ZNF471

Summary

ZNF471 (zinc finger protein 471, HGNC:23226) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger protein 471 (Q9BX82). 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 nucleus.

Source: NCBI Gene 57573 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 84 total
• MANE Select transcript: NM_020813

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23226
Approved symbol	ZNF471
Name	zinc finger protein 471
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1396, Z1971, Zfp78
Ensembl gene	ENSG00000196263
Ensembl biotype	protein_coding
OMIM	620162
Entrez	57573

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 12 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000308031, ENST00000591537, ENST00000591759, ENST00000593197, ENST00000858150, ENST00000858151, ENST00000858152, ENST00000858153, ENST00000858154, ENST00000858155, ENST00000962931, ENST00000962932, ENST00000962933

RefSeq mRNA: 2 — MANE Select: NM_020813 NM_001321768, NM_020813

CCDS: CCDS12945

Canonical transcript exons

ENST00000308031 — 5 exons

Exon	Start	End
ENSE00001177968	56518482	56518577
ENSE00001177972	56516275	56516401
ENSE00001177974	56507855	56507920
ENSE00001177981	56524324	56530212
ENSE00001177984	56511517	56511604

Expression profiles

Bgee: expression breadth ubiquitous, 223 present calls, max score 93.18.

FANTOM5 (CAGE): breadth broad, TPM avg 2.9065 / max 488.4674, expressed in 797 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177723	1.2498	484
177724	1.2222	334
177722	0.4345	213

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	93.18	gold quality
left ovary	UBERON:0002119	91.55	gold quality
right ovary	UBERON:0002118	90.21	gold quality
body of uterus	UBERON:0009853	87.94	gold quality
right hemisphere of cerebellum	UBERON:0014890	87.86	gold quality
tibial nerve	UBERON:0001323	87.31	gold quality
ovary	UBERON:0000992	87.10	gold quality
cortical plate	UBERON:0005343	86.97	gold quality
cerebellar hemisphere	UBERON:0002245	86.78	gold quality
cerebellar cortex	UBERON:0002129	86.62	gold quality
calcaneal tendon	UBERON:0003701	86.57	gold quality
lower esophagus muscularis layer	UBERON:0035833	86.34	gold quality
lower esophagus	UBERON:0013473	86.29	gold quality
endocervix	UBERON:0000458	85.93	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	85.93	gold quality
muscle layer of sigmoid colon	UBERON:0035805	85.44	gold quality
right lobe of thyroid gland	UBERON:0001119	85.40	gold quality
left lobe of thyroid gland	UBERON:0001120	85.19	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	85.14	gold quality
mucosa of stomach	UBERON:0001199	85.09	gold quality
cerebellum	UBERON:0002037	84.98	gold quality
popliteal artery	UBERON:0002250	84.83	gold quality
tibial artery	UBERON:0007610	84.81	gold quality
thyroid gland	UBERON:0002046	84.47	gold quality
aorta	UBERON:0000947	84.23	gold quality
artery	UBERON:0001637	84.21	gold quality
right frontal lobe	UBERON:0002810	84.21	gold quality
descending thoracic aorta	UBERON:0002345	83.83	gold quality
corpus callosum	UBERON:0002336	83.79	gold quality
ganglionic eminence	UBERON:0004023	83.79	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-CURD-6	yes	3706.68
E-ENAD-20	no	42.66
E-ANND-3	no	5.48
E-MTAB-6678	no	3.90

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA2554.1	ZNF471	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:39605320

miRNA regulators (miRDB)

116 targeting ZNF471, 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-340-5P	100.00	72.50	4437
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3605-5P	99.96	67.12	932
HSA-MIR-218-5P	99.93	72.22	2103
HSA-MIR-552-5P	99.93	68.56	1583
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-4648	99.91	67.00	710
HSA-MIR-3686	99.90	70.53	2432
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-374B-5P	99.90	69.98	2734
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-4503	99.85	71.45	1869
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-544A	99.84	68.66	1965
HSA-MIR-576-5P	99.84	70.46	2582
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-130B-5P	99.83	68.50	1888
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-6875-3P	99.82	70.26	2983
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-636	99.80	69.58	1500
HSA-MIR-6764-5P	99.75	67.89	2304

Literature-anchored findings (GeneRIF, showing 5)

• This is the first study to report hypermethylation of LRPPRC, RAB6C, and ZNF471 in squamous cell carcinoma of the tongue (PMID:28255813)
• ZNF471 acts as a tumor suppressor in gastric cancer by transcriptionally inhibiting downstream targets TFAP2A and PLS3. (PMID:29610526)
• The tumor suppressor Zinc finger protein 471 suppresses breast cancer growth and metastasis through inhibiting AKT and Wnt/beta-catenin signaling. (PMID:33203470)
• ZNF471 Interacts with BANP to Reduce Tumour Malignancy by Inactivating PI3K/AKT/mTOR Signalling but is Frequently Silenced by Aberrant Promoter Methylation in Renal Cell Carcinoma. (PMID:38169650)
• Suppression of N-Glycosylation of Zinc Finger Protein 471 Affects Proliferation, Invasion, and Docetaxel Sensitivity of Tongue Squamous Cell Carcinoma via Regulation of c-Myc. (PMID:38749608)

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 471 — Q9BX82 (reviewed: Q9BX82)

Alternative names: EZFIT-related protein 1

All UniProt accessions (2): K7EPX1, Q9BX82

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?
Q9BX82-1	1	yes
Q9BX82-2	2

RefSeq proteins (2): NP_001308697, NP_065864* (*=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 (26 total): zinc finger region 15, sequence variant 5, 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-Q9BX82-F1	72.57	0.29

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 62 (showing top): ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, VECCHI_GASTRIC_CANCER_EARLY_DN, STAT1_02, YKACATTT_UNKNOWN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, STAT1_03, PRC2_SUZ12_UP.V1_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, MIR607, MIR340_5P, MIR561_3P, MIR5590_3P, MIR142_5P, MIR3686, MIR218_5P

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

GO Molecular Function (6): 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)

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
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

430 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF471	SLFN12	Q8IYM2	458
ZNF471	KIAA1755	Q5JYT7	446
ZNF471	THOC5	Q13769	433
ZNF471	PACSIN2	Q9UNF0	417
ZNF471	CTSF	Q9UBX1	410
ZNF471	PLS3	P13797	386
ZNF471	TFAP2A	P05549	378
ZNF471	FOXI2	Q6ZQN5	374
ZNF471	SLC35A1	P78382	371
ZNF471	EVC2	Q86UK5	365
ZNF471	CXCL5	P42830	364
ZNF471	SUSD5	O60279	356
ZNF471	NR2F1	P10589	352
ZNF471	SMO	Q99835	349
ZNF471	SLFN12L	Q6IEE8	346

IntAct

11 interactions, top by confidence:

A	B	Type	Score
ZNF471	BANP	psi-mi:“MI:0915”(physical association)	0.570
MIS18A	ZNF471	psi-mi:“MI:0915”(physical association)	0.400
IGF1R	HAX1	psi-mi:“MI:0914”(association)	0.350
HNF4A	TAF4	psi-mi:“MI:2364”(proximity)	0.270
EPHA1	PIK3R2	psi-mi:“MI:2364”(proximity)	0.270
ZNF471		psi-mi:“MI:0915”(physical association)	0.000

BioGRID (17): ZNF471 (Two-hybrid), ZNF471 (Two-hybrid), ZNF471 (Two-hybrid), ZNF471 (Two-hybrid), CARD14 (Two-hybrid), COG7 (Two-hybrid), HAUS1 (Two-hybrid), GOLGA8EP (Two-hybrid), GOLGA8F (Two-hybrid), ZNF471 (Two-hybrid), ZNF471 (Two-hybrid), ZNF471 (Two-hybrid), ZNF471 (Two-hybrid), ZNF471 (Affinity Capture-Western), ZNF471 (Proximity Label-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, 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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	73
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1041 predictions. Top by Δscore:

Variant	Effect	Δscore
19:56507887:G:GT	donor_gain	0.9900
19:56507888:A:G	donor_gain	0.9900
19:56508034:G:GT	donor_gain	0.9900
19:56518477:T:G	acceptor_gain	0.9900
19:56518478:GTA:G	acceptor_loss	0.9900
19:56518479:TAGG:T	acceptor_loss	0.9900
19:56518480:A:AG	acceptor_gain	0.9900
19:56518481:G:A	acceptor_loss	0.9900
19:56518481:G:GG	acceptor_gain	0.9900
19:56518574:TCAGG:T	donor_loss	0.9900
19:56518578:G:GC	donor_loss	0.9900
19:56518579:T:G	donor_loss	0.9900
19:56507876:G:GT	donor_gain	0.9800
19:56507894:GC:G	donor_gain	0.9800
19:56507936:TTTGG:T	donor_gain	0.9800
19:56508001:TCGCG:T	donor_gain	0.9800
19:56511516:GCCTT:G	acceptor_gain	0.9800
19:56516177:T:G	acceptor_gain	0.9800
19:56518481:GGT:G	acceptor_gain	0.9800
19:56507891:A:T	donor_gain	0.9700
19:56507933:T:TA	donor_gain	0.9700
19:56507934:G:GA	donor_gain	0.9700
19:56507940:G:GT	donor_gain	0.9700
19:56507967:G:GT	donor_gain	0.9700
19:56508071:ACTCG:A	donor_gain	0.9700
19:56511515:A:AG	acceptor_gain	0.9700
19:56511516:G:GG	acceptor_gain	0.9700
19:56518474:ATAT:A	acceptor_gain	0.9700
19:56518481:GGTC:G	acceptor_gain	0.9700
19:56507892:GAGC:G	donor_gain	0.9600

AlphaMissense

4224 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:56525469:T:C	F468L	0.994
19:56525471:T:A	F468L	0.994
19:56525471:T:G	F468L	0.994
19:56525301:T:C	F412L	0.992
19:56525303:C:A	F412L	0.992
19:56525303:C:G	F412L	0.992
19:56525553:T:C	F496L	0.992
19:56525555:T:A	F496L	0.992
19:56525555:T:G	F496L	0.992
19:56525721:T:C	F552L	0.992
19:56525723:C:A	F552L	0.992
19:56525723:C:G	F552L	0.992
19:56525498:T:A	H477Q	0.991
19:56525498:T:G	H477Q	0.991
19:56525385:T:C	F440L	0.990
19:56525387:T:A	F440L	0.990
19:56525387:T:G	F440L	0.990
19:56525637:T:C	F524L	0.989
19:56525639:C:A	F524L	0.989
19:56525639:C:G	F524L	0.989
19:56524962:T:C	F299L	0.987
19:56524964:C:A	F299L	0.987
19:56524964:C:G	F299L	0.987
19:56525046:T:C	F327L	0.986
19:56525048:C:A	F327L	0.986
19:56525048:C:G	F327L	0.986
19:56525217:T:C	F384L	0.986
19:56525219:C:A	F384L	0.986
19:56525219:C:G	F384L	0.986
19:56525496:C:G	H477D	0.986

dbSNP variants (sampled 300 via entrez): RS1000124736 (19:56508616 C>T), RS1000129499 (19:56527727 T>A), RS1000183826 (19:56527541 C>G), RS1000185355 (19:56522255 C>T), RS1000196148 (19:56518394 T>C), RS1000397971 (19:56514172 G>A,T), RS1000508240 (19:56506157 C>T), RS1000617446 (19:56514320 C>A), RS1000648325 (19:56517192 A>G), RS1000867295 (19:56521588 G>A), RS1001128459 (19:56510082 G>A,C), RS1001350774 (19:56528027 C>T), RS1001436244 (19:56514743 A>G), RS1001466657 (19:56514977 A>G), RS1001482325 (19:56527731 A>G,T)

Disease associations

OMIM: gene MIM:620162 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
triphenyl phosphate	affects expression	1
bisphenol A	increases expression	1
arsenite	increases methylation, decreases expression	1
Benzo(a)pyrene	increases methylation	1
Doxorubicin	decreases expression	1
Nickel	decreases expression	1
Tretinoin	increases expression	1
Aflatoxin B1	decreases methylation	1
Asbestos, Crocidolite	decreases expression	1
Antirheumatic Agents	increases expression	1

Clinical trials (associated diseases)

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