ZNF480

Summary

ZNF480 (zinc finger protein 480, HGNC:23305) is a protein-coding gene on chromosome 19q13.41, encoding Zinc finger protein 480 (Q8WV37). Involved in transcriptional regulation as an activator.

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 cytosol and nucleoplasm.

Source: NCBI Gene 147657 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 78 total
• MANE Select transcript: NM_144684

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23305
Approved symbol	ZNF480
Name	zinc finger protein 480
Location	19q13.41
Locus type	gene with protein product
Status	Approved
Aliases	MGC32104
Ensembl gene	ENSG00000198464
Ensembl biotype	protein_coding
OMIM	613910
Entrez	147657

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 11 protein_coding, 1 nonsense_mediated_decay

ENST00000334564, ENST00000335090, ENST00000468240, ENST00000490272, ENST00000595962, ENST00000598016, ENST00000852522, ENST00000852523, ENST00000852524, ENST00000944566, ENST00000944567, ENST00000944568

RefSeq mRNA: 4 — MANE Select: NM_144684 NM_001297624, NM_001297625, NM_001412109, NM_144684

CCDS: CCDS12850, CCDS74437, CCDS77346

Canonical transcript exons

ENST00000595962 — 5 exons

Exon	Start	End
ENSE00002501787	52314153	52314279
ENSE00003147865	52321579	52325922
ENSE00003612625	52315834	52315962
ENSE00003660758	52300394	52300484
ENSE00003844712	52297169	52297223

Expression profiles

Bgee: expression breadth ubiquitous, 166 present calls, max score 86.39.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.5428 / max 107.3570, expressed in 1502 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177297	4.5428	1502

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	86.39	gold quality
calcaneal tendon	UBERON:0003701	85.65	gold quality
apex of heart	UBERON:0002098	85.26	gold quality
islet of Langerhans	UBERON:0000006	84.98	gold quality
right atrium auricular region	UBERON:0006631	84.66	gold quality
monocyte	CL:0000576	84.17	gold quality
leukocyte	CL:0000738	83.94	gold quality
gastrocnemius	UBERON:0001388	83.90	gold quality
mononuclear cell	CL:0000842	83.86	gold quality
muscle of leg	UBERON:0001383	83.30	gold quality
heart left ventricle	UBERON:0002084	82.75	gold quality
mucosa of transverse colon	UBERON:0004991	82.56	gold quality
ganglionic eminence	UBERON:0004023	82.14	gold quality
cortical plate	UBERON:0005343	81.83	gold quality
lower esophagus	UBERON:0013473	81.83	gold quality
lower esophagus muscularis layer	UBERON:0035833	81.83	gold quality
cardiac atrium	UBERON:0002081	81.65	gold quality
cardiac ventricle	UBERON:0002082	81.36	gold quality
rectum	UBERON:0001052	81.11	gold quality
colonic epithelium	UBERON:0000397	81.04	gold quality
hindlimb stylopod muscle	UBERON:0004252	80.95	gold quality
left adrenal gland cortex	UBERON:0035825	80.34	gold quality
left adrenal gland	UBERON:0001234	80.21	gold quality
heart	UBERON:0000948	79.76	gold quality
body of stomach	UBERON:0001161	79.72	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	79.64	gold quality
muscle layer of sigmoid colon	UBERON:0035805	79.59	gold quality
esophagus	UBERON:0001043	79.38	gold quality
right adrenal gland cortex	UBERON:0035827	79.22	gold quality
right adrenal gland	UBERON:0001233	79.11	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.55

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

Target	Regulation
AP1

miRNA regulators (miRDB)

110 targeting ZNF480, 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-3925-3P	100.00	69.95	1237
HSA-MIR-3064-3P	100.00	70.09	1254
HSA-MIR-3134	100.00	66.43	777
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-7152-3P	99.97	67.47	849
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-6753-3P	99.93	66.57	637
HSA-MIR-7107-3P	99.93	66.73	627
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-5195-3P	99.92	70.92	1877
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-6499-3P	99.90	66.38	1212
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-8062	99.88	68.43	995
HSA-MIR-3140-3P	99.88	68.47	2069
HSA-MIR-7978	99.86	66.90	856
HSA-MIR-659-3P	99.85	70.69	1620
HSA-MIR-629-3P	99.85	67.99	1875
HSA-MIR-5010-3P	99.83	70.60	2357
HSA-MIR-6844	99.82	70.69	2423
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-4799-5P	99.82	70.60	2663
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248

Literature-anchored findings (GeneRIF, showing 1)

• This supports the notion that de novo mutations in ZNF480 are extremely rare in schizophrenia (PMID:23425335)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	zfx	ENSDARG00000074453
danio_rerio		ENSDARG00000098424
mus_musculus	Zfy2	ENSMUSG00000000103
mus_musculus	Zfy1	ENSMUSG00000053211
rattus_norvegicus	Zfy1	ENSRNOG00000053042

Paralogs (38): ZFX (ENSG00000005889), ZBTB11 (ENSG00000066422), ZFAT (ENSG00000066827), ZFY (ENSG00000067646), ZNF586 (ENSG00000083828), IKZF5 (ENSG00000095574), ZNF419 (ENSG00000105136), ZNF549 (ENSG00000121406), ZSCAN20 (ENSG00000121903), ZNF304 (ENSG00000131845), PRDM15 (ENSG00000141956), ZNF660 (ENSG00000144792), ZNF711 (ENSG00000147180), ZNF773 (ENSG00000152439), ZNF256 (ENSG00000152454), ZNF837 (ENSG00000152475), ZNF691 (ENSG00000164011), ZNF610 (ENSG00000167554), E4F1 (ENSG00000167967), ZNF562 (ENSG00000171466), ZNF561 (ENSG00000171469), ZNF584 (ENSG00000171574), ZIK1 (ENSG00000171649), ZNF570 (ENSG00000171827), ZSCAN2 (ENSG00000176371), ZNF552 (ENSG00000178935), ZNF154 (ENSG00000179909), ZNF792 (ENSG00000180884), ZNF793 (ENSG00000188227), ZNF548 (ENSG00000188785), ZNF79 (ENSG00000196152), ZNF418 (ENSG00000196724), ZNF772 (ENSG00000197128), ZNF583 (ENSG00000198440), ZNF551 (ENSG00000204519), ZNF134 (ENSG00000213762), ZNF587B (ENSG00000269343), ZNF8 (ENSG00000278129)

Protein

Protein identifiers

Zinc finger protein 480 — Q8WV37 (reviewed: Q8WV37)

All UniProt accessions (4): Q8WV37, C9IZQ0, F8WEZ9, M0R367

UniProt curated annotations — full annotation on UniProt →

Function. Involved in transcriptional regulation as an activator.

Subcellular location. Nucleus.

Tissue specificity. Expressed in fetal heart, heart, skeletal muscle, pancreas and placenta.

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

Isoforms (3)

UniProt ID	Names	Canonical?
Q8WV37-1	1	yes
Q8WV37-2	2
Q8WV37-3	3

RefSeq proteins (4): NP_001284553, NP_001284554, NP_001399038, NP_653285* (*=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, PF13465

UniProt features (22 total): zinc finger region 12, cross-link 4, splice variant 2, sequence variant 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WV37-F1	70.95	0.35

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (4): 122, 125, 195, 220

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 57 (showing top): GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, OISHI_CHOLANGIOMA_STEM_CELL_LIKE_UP, KRAS.AMP.LUNG_UP.V1_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, NAB2_TARGET_GENES, ZNF350_TARGET_GENES, MIR335_3P, MIR6885_3P, MIR511_5P, MIR4762_3P, MIR6830_5P, MIR6516_5P, MIR6505_5P, MIR3925_3P, MIR5571_5P

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), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (4): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytosol (GO:0005829), nuclear lumen (GO:0031981)

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
cellular anatomical structure	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
binding	1
cation binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cytoplasm	1
nucleus	1
intracellular organelle lumen	1

Protein interactions and networks

STRING

416 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF480	PRR19	A6NJB7	397
ZNF480	KRTAP5-10	Q6L8G5	380
ZNF480	GIPC3	Q8TF64	380
ZNF480	ALS2CL	Q60I27	368
ZNF480	VSIG10L	Q86VR7	358
ZNF480	GPATCH4	Q5T3I0	308
ZNF480	FBXW12	Q6X9E4	301
ZNF480	USP17L17	D6RBQ6	297
ZNF480	DEFB126	Q9BYW3	277
ZNF480	ALDH16A1	Q8IZ83	275
ZNF480	NGRN	Q9NPE2	270
ZNF480	PLEKHA6	Q9Y2H5	269
ZNF480	SLC2A4RG	Q9NR83	254
ZNF480	DNTTIP2	Q5QJE6	250
ZNF480	TMBIM1	Q969X1	248

IntAct

11 interactions, top by confidence:

A	B	Type	Score
CCNDBP1	ZNF480	psi-mi:“MI:0915”(physical association)	0.560
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.530
ZNF480	KDM1A	psi-mi:“MI:0915”(physical association)	0.370
ZNF480	IPO8	psi-mi:“MI:0914”(association)	0.350
ZNF467	ZNF320	psi-mi:“MI:0914”(association)	0.350
NOTCH2	ZNF320	psi-mi:“MI:0914”(association)	0.350
LTBP2	ZNF320	psi-mi:“MI:0914”(association)	0.350
CUL9	NVL	psi-mi:“MI:0914”(association)	0.350
ZNF480	CCNDBP1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (11): ZNF480 (Two-hybrid), ZNF480 (Affinity Capture-MS), ZNF480 (Affinity Capture-MS), ZNF480 (Affinity Capture-MS), ZNF480 (Affinity Capture-MS), ZNF480 (Affinity Capture-MS), ZNF480 (Affinity Capture-MS), ZNF480 (Affinity Capture-MS), ZNF480 (Protein-RNA), ZNF480 (Affinity Capture-RNA), KDM1A (Two-hybrid)

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	62
Likely benign	2
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1351 predictions. Top by Δscore:

Variant	Effect	Δscore
19:52297219:GGCGC:G	donor_gain	0.9900
19:52297220:GCGC:G	donor_gain	0.9900
19:52297220:GCGCG:G	donor_gain	0.9900
19:52297222:GC:G	donor_gain	0.9900
19:52297224:G:GG	donor_gain	0.9900
19:52299347:A:AG	donor_gain	0.9900
19:52300306:GG:G	donor_gain	0.9900
19:52300307:GG:G	donor_gain	0.9900
19:52315828:A:AG	acceptor_gain	0.9900
19:52315829:A:G	acceptor_gain	0.9900
19:52315829:AACAG:A	acceptor_loss	0.9900
19:52315830:ACAG:A	acceptor_loss	0.9900
19:52315831:CAGGA:C	acceptor_loss	0.9900
19:52315832:A:AG	acceptor_gain	0.9900
19:52315833:G:GA	acceptor_loss	0.9900
19:52315833:G:GG	acceptor_gain	0.9900
19:52315833:GGA:G	acceptor_gain	0.9900
19:52315958:CACAG:C	donor_loss	0.9900
19:52315959:ACAG:A	donor_loss	0.9900
19:52315960:CAGGT:C	donor_loss	0.9900
19:52315962:GGTAA:G	donor_loss	0.9900
19:52315963:GTAA:G	donor_loss	0.9900
19:52315964:T:A	donor_loss	0.9900
19:52297221:CGC:C	donor_gain	0.9800
19:52297221:CGCG:C	donor_loss	0.9800
19:52297222:GCG:G	donor_gain	0.9800
19:52297223:CGT:C	donor_loss	0.9800
19:52297224:G:GA	donor_loss	0.9800
19:52297225:TGA:T	donor_loss	0.9800
19:52297226:G:GT	donor_loss	0.9800

AlphaMissense

3565 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:52322640:T:C	F464L	0.995
19:52322642:C:A	F464L	0.995
19:52322642:C:G	F464L	0.995
19:52322724:T:C	F492L	0.995
19:52322726:C:A	F492L	0.995
19:52322726:C:G	F492L	0.995
19:52322808:T:C	F520L	0.990
19:52322810:T:A	F520L	0.990
19:52322810:T:G	F520L	0.990
19:52322669:T:A	H473Q	0.988
19:52322669:T:G	H473Q	0.988
19:52322731:G:C	R494P	0.986
19:52322667:C:G	H473D	0.985
19:52322472:T:C	F408L	0.984
19:52322474:T:A	F408L	0.984
19:52322474:T:G	F408L	0.984
19:52322556:T:C	F436L	0.984
19:52322558:T:A	F436L	0.984
19:52322558:T:G	F436L	0.984
19:52322681:T:A	H477Q	0.984
19:52322681:T:G	H477Q	0.984
19:52322671:A:C	Q474P	0.982
19:52322429:T:A	H393Q	0.981
19:52322429:T:G	H393Q	0.981
19:52322659:T:C	L470P	0.981
19:52322641:T:C	F464S	0.980
19:52322753:T:A	H501Q	0.980
19:52322753:T:G	H501Q	0.980
19:52322667:C:A	H473N	0.979
19:52314186:T:C	F36L	0.978

dbSNP variants (sampled 300 via entrez): RS1000004859 (19:52313983 A>C), RS1000078366 (19:52312479 G>T), RS1000101457 (19:52320071 C>G), RS1000219687 (19:52309354 A>G), RS1000254206 (19:52296985 C>G,T), RS1000434555 (19:52302949 C>G,T), RS1000438241 (19:52313699 A>G), RS1000540829 (19:52298686 G>A), RS1000739234 (19:52310475 ATTTTT>A,ATTT,ATTTT,ATTTTTT,ATTTTTTT,ATTTTTTTTTTTTTTTTTTT), RS1000807273 (19:52303136 C>A,G,T), RS1001144550 (19:52299227 T>C,G), RS1001252276 (19:52309202 C>T), RS1001253671 (19:52295356 G>T), RS1001273608 (19:52303199 C>T), RS1001641493 (19:52303478 A>G)

Disease associations

OMIM: gene MIM:613910 | 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

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	affects cotreatment, increases abundance, increases oxidation, affects expression	2
Benzo(a)pyrene	affects methylation, decreases expression	2
Ozone	increases oxidation, increases abundance, affects expression, affects cotreatment	2
GSK-J4	decreases expression	1
TAK-243	increases sumoylation	1
dicrotophos	decreases expression	1
geldanamycin	increases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
bisphenol S	decreases methylation	1
(+)-JQ1 compound	increases expression	1
NSC668394	decreases expression	1
Temozolomide	increases expression	1
Vorinostat	decreases expression	1
Acetaminophen	decreases expression	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1
Clorgyline	increases expression	1
Dichlorodiphenyl Dichloroethylene	increases expression	1
Dimethyl Sulfoxide	increases expression	1
Endosulfan	decreases expression	1
Estradiol	decreases expression	1
Smoke	decreases expression	1
Valproic Acid	decreases methylation	1
Zinc	decreases expression	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	decreases expression	1
Volatile Organic Compounds	affects cotreatment, increases oxidation	1

Cellosaurus cell lines

3 cell lines: 3 embryonic stem cell

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_A8I0	SEES3-1V human ZNF480, clone1	Embryonic stem cell	Male
CVCL_A8I1	SEES3-1V human ZNF480, clone2	Embryonic stem cell	Male
CVCL_A8I2	SEES3-1V human ZNF480, clone3	Embryonic stem cell	Male

Clinical trials (associated diseases)

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