ZNF442

Summary

ZNF442 (zinc finger protein 442, HGNC:20877) is a protein-coding gene on chromosome 19p13.2, encoding Zinc finger protein 442 (Q9H7R0). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription 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 79973 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 92 total
• MANE Select transcript: NM_030824

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20877
Approved symbol	ZNF442
Name	zinc finger protein 442
Location	19p13.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ14356
Ensembl gene	ENSG00000198342
Ensembl biotype	protein_coding
Entrez	79973

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 retained_intron

ENST00000242804, ENST00000424168, ENST00000438182, ENST00000462995, ENST00000545749

RefSeq mRNA: 2 — MANE Select: NM_030824 NM_001363774, NM_030824

CCDS: CCDS12271, CCDS86707

Canonical transcript exons

ENST00000242804 — 6 exons

Exon	Start	End
ENSE00000950971	12363554	12363671
ENSE00001401270	12345944	12351318
ENSE00001514852	12364802	12365243
ENSE00001825985	12365533	12365683
ENSE00003653340	12352988	12353114
ENSE00003665193	12352010	12352070

Expression profiles

Bgee: expression breadth ubiquitous, 170 present calls, max score 84.50.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 2.5241 / max 85.6525, expressed in 960 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
179304	1.4237	638
179305	1.1004	626

Top tissues by expression

275 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	84.50	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.41	gold quality
hair follicle	UBERON:0002073	78.89	gold quality
calcaneal tendon	UBERON:0003701	78.34	gold quality
ventricular zone	UBERON:0003053	75.43	gold quality
tongue squamous epithelium	UBERON:0006919	72.01	gold quality
ganglionic eminence	UBERON:0004023	71.39	gold quality
left ovary	UBERON:0002119	70.29	gold quality
descending thoracic aorta	UBERON:0002345	69.62	gold quality
cortical plate	UBERON:0005343	69.46	gold quality
ovary	UBERON:0000992	69.10	gold quality
right ovary	UBERON:0002118	69.00	gold quality
popliteal artery	UBERON:0002250	68.86	gold quality
tibial artery	UBERON:0007610	68.81	gold quality
islet of Langerhans	UBERON:0000006	68.78	gold quality
diaphragm	UBERON:0001103	68.27	gold quality
pigmented layer of retina	UBERON:0001782	67.36	silver quality
right lobe of liver	UBERON:0001114	67.08	gold quality
smooth muscle tissue	UBERON:0001135	67.05	gold quality
germinal epithelium of ovary	UBERON:0001304	67.05	gold quality
aorta	UBERON:0000947	66.94	gold quality
colonic epithelium	UBERON:0000397	66.73	silver quality
tibial nerve	UBERON:0001323	65.92	gold quality
embryo	UBERON:0000922	65.63	gold quality
buccal mucosa cell	CL:0002336	65.52	gold quality
sural nerve	UBERON:0015488	65.27	silver quality
ectocervix	UBERON:0012249	65.19	gold quality
metanephros	UBERON:0000081	64.95	gold quality
stromal cell of endometrium	CL:0002255	64.94	gold quality
left coronary artery	UBERON:0001626	64.85	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-MTAB-10137	no	265.51
E-ANND-3	no	4.28

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

20 targeting ZNF442, 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-203A-3P	99.49	70.56	2806
HSA-MIR-3940-5P	99.14	65.26	493
HSA-MIR-4507	99.14	65.27	515
HSA-MIR-331-3P	98.76	64.91	793
HSA-MIR-4752	98.71	68.04	833
HSA-MIR-3691-5P	98.62	65.88	552
HSA-MIR-3188	98.58	65.60	878
HSA-MIR-7114-5P	98.51	67.87	1349
HSA-MIR-4722-5P	98.46	66.34	1611
HSA-MIR-376B-5P	98.46	66.40	606
HSA-MIR-376C-5P	98.46	66.64	589
HSA-MIR-6801-3P	98.04	64.64	805
HSA-MIR-6810-3P	97.96	64.57	1023
HSA-MIR-6824-5P	97.41	68.43	583
HSA-MIR-7855-5P	97.39	67.18	925
HSA-MIR-8056	97.15	64.49	769
HSA-MIR-584-5P	95.82	68.05	848
HSA-MIR-4278	95.28	65.49	351
HSA-MIR-5191	95.22	64.69	354
HSA-MIR-6732-5P	93.97	64.65	422

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp961	ENSMUSG00000052446
rattus_norvegicus	Zfp617	ENSRNOG00000049856

Paralogs (15): ZNF14 (ENSG00000105708), ZNF57 (ENSG00000171970), ZNF791 (ENSG00000173875), ZNF443 (ENSG00000180855), ZNF101 (ENSG00000181896), ZNF563 (ENSG00000188868), ZNF799 (ENSG00000196466), ZNF700 (ENSG00000196757), ZNF441 (ENSG00000197044), ZNF433 (ENSG00000197647), ZNF44 (ENSG00000197857), ZNF823 (ENSG00000197933), ZNF844 (ENSG00000223547), ZNF709 (ENSG00000242852), ZNF878 (ENSG00000257446)

Protein

Protein identifiers

Zinc finger protein 442 — Q9H7R0 (reviewed: Q9H7R0)

All UniProt accessions (2): C9JC15, Q9H7R0

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?
Q9H7R0-1	1	yes
Q9H7R0-2	2

RefSeq proteins (2): NP_001350703, NP_110451* (*=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, PF13894, PF13912

UniProt features (26 total): zinc finger region 16, sequence variant 7, chain 1, domain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H7R0-F1	70.33	0.09

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 33 (showing top): chr19p13, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, KAT5_TARGET_GENES, NKX2_3_TARGET_GENES, PRKDC_TARGET_GENES, ZNF184_TARGET_GENES, ZNF563_TARGET_GENES, MIR7114_5P, MIR6810_3P, MIR6801_3P, MIR8056, GSE14000_UNSTIM_VS_16H_LPS_DC_TRANSLATED_RNA_DN, BLANCO_MELO_COVID19_SARS_COV_2_INFECTION_CALU3_CELLS_UP, BLANCO_MELO_BRONCHIAL_EPITHELIAL_CELLS_INFLUENZA_A_DEL_NS1_INFECTION_UP

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 transcription regulatory region sequence-specific DNA binding (GO:0000977), 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 (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
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
transcription cis-regulatory region binding	1
chromatin	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	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

Protein interactions and networks

STRING

252 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF442	SLC25A44	Q96H78	480
ZNF442	PTPRH	Q9HD43	431
ZNF442	RNF39	Q9H2S5	419
ZNF442	PM20D1	Q6GTS8	400
ZNF442	PXT1	Q8NFP0	398
ZNF442	TMEM125	Q96AQ2	398
ZNF442	ACTL9	Q8TC94	381
ZNF442	KCTD20	Q7Z5Y7	377
ZNF442	ADCK5	Q3MIX3	370
ZNF442	STK38	Q15208	366
ZNF442	ARK2C	Q6ZSG1	359
ZNF442	SLC44A5	Q8NCS7	320
ZNF442	ZNF644	Q9H582	308
ZNF442	ERGIC3	Q9Y282	297
ZNF442	MT1B	P07438	277

IntAct

4 interactions, top by confidence:

A	B	Type	Score
ZNF442	HNRNPU	psi-mi:“MI:0915”(physical association)	0.400
ZNF442	CBX3	psi-mi:“MI:0914”(association)	0.350
ATG16L1	ESYT2	psi-mi:“MI:0914”(association)	0.350

BioGRID (2): ZNF442 (Proximity Label-MS), ZNF442 (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: A0JPK3, A8MT65, C9JN71, E9QAG8, G3X9G7, O75820, P16373, P16374, P16415, P17017, P17024, P17025, P51815, P52737, Q08AG5, Q08ER8, Q0D2J5, Q15973, Q2M218, Q3KP31, Q3V080, Q494X3, Q4R4C7, Q5MYW4, Q5R9F0, Q5R9S5, Q5REI6, Q5REK1, Q68EA5, Q6P560, Q6P5C7, Q6ZQV5, Q7L945, Q86T29, Q8BGV5, Q8C6P8, Q8IYI8, Q8IZC7, Q8N7K0, Q8N972

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	87
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

567 predictions. Top by Δscore:

Variant	Effect	Δscore
19:12351316:CAT:C	acceptor_gain	0.9900
19:12351319:C:CC	acceptor_gain	0.9900
19:12352005:ATTAC:A	donor_loss	0.9900
19:12352006:TTA:T	donor_loss	0.9900
19:12352007:TA:T	donor_loss	0.9900
19:12352008:A:C	donor_loss	0.9900
19:12352009:C:CT	donor_loss	0.9900
19:12352013:AGGCT:A	donor_gain	0.9900
19:12352020:T:TA	donor_gain	0.9900
19:12353125:CCACA:C	acceptor_gain	0.9900
19:12353126:CACA:C	acceptor_gain	0.9900
19:12365529:TCA:T	donor_loss	0.9900
19:12365530:CA:C	donor_loss	0.9900
19:12365531:A:AC	donor_gain	0.9900
19:12365531:ACCA:A	donor_loss	0.9900
19:12365532:C:CC	donor_gain	0.9900
19:12351318:TC:T	acceptor_loss	0.9800
19:12352066:CATTC:C	acceptor_gain	0.9800
19:12352070:CCTAA:C	acceptor_loss	0.9800
19:12352072:T:C	acceptor_loss	0.9800
19:12352078:G:C	acceptor_gain	0.9800
19:12352982:TTTTA:T	donor_loss	0.9800
19:12352983:TTTAC:T	donor_loss	0.9800
19:12352984:TTA:T	donor_loss	0.9800
19:12352985:TA:T	donor_loss	0.9800
19:12352986:A:AG	donor_loss	0.9800
19:12352987:C:G	donor_loss	0.9800
19:12353126:C:T	acceptor_gain	0.9800
19:12353129:A:C	acceptor_gain	0.9800
19:12353796:T:TG	acceptor_gain	0.9800

AlphaMissense

4210 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:12350679:G:C	F302L	0.987
19:12350679:G:T	F302L	0.987
19:12350681:A:G	F302L	0.987
19:12350847:G:C	F246L	0.987
19:12350847:G:T	F246L	0.987
19:12350849:A:G	F246L	0.987
19:12353080:A:G	F38S	0.984
19:12350010:G:C	F525L	0.983
19:12350010:G:T	F525L	0.983
19:12350012:A:G	F525L	0.983
19:12350595:A:C	F330L	0.983
19:12350595:A:T	F330L	0.983
19:12350597:A:G	F330L	0.983
19:12353079:G:C	F38L	0.983
19:12353079:G:T	F38L	0.983
19:12353081:A:G	F38L	0.983
19:12349926:G:C	F553L	0.981
19:12349926:G:T	F553L	0.981
19:12349928:A:G	F553L	0.981
19:12350511:A:C	F358L	0.980
19:12350511:A:T	F358L	0.980
19:12350513:A:G	F358L	0.980
19:12350094:G:C	F497L	0.977
19:12350094:G:T	F497L	0.977
19:12350096:A:G	F497L	0.977
19:12350259:G:C	F442L	0.977
19:12350259:G:T	F442L	0.977
19:12350261:A:G	F442L	0.977
19:12350763:G:C	F274L	0.977
19:12350763:G:T	F274L	0.977

dbSNP variants (sampled 300 via entrez): RS1000029896 (19:12361843 C>A,T), RS1000045622 (19:12373533 C>T), RS1000443347 (19:12361244 A>C), RS1000672838 (19:12370933 A>G), RS1000682942 (19:12349032 A>AG), RS1000823632 (19:12370694 G>C), RS1000905347 (19:12347757 A>G), RS1000948853 (19:12370344 A>C), RS1001034592 (19:12360353 C>A,T), RS1001124022 (19:12365227 G>A), RS1001324134 (19:12367813 C>T), RS1001341096 (19:12373434 T>C), RS1001453776 (19:12373055 A>T), RS1001569831 (19:12350443 T>A,C,G), RS1001620025 (19:12362468 G>A,T)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

22 total (human), top 22 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
cinnamaldehyde	increases expression	1
potassium chromate(VI)	affects cotreatment, increases expression	1
resorcinol	decreases expression	1
epigallocatechin gallate	increases expression, affects cotreatment	1
Grape Seed Proanthocyanidins	decreases expression, affects cotreatment	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	decreases expression	1
Leflunomide	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	decreases methylation	1
Catechin	affects cotreatment, decreases expression	1
Doxorubicin	decreases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Urethane	increases expression	1
Valproic Acid	increases methylation	1
Cyclosporine	increases expression	1
Aflatoxin B1	affects expression	1
Okadaic Acid	increases expression	1
Acrylamide	increases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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