ZNF790

Summary

ZNF790 (zinc finger protein 790, HGNC:33114) is a protein-coding gene on chromosome 19q13.12, encoding Zinc finger protein 790 (Q6PG37). 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 388536 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 94 total
• MANE Select transcript: NM_206894

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33114
Approved symbol	ZNF790
Name	zinc finger protein 790
Location	19q13.12
Locus type	gene with protein product
Status	Approved
Aliases	MGC62100, FLJ20350
Ensembl gene	ENSG00000197863
Ensembl biotype	protein_coding
Entrez	388536

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 16 protein_coding

ENST00000356725, ENST00000525288, ENST00000527645, ENST00000528994, ENST00000586323, ENST00000613249, ENST00000614179, ENST00000615484, ENST00000867320, ENST00000867321, ENST00000867322, ENST00000867323, ENST00000932990, ENST00000951466, ENST00000951467, ENST00000951468

RefSeq mRNA: 4 — MANE Select: NM_206894 NM_001242800, NM_001242801, NM_001242802, NM_206894

CCDS: CCDS12496

Canonical transcript exons

ENST00000356725 — 5 exons

Exon	Start	End
ENSE00001376731	36823285	36823380
ENSE00001412573	36817428	36820114
ENSE00001421107	36823667	36823790
ENSE00001423638	36825611	36825692
ENSE00001426574	36838337	36838387

Expression profiles

Bgee: expression breadth ubiquitous, 137 present calls, max score 98.86.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.0021 / max 120.3700, expressed in 1535 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
180694	1.9508	1025
180696	1.4674	737
180697	1.1672	649
180695	0.4166	224

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
quadriceps femoris	UBERON:0001377	98.86	gold quality
cerebellar vermis	UBERON:0004720	98.52	gold quality
calcaneal tendon	UBERON:0003701	84.21	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.17	gold quality
right testis	UBERON:0004534	81.28	gold quality
corpus callosum	UBERON:0002336	81.17	gold quality
testis	UBERON:0000473	80.63	gold quality
left testis	UBERON:0004533	80.56	gold quality
colonic epithelium	UBERON:0000397	78.70	gold quality
endometrium	UBERON:0001295	78.59	gold quality
cortical plate	UBERON:0005343	77.83	gold quality
islet of Langerhans	UBERON:0000006	77.33	gold quality
skeletal muscle tissue	UBERON:0001134	77.30	gold quality
adrenal tissue	UBERON:0018303	77.26	gold quality
muscle tissue	UBERON:0002385	76.96	gold quality
kidney	UBERON:0002113	76.56	gold quality
ganglionic eminence	UBERON:0004023	76.48	gold quality
lower esophagus mucosa	UBERON:0035834	76.05	gold quality
right adrenal gland cortex	UBERON:0035827	75.77	gold quality
ventricular zone	UBERON:0003053	75.76	gold quality
adrenal gland	UBERON:0002369	75.74	gold quality
liver	UBERON:0002107	75.71	gold quality
adult mammalian kidney	UBERON:0000082	75.65	gold quality
popliteal artery	UBERON:0002250	75.55	gold quality
tibial artery	UBERON:0007610	75.55	gold quality
urinary bladder	UBERON:0001255	75.51	gold quality
left adrenal gland	UBERON:0001234	75.46	gold quality
thyroid gland	UBERON:0002046	75.41	gold quality
lower esophagus	UBERON:0013473	75.38	gold quality
lower esophagus muscularis layer	UBERON:0035833	75.38	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-CURD-10	no	94.69
E-ANND-3	no	3.87

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

10 targeting ZNF790, 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-489-3P	99.80	66.46	839
HSA-MIR-3913-3P	99.74	66.53	938
HSA-MIR-1252-3P	99.55	67.71	2862
HSA-MIR-155-3P	99.03	67.99	924
HSA-MIR-670-3P	99.03	68.88	2404
HSA-MIR-4326	98.97	67.63	962
HSA-MIR-4297	98.77	66.95	2013
HSA-MIR-5581-5P	97.91	66.50	965
HSA-MIR-937-5P	97.43	68.39	667
HSA-MIR-5702	96.68	68.21	958

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 790 — Q6PG37 (reviewed: Q6PG37)

All UniProt accessions (5): E9PL27, E9PQ03, E9PRR6, Q6PG37, K7EQ58

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 (4): NP_001229729, NP_001229730, NP_001229731, NP_996777* (*=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 (17 total): zinc finger region 13, sequence variant 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6PG37-F1	64.72	0.08

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 70 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, DYRK1A_TARGET_GENES, HMG20B_TARGET_GENES, PAX7_TARGET_GENES, ZFP28_TARGET_GENES, ZFP3_TARGET_GENES, ZNF169_TARGET_GENES, ZNF257_TARGET_GENES, ZNF322_TARGET_GENES, ZNF329_TARGET_GENES, ZNF391_TARGET_GENES, ZNF410_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 (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 (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
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

328 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF790	KIAA1143	Q96AT1	507
ZNF790	OR13C8	Q8NGS7	507
ZNF790	ZNF521	Q96K83	411
ZNF790	ZNF148	Q9UQR1	405
ZNF790	JAKMIP2	Q96AA8	395
ZNF790	ZNF853	P0CG23	389
ZNF790	CC2D1B	Q5T0F9	379
ZNF790	MSH3	P20585	363
ZNF790	MSH6	P52701	353
ZNF790	EPHB2	P29323	353
ZNF790	SNX30	Q5VWJ9	324
ZNF790	POF1B	Q8WVV4	324
ZNF790	DIP2C	Q9Y2E4	306
ZNF790	ZNF608	Q9ULD9	292
ZNF790	GLRB	P48167	287

IntAct

5 interactions, top by confidence:

A	B	Type	Score
TERF1	ZNF790	psi-mi:“MI:0915”(physical association)	0.370
TINF2	ZNF790	psi-mi:“MI:0915”(physical association)	0.370
ZNF790	ACD	psi-mi:“MI:0915”(physical association)	0.370
POT1	ZNF790	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (4): ZNF790 (Two-hybrid), ZNF790 (Two-hybrid), ZNF790 (Two-hybrid), ZNF790 (Two-hybrid)

ESM2 similar proteins: A0A087WUV0, A0JNB1, A2VDP4, B2RUI1, P0CG31, P10072, P17025, P17036, P17097, P18733, P51814, Q08ER8, Q09FC8, Q0VGE8, Q14590, Q15937, Q16600, Q2M3X9, Q4V8A8, Q5CZA5, Q5R8G9, Q5RBX0, Q5VIY5, Q68DI1, Q6J6I6, Q6NX49, Q6P1L6, Q6PG37, Q6ZMS4, Q6ZMW2, Q80YP6, Q86UD4, Q86Y25, Q8IZ26, Q8N184, Q8NB42, Q8NEK5, Q8TAF7, Q8TF47, Q8WXB4

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	82
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

663 predictions. Top by Δscore:

Variant	Effect	Δscore
19:36823662:CTTA:C	donor_loss	1.0000
19:36823663:TTACC:T	donor_loss	1.0000
19:36823664:TA:T	donor_loss	1.0000
19:36823665:A:AC	donor_gain	1.0000
19:36823665:AC:A	donor_gain	1.0000
19:36823666:C:CC	donor_gain	1.0000
19:36823666:CC:C	donor_gain	1.0000
19:36823786:ATCAA:A	acceptor_gain	1.0000
19:36823787:TCAA:T	acceptor_gain	1.0000
19:36823788:CAA:C	acceptor_gain	1.0000
19:36823788:CAAC:C	acceptor_gain	1.0000
19:36823789:AA:A	acceptor_gain	1.0000
19:36823790:ACT:A	acceptor_loss	1.0000
19:36823791:C:CC	acceptor_gain	1.0000
19:36823791:C:CG	acceptor_loss	1.0000
19:36823794:T:C	acceptor_gain	1.0000
19:36823794:T:TC	acceptor_gain	1.0000
19:36825609:A:AC	donor_gain	1.0000
19:36825610:C:CC	donor_gain	1.0000
19:36825626:A:C	donor_gain	1.0000
19:36825688:CAGAG:C	acceptor_gain	1.0000
19:36825693:C:CC	acceptor_gain	1.0000
19:36823665:ACC:A	donor_gain	0.9900
19:36823666:CCC:C	donor_gain	0.9900
19:36823666:CCCA:C	donor_gain	0.9900
19:36823666:CCCAG:C	donor_gain	0.9900
19:36823790:ACTGT:A	acceptor_gain	0.9900
19:36823791:CTGTT:C	acceptor_gain	0.9900
19:36825689:AGAG:A	acceptor_gain	0.9900
19:36825690:GAG:G	acceptor_gain	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000018264 (19:36817730 A>G), RS1000114845 (19:36833419 A>C), RS1000315467 (19:36817333 A>G), RS1000316464 (19:36849642 C>A,T), RS1000356178 (19:36827246 C>T), RS1000394397 (19:36833706 G>A), RS1000439387 (19:36842564 A>G), RS1000602834 (19:36836169 A>G), RS1000675944 (19:36828444 C>A), RS1000703677 (19:36829177 A>G,T), RS1000719301 (19:36839248 TATC>T), RS1000854739 (19:36823118 A>G), RS1000893485 (19:36842894 A>G), RS1000906856 (19:36823459 G>A,C), RS1000917358 (19:36851158 TAG>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

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects cotreatment, increases abundance, increases expression	2
Benzo(a)pyrene	affects response to substance, decreases expression, decreases methylation	2
GSK-J4	decreases expression	1
TAK-243	increases sumoylation	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
beta-lapachone	decreases expression	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
Acrolein	increases oxidation, increases abundance, affects cotreatment	1
Air Pollutants	affects cotreatment, increases abundance, increases oxidation	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Manganese	increases abundance, increases expression, affects cotreatment	1
Ozone	affects cotreatment, increases oxidation, increases abundance	1
Cadmium Chloride	decreases expression	1
Okadaic Acid	decreases expression	1
Lactic Acid	decreases expression	1
Volatile Organic Compounds	affects cotreatment, increases oxidation	1

Clinical trials (associated diseases)

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