugenol	decreases expression	1
triphenyl phosphate	affects expression	1
nickel sulfate	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, decreases expression	1
clothianidin	increases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol S	increases methylation	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Atrazine	increases expression	1
Benzo(a)pyrene	affects methylation	1
Vanadates	decreases expression	1
Aflatoxin B1	decreases methylation	1
Cadmium Chloride	increases expression	1
Okadaic Acid	increases expression	1
Particulate Matter	increases expression	1

Clinical trials (associated diseases)

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