ZNF799

gene
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Also known as HIT-40MGC71805

Summary

ZNF799 (zinc finger protein 799, HGNC:28071) is a protein-coding gene on chromosome 19p13.2, encoding Zinc finger protein 799 (Q96GE5). 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 90576 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): Tourette syndrome (No Known Disease Relationship, GenCC)
  • GWAS associations: 4
  • Clinical variants (ClinVar): 116 total
  • MANE Select transcript: NM_001080821

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28071
Approved symbolZNF799
Namezinc finger protein 799
Location19p13.2
Locus typegene with protein product
StatusApproved
AliasesHIT-40, MGC71805
Ensembl geneENSG00000196466
Ensembl biotypeprotein_coding
OMIM619916
Entrez90576

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 retained_intron

ENST00000419318, ENST00000430385, ENST00000460935, ENST00000595766

RefSeq mRNA: 3 — MANE Select: NM_001080821 NM_001080821, NM_001322497, NM_001322498

CCDS: CCDS45989, CCDS82297

Canonical transcript exons

ENST00000430385 — 4 exons

ExonStartEnd
ENSE000016878221240106812401271
ENSE000035863441239329712393423
ENSE000036639831239001612392206
ENSE000036808201239260312392663

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 82.37.

FANTOM5 (CAGE): breadth broad, TPM avg 1.3522 / max 21.8568, expressed in 742 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1793071.3522742

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047382.37gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099180.18gold quality
endometriumUBERON:000129578.38gold quality
calcaneal tendonUBERON:000370176.64gold quality
granulocyteCL:000009476.05gold quality
placentaUBERON:000198775.34gold quality
left adrenal glandUBERON:000123474.81gold quality
left ovaryUBERON:000211974.76gold quality
right ovaryUBERON:000211874.55gold quality
right adrenal glandUBERON:000123374.47gold quality
left adrenal gland cortexUBERON:003582574.47gold quality
ovaryUBERON:000099274.29gold quality
sural nerveUBERON:001548874.22gold quality
mucosa of transverse colonUBERON:000499174.15gold quality
islet of LangerhansUBERON:000000674.07gold quality
right adrenal gland cortexUBERON:003582773.78gold quality
adrenal glandUBERON:000236973.62gold quality
ventricular zoneUBERON:000305372.77gold quality
leukocyteCL:000073872.69gold quality
rectumUBERON:000105272.53gold quality
right lobe of liverUBERON:000111472.44gold quality
monocyteCL:000057672.31gold quality
metanephros cortexUBERON:001053372.05gold quality
fallopian tubeUBERON:000388971.87gold quality
cortex of kidneyUBERON:000122571.57gold quality
smooth muscle tissueUBERON:000113571.53gold quality
pancreasUBERON:000126471.15gold quality
thoracic mammary glandUBERON:000520071.14gold quality
lymph nodeUBERON:000002971.00gold quality
cortical plateUBERON:000534370.76gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

44 targeting ZNF799, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4262100.0073.263931
HSA-MIR-188-3P100.0068.761240
HSA-MIR-3163100.0077.238605
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-450099.9972.722367
HSA-MIR-6759-5P99.9966.54785
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-LET-7A-5P99.9872.291790
HSA-LET-7B-5P99.9872.311790
HSA-LET-7C-5P99.9872.291790
HSA-LET-7E-5P99.9872.291790
HSA-LET-7F-5P99.9872.561784
HSA-LET-7G-5P99.9872.371784
HSA-LET-7I-5P99.9872.371788
HSA-MIR-98-5P99.9872.331787
HSA-LET-7D-5P99.9671.761632
HSA-MIR-445899.9671.641650
HSA-MIR-381-3P99.9371.872854
HSA-MIR-30099.9271.762856
HSA-MIR-202-3P99.8471.411290
HSA-MIR-510-3P99.5470.062965
HSA-MIR-217-5P99.4969.931419
HSA-MIR-208A-5P99.4270.831913
HSA-MIR-208B-5P99.4270.831952
HSA-MIR-428499.3665.251293
HSA-MIR-1912-3P99.3267.40936
HSA-MIR-3064-5P99.2666.131497

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusZfp961ENSMUSG00000052446
rattus_norvegicusZfp617ENSRNOG00000049856

Paralogs (15): ZNF14 (ENSG00000105708), ZNF57 (ENSG00000171970), ZNF791 (ENSG00000173875), ZNF443 (ENSG00000180855), ZNF101 (ENSG00000181896), ZNF563 (ENSG00000188868), ZNF700 (ENSG00000196757), ZNF441 (ENSG00000197044), ZNF433 (ENSG00000197647), ZNF44 (ENSG00000197857), ZNF823 (ENSG00000197933), ZNF442 (ENSG00000198342), ZNF844 (ENSG00000223547), ZNF709 (ENSG00000242852), ZNF878 (ENSG00000257446)

Protein

Protein identifiers

Zinc finger protein 799Q96GE5 (reviewed: Q96GE5)

Alternative names: Zinc finger protein 842

All UniProt accessions (3): D3YTF2, Q96GE5, M0R0E1

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 IDNamesCanonical?
Q96GE5-11yes
Q96GE5-22

RefSeq proteins (3): NP_001074290, NP_001309426, NP_001309427 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001909KRABDomain
IPR013087Znf_C2H2_typeDomain
IPR036051KRAB_dom_sfHomologous_superfamily
IPR036236Znf_C2H2_sfHomologous_superfamily

Pfam: PF00096, PF01352, PF13912

UniProt features (24 total): zinc finger region 18, sequence variant 2, chain 1, domain 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96GE5-F170.870.00

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-212436Generic Transcription Pathway

MSigDB gene sets: 61 (showing top): chr19p13, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, RAPA_EARLY_UP.V1_DN, P53_DN.V1_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, CEBPZ_TARGET_GENES, DACH1_TARGET_GENES, E2F2_TARGET_GENES, PRKDC_TARGET_GENES, ZNF350_TARGET_GENES, ZNF768_TARGET_GENES, MIR208B_5P, MIR208A_5P, MIR153_3P, MIR202_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 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:

CategoryPathways
RNA Polymerase II Transcription1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of DNA-templated transcription1
transcription by RNA polymerase II1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
transcription cis-regulatory region binding1
chromatin1
RNA polymerase II transcription regulatory region sequence-specific DNA binding1
DNA-binding transcription factor activity1
regulation of transcription by RNA polymerase II1
transition metal ion binding1
nucleic acid binding1
cation binding1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

344 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZNF799TAS2R46P59540479
ZNF799SERPINB11Q96P15477
ZNF799KHDC1Q4VXA5476
ZNF799JCADQ9P266439
ZNF799SDK2Q58EX2419
ZNF799KCNG4Q8TDN1395
ZNF799BBS9P78514349
ZNF799GRK4P32298324
ZNF799RPL14P50914323
ZNF799VPS33AQ96AX1280
ZNF799BHMTQ93088279
ZNF799DOK6Q6PKX4258
ZNF799CCDC102BQ68D86254
ZNF799ACADVLP49748252
ZNF799RABEP2Q9H5N1247

IntAct

4 interactions, top by confidence:

ABTypeScore
TRIM28ZNF320psi-mi:“MI:0914”(association)0.530
ECE1ZNF799psi-mi:“MI:0915”(physical association)0.370
ZNF799CSNK2A1psi-mi:“MI:0914”(association)0.350

BioGRID (2): ZNF799 (Affinity Capture-MS), ZNF799 (Affinity Capture-MS)

ESM2 similar proteins: A6NDX5, A6NK75, A6NNF4, A6NP11, B4DXR9, B7Z6K7, C9JN71, O43361, O75290, O75373, P0CJ79, P0DKX0, P17019, P17021, P17035, P17039, P35789, Q02386, Q03938, Q08AN1, Q13106, Q15928, Q3ZCX4, Q5R9F0, Q5SXM1, Q68EA5, Q6P9A1, Q6PDB4, Q6ZN06, Q6ZN08, Q6ZNG1, Q76KX8, Q86V71, Q86XN6, Q8IYB9, Q8N4W9, Q8NEP9, Q8TBZ8, Q8TC21, Q8TF32

Diamond homologs: A0JPK3, A2RRD8, A2VDQ7, A3KN32, A8MUZ8, A8MWA4, C9JN71, E9QAG8, O60384, O60765, O75820, P0CH99, P0CI00, P10076, P10755, P15621, P16374, P16415, P17017, P17024, P51523, P52737, P52740, Q06730, Q06732, Q08AG5, Q0D2J5, Q13106, Q13360, Q15928, Q15935, Q15973, Q32M78, Q3KP31, Q4R4C7, Q4R6J4, Q4R882, Q5R9F0, Q5RC79, Q5REI6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance111
Likely benign5
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

608 predictions. Top by Δscore:

VariantEffectΔscore
19:12392659:CATTC:Cacceptor_gain1.0000
19:12392662:TCC:Tacceptor_loss1.0000
19:12392664:CTAAA:Cacceptor_loss1.0000
19:12393291:CCTTA:Cdonor_loss1.0000
19:12393292:CTTA:Cdonor_loss1.0000
19:12393293:TTA:Tdonor_loss1.0000
19:12393294:TA:Tdonor_loss1.0000
19:12393295:A:Cdonor_loss1.0000
19:12393295:A:Tdonor_loss1.0000
19:12393296:C:CTdonor_loss1.0000
19:12393296:CCTA:Cdonor_gain1.0000
19:12393434:CCACA:Cacceptor_gain1.0000
19:12393435:C:CTacceptor_gain1.0000
19:12393435:C:Tacceptor_gain1.0000
19:12393435:CACA:Cacceptor_gain1.0000
19:12393437:C:CTacceptor_gain1.0000
19:12393438:A:Cacceptor_gain1.0000
19:12393440:G:GCacceptor_gain1.0000
19:12393443:C:CTacceptor_gain1.0000
19:12393444:A:Tacceptor_gain1.0000
19:12401064:GCAC:Gdonor_loss1.0000
19:12401065:CACC:Cdonor_loss1.0000
19:12401065:CACCA:Cdonor_loss1.0000
19:12401066:A:Tdonor_loss1.0000
19:12401067:C:CGdonor_loss1.0000
19:12392204:CAT:Cacceptor_gain0.9900
19:12392207:C:CCacceptor_gain0.9900
19:12392598:ATTAC:Adonor_loss0.9900
19:12392599:TTACC:Tdonor_loss0.9900
19:12392600:TA:Tdonor_loss0.9900

AlphaMissense

4306 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:12390859:G:CF513L0.988
19:12390859:G:TF513L0.988
19:12390861:A:GF513L0.988
19:12390775:G:CF541L0.986
19:12390775:G:TF541L0.986
19:12390777:A:GF541L0.986
19:12390943:G:CF485L0.982
19:12390943:G:TF485L0.982
19:12390945:A:GF485L0.982
19:12391192:A:CF402L0.980
19:12391192:A:TF402L0.980
19:12391194:A:GF402L0.980
19:12390691:G:CF569L0.974
19:12390691:G:TF569L0.974
19:12390693:A:GF569L0.974
19:12391360:A:CF346L0.972
19:12391360:A:TF346L0.972
19:12391362:A:GF346L0.972
19:12391696:A:CF234L0.972
19:12391696:A:TF234L0.972
19:12391698:A:GF234L0.972
19:12393388:G:CF13L0.971
19:12393388:G:TF13L0.971
19:12393390:A:GF13L0.971
19:12391528:G:CF290L0.969
19:12391528:G:TF290L0.969
19:12391530:A:GF290L0.969
19:12391027:A:CF457L0.968
19:12391027:A:TF457L0.968
19:12391029:A:GF457L0.968

dbSNP variants (sampled 300 via entrez): RS1000356080 (19:12397842 A>G), RS1000442609 (19:12408996 T>C), RS1000665602 (19:12398096 A>G), RS1000836911 (19:12401246 T>A,C,G), RS1000897738 (19:12407214 G>A,C), RS1001045039 (19:12407611 CTCTT>C), RS1001520630 (19:12397586 G>A,C,T), RS1001583301 (19:12410073 G>A,T), RS1001596051 (19:12416461 C>A,T), RS1001725722 (19:12402360 C>T), RS1002134571 (19:12391824 G>A,T), RS1002177585 (19:12407289 C>A,T), RS1002230480 (19:12401873 T>C), RS1002381761 (19:12412827 G>T), RS1002442925 (19:12392142 G>A,C)

Disease associations

OMIM: gene MIM:619916 | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
Tourette syndromeNo Known Disease RelationshipUnknown

Mondo (1): Tourette syndrome (MONDO:0007661)

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

StudyTraitp-value
GCST009439_9Age-related cognitive decline (language) (slope of z-scores)4.000000e-06
GCST010118_71Type 2 diabetes2.000000e-08
GCST90002393_642Monocyte count1.000000e-11
GCST90020029_16Waist circumference adjusted for body mass index1.000000e-08

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0007710cognitive decline measurement
EFO:0005091monocyte count
EFO:0007789BMI-adjusted waist circumference

MeSH disease descriptors (1)

DescriptorNameTree numbers
D005879Tourette SyndromeC10.228.140.079.898; C10.228.662.825.800; C10.574.500.850; C16.320.400.820; F03.625.992.850

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

ChemicalActions (top 5)PubMed papers
aristolochic acid Iincreases expression1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
TAK-243increases sumoylation1
triphenyl phosphateaffects expression1
bisphenol Adecreases methylation1
arseniteaffects binding, decreases reaction1
2-amino-3,8-dimethylimidazo(4,5-f)quinoxalineincreases expression1
di-n-butylphosphoric acidaffects expression1
MT19c compoundincreases expression1
Sunitinibincreases expression1
Leflunomideincreases expression1
Air Pollutants, Occupationaldecreases expression1
Benzo(a)pyreneaffects methylation1
Nickeldecreases expression1
Smokedecreases expression1
Tetrachlorodibenzodioxinaffects expression1
Okadaic Acidincreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00152750PHASE4UNKNOWNStudy of Clonidine on Sleep Architecture in Children With Tourette’s Syndrome (TS) and Comorbid ADHD
NCT00226824PHASE4TERMINATEDSafety Study of Galantamine in Tic Disorders
NCT00241176PHASE4COMPLETEDOpen Label Trial of Aripiprazole in Children and Adolescents With Tourette’s Disorder
NCT00370838PHASE4COMPLETEDComparison of Keppra and Clonidine in the Treatment of Tics
NCT01018056PHASE4COMPLETEDDeveloping New Treatments for Tourette Syndrome: Therapeutic Trials With Modulators of Glutamatergic Neurotransmission
NCT01547000PHASE4COMPLETEDGuanfacine in Children With Tic Disorders
NCT03239210PHASE4COMPLETEDEffects of Ondansetron in Obsessive-compulsive and Tic Disorders
NCT00004376PHASE3COMPLETEDPhase III Randomized, Double-Blind, Placebo-Controlled Study of Guanfacine for Tourette Syndrome and Attention Deficit Hyperactivity Disorder
NCT00206323PHASE3COMPLETEDA Randomized, Placebo-controlled, Tourette Syndrome Study.
NCT00206336PHASE3COMPLETEDAn Open-label Study to Determine the Efficacy and Safety of Topiramate in the Treatment of Tourette Syndrome.
NCT00478842PHASE3COMPLETEDPallidal Stimulation and Gilles de la Tourette Syndrome
NCT00681863PHASE3TERMINATEDOpen-label Extension Study of Pramipexole in the Treatment of Children and Adolescents With Tourette Syndrome
NCT01501695PHASE3COMPLETEDPhase III Study of 5LGr to Treat Tic Disorder
NCT03087201PHASE3COMPLETEDCANNAbinoids in the Treatment of TICS (CANNA-TICS)
NCT03487783PHASE3COMPLETEDAripiprazole Oral Solution in the Treatment of Children and Adolescents With Tourette’s Syndrome
NCT03567291PHASE3TERMINATEDEvaluation of Safety and Tolerability of Long-term TEV-50717 (Deutetrabenazine) for Treatment of Tourette Syndrome in Children and Adolescents
NCT03571256PHASE3COMPLETEDA Study to Test if TEV-50717 is Effective in Relieving Tics Associated With Tourette Syndrome (TS)
NCT06021522PHASE3ACTIVE_NOT_RECRUITINGA Study to Evaluate Long-term Safety of Ecopipam Tablets in Children, Adolescents and Adults With Tourette’s Disorder
NCT00004393PHASE2COMPLETEDPhase II Double Blind Placebo Controlled Trial of Risperidone in Tourette Syndrome
NCT00004652PHASE2COMPLETEDPhase II Pilot Controlled Study of Short Vs Longer Term Pimozide (Orap) Therapy in Tourette Syndrome
NCT00231985PHASE2COMPLETEDEffectiveness of Behavior Therapy and Psychosocial Therapy for the Treatment of Tourette Syndrome and Chronic Tic Disorder
NCT00311909PHASE2COMPLETEDThalamic Deep Brain Stimulation for Tourette Syndrome
NCT00529308PHASE2COMPLETEDTranscranial Magnetic Stimulation (TMS) for Individuals With Tourette’s Syndrome
NCT00558467PHASE2COMPLETEDPramipexole Pilot Phase II Study in Children and Adolescents With Tourette Disorder According to DSM-IV Criteria
NCT01043549PHASE2TERMINATEDRepetitive Transcranial Magnetic Stimulation of the Posterior Parietal Cortex in Patients Suffering From Gilles de la Tourette Syndrome
NCT01133353PHASE2WITHDRAWNA Study of the Effectiveness and Safety of Tetrabenazine MR in Pediatric Subjects With Tourette’s Syndrome
NCT01475383PHASE2WITHDRAWNStudy Evaluating The Safety And Efficacy Of PF-03654746 In Adult Subjects With Tourette’s Syndrome
NCT01647269PHASE2COMPLETEDA Trial of Bilateral Deep Brain Stimulation to the Globus Pallidus Internum in Tourette Syndrome
NCT01904773PHASE2COMPLETEDSafety, Tolerability, Pharmacokinetic, and Efficacy Study of AZD5213 in Adolescents With Tourette’s Disorder
NCT02102698PHASE2COMPLETEDEcopipam Treatment of Tourette’s Syndrome in Subjects 7-17 Years
NCT02217007PHASE2WITHDRAWNA Trial Evaluating the Efficacy, Safety, and Pharmacokinetics of SNC-102 in Subjects With Tourette Syndrome
NCT02247206PHASE2COMPLETEDVoIP Delivered Behavior Therapy for Tourette Syndrome
NCT02581865PHASE2COMPLETEDSafety and Efficacy Study of NBI-98854 in Adults With Tourette Syndrome
NCT02619084PHASE2COMPLETEDSubthalamic Stimulation in Tourette’s Syndrome
NCT02679079PHASE2COMPLETEDSafety and Efficacy Study of NBI-98854 in Children and Adolescents With Tourette Syndrome
NCT02879578PHASE2COMPLETEDSafety and Tolerability Study of NBI-98854 for the Treatment of Subjects With Tourette Syndrome
NCT03066193PHASE2COMPLETEDEfficacy of a Therapeutic Combination of Dronabinol and PEA for Tourette Syndrome
NCT03247244PHASE2TERMINATEDSafety and Efficacy of Cannabis in Tourette Syndrome
NCT03325010PHASE2COMPLETEDSafety, Tolerability, and Efficacy of NBI-98854 for the Treatment of Pediatric Subjects With Tourette Syndrome
NCT03444038PHASE2COMPLETEDOpen-Label Safety and Tolerability Study of NBI-98854 for the Treatment of Pediatric Subjects With Tourette Syndrome
  • Associated diseases: Tourette syndrome
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): Tourette syndrome