ZNF639

gene
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Also known as ANC-2H01ZASC1

Summary

ZNF639 (zinc finger protein 639, HGNC:30950) is a protein-coding gene on chromosome 3q26.33, encoding Zinc finger protein 639 (Q9UID6). Binds DNA and may function as a transcriptional repressor.

This gene encodes a member of the Kruppel-like zinc finger family of proteins. Amplification and overexpression of this gene have been observed in esophageal squamous cell carcinoma. The encoded protein has been shown to bind DNA in a sequence-specific manner and may regulate HIV-1 gene expression. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 51193 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 48 total
  • MANE Select transcript: NM_001303426

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30950
Approved symbolZNF639
Namezinc finger protein 639
Location3q26.33
Locus typegene with protein product
StatusApproved
AliasesANC-2H01, ZASC1
Ensembl geneENSG00000121864
Ensembl biotypeprotein_coding
OMIM619214
Entrez51193

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 13 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000326361, ENST00000466264, ENST00000466663, ENST00000481587, ENST00000483460, ENST00000484866, ENST00000491818, ENST00000494234, ENST00000496856, ENST00000621687, ENST00000908082, ENST00000908083, ENST00000908084, ENST00000908085, ENST00000971543

RefSeq mRNA: 10 — MANE Select: NM_001303426 NM_001303425, NM_001303426, NM_001375800, NM_001375802, NM_001375803, NM_001375804, NM_001375805, NM_001375806, NM_001375807, NM_016331

CCDS: CCDS3227

Canonical transcript exons

ENST00000496856 — 6 exons

ExonStartEnd
ENSE00001268779179333269179338583
ENSE00001268789179328283179328351
ENSE00001512751179327561179327631
ENSE00001819600179323031179323291
ENSE00003570719179332989179333123
ENSE00003661548179329618179329728

Expression profiles

Bgee: expression breadth ubiquitous, 264 present calls, max score 95.00.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.0568 / max 134.4453, expressed in 1786 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
3992410.16991762
399232.88681431

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cortical plateUBERON:000534395.00gold quality
calcaneal tendonUBERON:000370194.23gold quality
ganglionic eminenceUBERON:000402393.36gold quality
ventricular zoneUBERON:000305392.99gold quality
islet of LangerhansUBERON:000000692.29gold quality
adrenal tissueUBERON:001830392.08gold quality
mucosa of stomachUBERON:000119992.00gold quality
tibial arteryUBERON:000761091.56gold quality
popliteal arteryUBERON:000225091.55gold quality
descending thoracic aortaUBERON:000234591.39gold quality
biceps brachiiUBERON:000150791.31gold quality
aortaUBERON:000094791.30gold quality
synovial jointUBERON:000221791.02gold quality
thoracic aortaUBERON:000151590.98gold quality
caput epididymisUBERON:000435890.94gold quality
seminal vesicleUBERON:000099890.91gold quality
ascending aortaUBERON:000149690.90gold quality
right coronary arteryUBERON:000162590.79gold quality
skin of hipUBERON:000155490.78gold quality
cartilage tissueUBERON:000241890.73gold quality
tendonUBERON:000004390.63gold quality
body of uterusUBERON:000985390.47gold quality
cauda epididymisUBERON:000436090.41gold quality
lower esophagus muscularis layerUBERON:003583390.41gold quality
left uterine tubeUBERON:000130390.40gold quality
endocervixUBERON:000045890.39gold quality
upper leg skinUBERON:000426290.39gold quality
lower esophagusUBERON:001347390.38gold quality
rectumUBERON:000105290.37gold quality
endometriumUBERON:000129590.37gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes5.60

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

69 targeting ZNF639, 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-4795-3P100.0074.624024
HSA-MIR-4533100.0069.482758
HSA-MIR-428299.9975.366408
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-MIR-1213699.9872.815713
HSA-MIR-548AN99.9770.912817
HSA-MIR-6793-5P99.9765.95758
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-548AT-5P99.9670.832666
HSA-MIR-548J-3P99.9472.614881
HSA-MIR-548AE-3P99.9372.664867
HSA-MIR-548AH-3P99.9372.544872
HSA-MIR-548AM-3P99.9372.544872
HSA-MIR-548AQ-3P99.9372.664867
HSA-MIR-314399.9371.963104
HSA-MIR-515-5P99.9269.822343
HSA-MIR-519E-5P99.9269.622358
HSA-MIR-368699.9070.532432
HSA-MIR-627-3P99.9071.423316
HSA-MIR-6780A-5P99.8866.692776
HSA-MIR-391999.8769.452489
HSA-MIR-489-3P99.8066.46839
HSA-MIR-1273H-5P99.7766.322471
HSA-MIR-3913-3P99.7466.53938
HSA-MIR-371499.7170.742671
HSA-MIR-494-3P99.7071.452795
HSA-MIR-30B-3P99.7065.762325

Literature-anchored findings (GeneRIF, showing 2)

  • ZASC1 copy number that increased from primary to recurrent tumor suggested the importance of ZASC1 in tumor progression. The increase of ZASC1 gene copy number in recurrent tumors was associated with the consumption of betel quid in patients. (PMID:20646234)
  • ZASC1 as novel regulator of HIV-1 gene expression that functions through the DNA-dependent, RNA-independent recruitment of TAT/P-TEFb to the HIV-1 promoter. (PMID:24204263)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
mus_musculusZfp639ENSMUSG00000027667
rattus_norvegicusZfp639ENSRNOG00000043053
drosophila_melanogasterCG14442FBGN0029893
drosophila_melanogasterCG14440FBGN0029894

Paralogs (11): IKZF2 (ENSG00000030419), ZNF821 (ENSG00000102984), IKZF4 (ENSG00000123411), ZNF382 (ENSG00000161298), IKZF3 (ENSG00000161405), ZNF613 (ENSG00000176024), IKZF1 (ENSG00000185811), ZNF567 (ENSG00000189042), ZNF649 (ENSG00000198093), ZNF564 (ENSG00000249709), ZNF350 (ENSG00000256683)

Protein

Protein identifiers

Zinc finger protein 639Q9UID6 (reviewed: Q9UID6)

Alternative names: Zinc finger protein ANC_2H01, Zinc finger protein ZASC1

All UniProt accessions (5): C9IZP0, C9J3R1, Q9UID6, J3KR59, J3KR68

UniProt curated annotations — full annotation on UniProt →

Function. Binds DNA and may function as a transcriptional repressor.

Subunit / interactions. Interacts with CTNNA2.

Subcellular location. Nucleus.

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

RefSeq proteins (10): NP_001290354, NP_001290355, NP_001362729, NP_001362731, NP_001362732, NP_001362733, NP_001362734, NP_001362735, NP_001362736, NP_057415 (=MANE)

Domains & families (InterPro)

IDNameType
IPR013087Znf_C2H2_typeDomain
IPR036236Znf_C2H2_sfHomologous_superfamily
IPR050527

Pfam: PF00096

UniProt features (18 total): zinc finger region 8, cross-link 4, region of interest 2, modified residue 2, chain 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UID6-F153.240.00

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 (6): 60, 88, 76, 177, 181, 226

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 133 (showing top): GOBP_HOST_MEDIATED_ACTIVATION_OF_VIRAL_TRANSCRIPTION, GOBP_GROWTH, GOBP_HOST_MEDIATED_SUPPRESSION_OF_VIRAL_TRANSCRIPTION, GOBP_MODULATION_OF_PROCESS_OF_ANOTHER_ORGANISM, chr3q26, GOBP_HOST_MEDIATED_PERTURBATION_OF_VIRAL_PROCESS, WEI_MYCN_TARGETS_WITH_E_BOX, GOBP_POSITIVE_REGULATION_OF_CELL_GROWTH, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_UP, GOBP_BIOLOGICAL_PROCESS_INVOLVED_IN_INTERACTION_WITH_HOST, GOBP_VIRAL_LIFE_CYCLE, GOBP_HOST_MEDIATED_ACTIVATION_OF_VIRAL_PROCESS, GOBP_POSITIVE_REGULATION_OF_GROWTH, MODULE_277, GOBP_CELL_GROWTH

GO Biological Process (7): regulation of transcription by RNA polymerase II (GO:0006357), positive regulation of cell growth (GO:0030307), host-mediated suppression of viral transcription (GO:0043922), host-mediated activation of viral transcription (GO:0043923), negative regulation of DNA-templated transcription (GO:0045892), positive regulation of transcription by RNA polymerase II (GO:0045944), symbiont entry into host cell (GO:0046718)

GO Molecular Function (8): transcription cis-regulatory region binding (GO:0000976), RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), DNA-binding transcription factor activity (GO:0003700), zinc ion binding (GO:0008270), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (2): nucleus (GO:0005634), nucleoplasm (GO:0005654)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of DNA-templated transcription3
transcription by RNA polymerase II2
host-mediated perturbation of viral transcription2
RNA polymerase II transcription regulatory region sequence-specific DNA binding2
regulation of cell growth1
cell growth1
positive regulation of growth1
positive regulation of cellular process1
host-mediated suppression of viral proces1
host-mediated activation of viral process1
DNA-templated transcription1
negative regulation of RNA biosynthetic process1
regulation of transcription by RNA polymerase II1
positive regulation of DNA-templated transcription1
viral life cycle1
symbiont entry into host1
transcription regulatory region nucleic acid binding1
sequence-specific double-stranded DNA binding1
cis-regulatory region sequence-specific DNA binding1
DNA-binding transcription factor activity, RNA polymerase II-specific1
DNA-binding transcription activator activity1
positive regulation of transcription by RNA polymerase II1
transcription cis-regulatory region binding1
transcription regulator activity1
transition metal ion binding1
nucleic acid binding1
binding1
cation binding1
intracellular membrane-bounded organelle1
nuclear lumen1
cellular anatomical structure1

Protein interactions and networks

STRING

770 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZNF639CTNNA2P26232569
ZNF639ZBTB2Q8N680487
ZNF639HDAC1Q13547417
ZNF639ZBTB5O15062415
ZNF639ZBTB25P24278415
ZNF639SCRN3Q0VDG4414
ZNF639K7ESF6K7ESF6385
ZNF639ZNF44P15621385
ZNF639ZNF629Q9UEG4383
ZNF639ZNF436Q9C0F3383
ZNF639ZNF569Q5MCW4383
ZNF639ZNF501Q96CX3378
ZNF639DCUN1D1Q96GG9374
ZNF639AFF1P51825329
ZNF639ANKRD54Q6NXT1323

IntAct

83 interactions, top by confidence:

ABTypeScore
HDAC1CDK2AP1psi-mi:“MI:0914”(association)0.840
RBBP4CDK2AP1psi-mi:“MI:0914”(association)0.790
ZNF639PNKPpsi-mi:“MI:0915”(physical association)0.720
PNKPZNF639psi-mi:“MI:0915”(physical association)0.720
ZBTB2ZNF639psi-mi:“MI:0915”(physical association)0.670
ZBTB2ZBTB25psi-mi:“MI:0914”(association)0.670
ZNF639CTNNA2psi-mi:“MI:0915”(physical association)0.600
ZNF639CTNNA2psi-mi:“MI:0403”(colocalization)0.600
PRPF18ZNF639psi-mi:“MI:0915”(physical association)0.560
MPP1ZNF639psi-mi:“MI:0915”(physical association)0.560
ZBTB24ZNF639psi-mi:“MI:0915”(physical association)0.560
ZNF250ZNF639psi-mi:“MI:0915”(physical association)0.560
MCRS1ZNF639psi-mi:“MI:0915”(physical association)0.560
ZNF792ZNF639psi-mi:“MI:0915”(physical association)0.560
ZNF837ZNF639psi-mi:“MI:0915”(physical association)0.560
ELAVL4ZNF639psi-mi:“MI:0915”(physical association)0.560
RASSF8CORO1Apsi-mi:“MI:0914”(association)0.530
MBD3L1CDK2AP1psi-mi:“MI:0914”(association)0.530
RIN3ZNF639psi-mi:“MI:0915”(physical association)0.370
Mta1MTA3psi-mi:“MI:0914”(association)0.350
Zbtb2ENO1psi-mi:“MI:0914”(association)0.350

BioGRID (37): ZNF639 (Two-hybrid), ZNF639 (Affinity Capture-MS), ZNF639 (Affinity Capture-MS), ZNF639 (Two-hybrid), ZNF639 (Affinity Capture-MS), ZNF639 (Affinity Capture-MS), ZNF639 (Affinity Capture-MS), ZNF639 (Affinity Capture-MS), ZNF639 (Affinity Capture-MS), ZNF639 (Affinity Capture-MS), ZNF639 (Synthetic Lethality), ZNF639 (Two-hybrid), ZNF639 (Two-hybrid), MPP1 (Two-hybrid), ZNF837 (Two-hybrid)

ESM2 similar proteins: A0A0A6YYL3, A5PK30, A7KBS4, B3NP26, B4GBA9, B4HMH2, B4P8I0, B4QIJ9, B7ZQJ9, E1JH25, G3X9G7, H3BUK9, P10925, P18853, P20662, P98182, Q09377, Q0VCB0, Q10127, Q19203, Q290S5, Q2EI20, Q2EI21, Q4R6J4, Q5NVT2, Q5PPG4, Q5SVQ8, Q5T5D7, Q5UR86, Q65XX7, Q6IQ21, Q6NRM8, Q7JUR5, Q7K4M4, Q7Z142, Q8BIQ8, Q8C0P7, Q8IRH5, Q8NAP3, Q8T053

Diamond homologs: A5PK30, P80944, Q29419, Q5PPG4, Q99KZ6, Q9UID6, A1L2U9, A2A884, A2ANX9, A7Y7X5, A8K8V0, B1WAZ8, B1WBU4, E9PZZ1, G5EBU4, O15391, O60315, O62836, O75362, O95863, P08048, P0CS62, P0CS63, P10925, P15822, P17010, P17012, P20662, P22227, P25490, P31509, P31629, P36197, P52739, P56270, P56670, P56671, P60319, Q00899, Q00900

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 43 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
NuRD complex assembly527.1×2e-04

GO biological processes:

GO termPartnersFoldFDR
chromatin remodeling59.3×1e-02

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance43
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

745 predictions. Top by Δscore:

VariantEffectΔscore
3:179327632:G:GGdonor_gain1.0000
3:179328273:C:Aacceptor_gain1.0000
3:179328278:TTTA:Tacceptor_loss1.0000
3:179328279:TTAG:Tacceptor_loss1.0000
3:179328280:TA:Tacceptor_loss1.0000
3:179328281:A:AGacceptor_gain1.0000
3:179328282:G:GAacceptor_gain1.0000
3:179328282:GAT:Gacceptor_gain1.0000
3:179328282:GATT:Gacceptor_gain1.0000
3:179328349:CAGG:Cdonor_loss1.0000
3:179328350:AGGTC:Adonor_loss1.0000
3:179328352:G:Adonor_loss1.0000
3:179328353:T:Gdonor_loss1.0000
3:179329610:A:AGacceptor_gain1.0000
3:179329611:T:Gacceptor_gain1.0000
3:179329612:GTTCA:Gacceptor_loss1.0000
3:179329614:TCAG:Tacceptor_loss1.0000
3:179329615:CA:Cacceptor_loss1.0000
3:179329616:A:AGacceptor_gain1.0000
3:179329616:AGA:Aacceptor_loss1.0000
3:179329617:G:GGacceptor_gain1.0000
3:179329617:G:GTacceptor_loss1.0000
3:179329724:CAAAG:Cdonor_loss1.0000
3:179329725:AAAGG:Adonor_loss1.0000
3:179329726:AAGGT:Adonor_loss1.0000
3:179329727:AG:Adonor_loss1.0000
3:179329728:GG:Gdonor_loss1.0000
3:179329729:G:GAdonor_loss1.0000
3:179329730:T:Adonor_loss1.0000
3:179332983:TTACA:Tacceptor_loss1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000181287 (3:179327958 T>C,G), RS1000412720 (3:179327198 A>G), RS1000465009 (3:179326960 TGG>T), RS1000630852 (3:179332932 A>C,G), RS1000661897 (3:179332503 A>G), RS1000678846 (3:179332911 TAA>T), RS1000788363 (3:179326785 C>A), RS1000937740 (3:179321622 T>C), RS1000944913 (3:179338262 G>A), RS1001072997 (3:179322046 T>C), RS1001326835 (3:179323213 C>A,G), RS1001519785 (3:179327869 G>A), RS1001534535 (3:179327543 T>C), RS1001619768 (3:179331516 C>A,T), RS1001652253 (3:179337733 A>G)

Disease associations

OMIM: gene MIM:619214 | disease phenotypes: MIM:158350

GenCC curated gene-disease

Mondo (1): Cowden disease (MONDO:0016063)

Orphanet (1): Cowden syndrome (Orphanet:201)

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST007059_17Response to antidepressants (symptom improvement)3.000000e-06
GCST010273_7Gout (normal type)5.000000e-07

MeSH disease descriptors (1)

DescriptorNameTree numbers
D006223Hamartoma Syndrome, MultipleC04.445.435; C04.651.435; C04.700.435; C16.320.700.435

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.

ChemicalActions (top 5)PubMed papers
Valproic Aciddecreases expression, decreases methylation, affects expression4
Cadmium Chloridedecreases expression2
Particulate Matterdecreases expression, increases abundance, increases expression2
aristolochic acid Idecreases expression1
FR900359increases phosphorylation1
TAK-243increases sumoylation1
dicrotophosdecreases expression1
trichostatin Aaffects expression1
cinnamaldehydeincreases expression1
mono-(2-ethylhexyl)phthalateincreases expression1
sodium arsenitedecreases expression1
K 7174increases expression1
jinfukangdecreases expression1
Vorinostatincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Vehicle Emissionsincreases expression, increases abundance1
Caffeinedecreases phosphorylation1
Doxorubicindecreases expression1
Formaldehydedecreases expression1
Hydrogen Peroxideincreases expression1
Methotrexateincreases expression1
Methyl Methanesulfonatedecreases expression1
Phenobarbitalaffects expression1
Quercetindecreases expression1
Urethanedecreases expression1
Cyclosporineincreases expression1
Aflatoxin M1decreases expression1
Copper Sulfatedecreases expression1

Cellosaurus cell lines

2 cell lines: 1 cancer cell line, 1 transformed cell line

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

CellosaurusNameCategorySex
CVCL_HA06K562 eGFP-ZNF639Cancer cell lineFemale
CVCL_HD35HEK293 eGFP-ZNF639Transformed cell lineFemale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT03306446PHASE4UNKNOWNChanging the coUrse of cRohn’s Disease With an Early Use of Adalimumab
NCT00971789PHASE2COMPLETEDSirolimus to Treat Cowden Syndrome and Other PTEN Hamartomatous Tumor Syndromes
NCT04094675PHASE2COMPLETEDSirolimus for Cowden Syndrome With Colon Polyposis
NCT00620594PHASE1COMPLETEDA Phase I/II Study of BEZ235 in Patients With Advanced Solid Malignancies Enriched by Patients With Advanced Breast Cancer
NCT01757964PHASE1COMPLETEDBacteriotherapy in Pediatric Inflammatory Bowel Disease
NCT07218575PHASE2/PHASE3NOT_YET_RECRUITINGDouble-Blind Trial of Everolimus for Improving Social Abilities in PTEN Germline Mutations
NCT00600275PHASE1/PHASE2COMPLETEDA Phase I/II Study of BGT226 in Adult Patients With Advanced Solid Malignancies Including Patients With Advanced Breast Cancer
NCT02856763Not specifiedCOMPLETEDPredictive Factors of ANTI-TNF Response in Luminal Crohn’s Disease Complicated by Abscess
NCT03487900Not specifiedUNKNOWNIs the Endoscopic Remission Evaluation, Using the CREDO 1 Index / Score in CD Patients in Clinical Remission at Baseline, Predictive of Sustained Clinical Remission Using a 2-year Follow up
NCT03498625Not specifiedCOMPLETEDCrohn’s Disease Endoscopic REmission Definition in an Objective Way
NCT03702309Not specifiedRECRUITINGLiquid Biopsy Evaluation and Repository Development at Princess Margaret
NCT06163365Not specifiedUNKNOWNInherited Cancer Early Diagnosis (ICED) Study
NCT06523582Not specifiedRECRUITINGGenetic Bases of Neuroendocrine Neoplasms in Mexican Patients
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): Cowden disease