ZNF664

gene
On this page

Also known as ZFOC1DKFZp761B128

Summary

ZNF664 (zinc finger protein 664, HGNC:25406) is a protein-coding gene on chromosome 12q24.31, encoding Zinc finger protein 664 (Q8N3J9). 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 DNA-templated transcription. Located in nucleus.

Source: NCBI Gene 144348 — RefSeq curated summary.

At a glance

  • GWAS associations: 67
  • Clinical variants (ClinVar): 18 total
  • MANE Select transcript: NM_152437

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25406
Approved symbolZNF664
Namezinc finger protein 664
Location12q24.31
Locus typegene with protein product
StatusApproved
AliasesZFOC1, DKFZp761B128
Ensembl geneENSG00000179195
Ensembl biotypeprotein_coding
OMIM617890
Entrez144348

Gene structure

Transcript identifiers

Ensembl transcripts: 60 — 50 protein_coding, 8 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000337815, ENST00000392404, ENST00000537532, ENST00000538932, ENST00000539257, ENST00000539501, ENST00000539644, ENST00000540009, ENST00000540498, ENST00000541448, ENST00000542493, ENST00000542820, ENST00000543017, ENST00000546098, ENST00000901659, ENST00000901660, ENST00000901661, ENST00000901662, ENST00000901663, ENST00000901664, ENST00000901665, ENST00000901666, ENST00000901667, ENST00000901668, ENST00000901669, ENST00000901670, ENST00000901671, ENST00000901672, ENST00000901673, ENST00000901674, ENST00000901675, ENST00000901676, ENST00000901677, ENST00000901678, ENST00000901679, ENST00000901680, ENST00000901681, ENST00000901682, ENST00000901683, ENST00000901684, ENST00000901685, ENST00000901686, ENST00000901687, ENST00000901688, ENST00000901689, ENST00000901690, ENST00000901691, ENST00000901692, ENST00000901693, ENST00000901694, ENST00000901695, ENST00000901696, ENST00000901697, ENST00000915687, ENST00000915688, ENST00000915689, ENST00000915690, ENST00000963055, ENST00000963056, ENST00000963057

RefSeq mRNA: 2 — MANE Select: NM_152437 NM_001204298, NM_152437

CCDS: CCDS9257

Canonical transcript exons

ENST00000337815 — 5 exons

ExonStartEnd
ENSE00001285710124011381124011441
ENSE00001285732123988043123988138
ENSE00002318983123973215123973352
ENSE00003624130123973886123974020
ENSE00003841583124011546124015427

Expression profiles

Bgee: expression breadth ubiquitous, 255 present calls, max score 99.39.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 44.1554 / max 333.6317, expressed in 1813 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
12861344.15541813
1286121.1151694
1286150.290493

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ileal mucosaUBERON:000033199.39gold quality
secondary oocyteCL:000065599.14gold quality
bronchial epithelial cellCL:000232898.90gold quality
kidney epitheliumUBERON:000481998.86gold quality
left ventricle myocardiumUBERON:000656698.82gold quality
jejunal mucosaUBERON:000039998.78gold quality
cardiac muscle of right atriumUBERON:000337998.78gold quality
bronchusUBERON:000218598.77gold quality
germinal epithelium of ovaryUBERON:000130498.27gold quality
corpus epididymisUBERON:000435998.25gold quality
lateral globus pallidusUBERON:000247698.24gold quality
mucosa of paranasal sinusUBERON:000503098.23gold quality
pigmented layer of retinaUBERON:000178298.19gold quality
epithelium of nasopharynxUBERON:000195198.17gold quality
subthalamic nucleusUBERON:000190698.15gold quality
globus pallidusUBERON:000187598.08gold quality
mucosa of sigmoid colonUBERON:000499398.08gold quality
palpebral conjunctivaUBERON:000181298.07gold quality
caput epididymisUBERON:000435898.07gold quality
C1 segment of cervical spinal cordUBERON:000646998.05gold quality
medial globus pallidusUBERON:000247798.04gold quality
parotid glandUBERON:000183198.01gold quality
inferior vagus X ganglionUBERON:000536397.98gold quality
postcentral gyrusUBERON:000258197.91gold quality
spinal cordUBERON:000224097.89gold quality
visceral pleuraUBERON:000240197.88gold quality
parietal pleuraUBERON:000240097.85gold quality
duodenumUBERON:000211497.84gold quality
ganglionic eminenceUBERON:000402397.81gold quality
colonic mucosaUBERON:000031797.76gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes15.74
E-MTAB-6678no3.33

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

85 targeting ZNF664, 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-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-3134100.0066.43777
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-340-5P100.0072.504437
HSA-MIR-12118100.0065.881270
HSA-MIR-4262100.0073.263931
HSA-MIR-3120-5P100.0065.56965
HSA-MIR-3667-3P99.9967.171636
HSA-MIR-453499.9966.581907
HSA-MIR-366299.9973.825684
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-MIR-548P99.9872.253784
HSA-MIR-3173-3P99.9866.491217
HSA-MIR-6891-5P99.9866.531372
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-60799.9773.625593
HSA-MIR-9-3P99.9670.882068
HSA-MIR-495-3P99.9672.814197
HSA-MIR-568899.9673.234504
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-4760-3P99.9370.502385
HSA-MIR-311999.9271.342390
HSA-MIR-129799.9173.413162
HSA-MIR-367199.9073.043897
HSA-MIR-182-5P99.8774.032589
HSA-MIR-450399.8571.451869

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
mus_musculusZfp664ENSMUSG00000079215
rattus_norvegicusZfp664ENSRNOG00000064009
drosophila_melanogasterCG18476FBGN0037931
drosophila_melanogasterCG10669FBGN0039329

Paralogs (5): ZNF648 (ENSG00000179930), ZNF721 (ENSG00000182903), ZFP62 (ENSG00000196670), ZNF485 (ENSG00000198298), ZNF808 (ENSG00000198482)

Protein

Protein identifiers

Zinc finger protein 664Q8N3J9 (reviewed: Q8N3J9)

Alternative names: Zinc finger protein 176, Zinc finger protein from organ of Corti

All UniProt accessions (1): Q8N3J9

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 (2): NP_001191227, NP_689650* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR013087Znf_C2H2_typeDomain
IPR036236Znf_C2H2_sfHomologous_superfamily

Pfam: PF00096

UniProt features (16 total): zinc finger region 9, sequence conflict 5, chain 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N3J9-F191.400.77

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 (1): 257

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-212436Generic Transcription Pathway

MSigDB gene sets: 103 (showing top): AAGTCCA_MIR422B_MIR422A, CTAGGAA_MIR384, SOX9_B1, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN, SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX1_UP, SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX4_DN, TGGNNNNNNKCCAR_UNKNOWN, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, GRYDER_PAX3FOXO1_TOP_ENHANCERS, TCCCRNNRTGC_UNKNOWN, chr12q24, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GRYDER_PAX3FOXO1_ENHANCERS_KO_DOWN, ERR1_Q2, STK33_DN

GO Biological Process (2): regulation of DNA-templated transcription (GO:0006355), regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (6): 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), protein binding (GO:0005515), 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
RNA polymerase II transcription regulatory region sequence-specific DNA binding2
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
regulation of DNA-templated transcription1
transcription by RNA polymerase II1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
regulation of transcription by RNA polymerase II1
transition metal ion binding1
nucleic acid binding1
binding1
cation binding1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

562 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZNF664CCDC92Q53HC0797
ZNF664DNAH10Q8IVF4702
ZNF664RFLNAQ6ZTI6543
ZNF664GALNT2Q10471448
ZNF664NT5DC2Q9H857448
ZNF664OR56B1Q8NGI3447
ZNF664SORCS1Q8WY21446
ZNF664CMIPQ8IY22442
ZNF664C5orf67F2Z3F1431
ZNF664COBLL1Q53SF7419
ZNF664TRIB1Q96RU8418
ZNF664ARL15Q9NXU5416
ZNF664FOXN3O00409413
ZNF664TEX19Q8NA77398
ZNF664SECTM1Q8WVN6374

IntAct

34 interactions, top by confidence:

ABTypeScore
MPDZSMCHD1psi-mi:“MI:0914”(association)0.590
CIB3ZNF664psi-mi:“MI:0915”(physical association)0.560
ZNF664psi-mi:“MI:0915”(physical association)0.560
CABP5ZNF664psi-mi:“MI:0915”(physical association)0.560
ZNF664ZNF330psi-mi:“MI:0915”(physical association)0.560
ZNF664CIB3psi-mi:“MI:0915”(physical association)0.560
ZNF664CABP5psi-mi:“MI:0915”(physical association)0.560
GADD45GZNF664psi-mi:“MI:0915”(physical association)0.560
VWCEZNF316psi-mi:“MI:0914”(association)0.530
IGFBP1SUSD5psi-mi:“MI:0914”(association)0.530
RETNGLI4psi-mi:“MI:0914”(association)0.530
RGS20PGPpsi-mi:“MI:0914”(association)0.350
ZNF227ZNF664psi-mi:“MI:0914”(association)0.350
NOTCH2ZNF320psi-mi:“MI:0914”(association)0.350
LTBP2ZNF320psi-mi:“MI:0914”(association)0.350
FBLN2ZNF316psi-mi:“MI:0914”(association)0.350
ST14LIPT2psi-mi:“MI:0914”(association)0.350
ZNF664GAPDHSpsi-mi:“MI:0914”(association)0.350
TRAK1PEX14psi-mi:“MI:0914”(association)0.350
LY6HNXPH4psi-mi:“MI:0914”(association)0.350
NFIBpsi-mi:“MI:0914”(association)0.350
ZNF330ZNF664psi-mi:“MI:0915”(physical association)0.000
GADD45GZNF664psi-mi:“MI:0915”(physical association)0.000

BioGRID (32): ZNF664 (Affinity Capture-MS), ZNF664 (Affinity Capture-MS), ZNF664 (Affinity Capture-MS), ZNF664 (Affinity Capture-MS), ZNF664 (Affinity Capture-MS), ZNF664 (Affinity Capture-MS), ZNF664 (Two-hybrid), ZNF664 (Two-hybrid), ZNF664 (Two-hybrid), ZNF664 (Two-hybrid), KRTAP10-1 (Two-hybrid), ZNF664 (Affinity Capture-RNA), ZNF664 (Affinity Capture-MS), STRIP1 (Affinity Capture-MS), ZNF664 (Affinity Capture-MS)

ESM2 similar proteins: O73694, P18712, P18717, P18719, P18720, P18721, P18722, P18724, P18727, P18730, P18731, P18732, P18734, P18735, P18738, P18740, P18741, P18742, P18743, P18744, P18750, P24399, P26634, P26635, P31507, P31508, P31509, Q01779, Q01792, Q01793, Q01797, Q01799, Q01800, Q01871, Q01872, Q02025, Q02026, Q02027, Q02034, Q02035

Diamond homologs: Q4VA44, Q5RAM9, Q60493, Q8N3J9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance17
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1338 predictions. Top by Δscore:

VariantEffectΔscore
12:123974018:CAGGT:Cdonor_loss1.0000
12:123974019:AGG:Adonor_loss1.0000
12:123974020:GGT:Gdonor_loss1.0000
12:123976224:G:GTdonor_gain1.0000
12:123973301:G:Tdonor_gain0.9900
12:123973350:GGA:Gdonor_gain0.9900
12:123973351:GAG:Gdonor_gain0.9900
12:123973353:G:GGdonor_gain0.9900
12:123974018:CAGG:Cdonor_loss0.9900
12:123974021:GT:Gdonor_loss0.9900
12:123974021:GTA:Gdonor_loss0.9900
12:123974022:T:Gdonor_loss0.9900
12:123976203:T:Gdonor_gain0.9900
12:124011379:A:AGacceptor_gain0.9900
12:124011380:G:GGacceptor_gain0.9900
12:123973351:GA:Gdonor_gain0.9800
12:123976224:G:Tdonor_gain0.9800
12:123976239:G:Tdonor_gain0.9800
12:123989289:T:Gacceptor_gain0.9800
12:124011437:AAAAG:Adonor_loss0.9800
12:124011438:AAAG:Adonor_loss0.9800
12:124011439:AAGG:Adonor_loss0.9800
12:124011440:AG:Adonor_loss0.9800
12:124011440:AGG:Adonor_loss0.9800
12:124011441:G:GTdonor_loss0.9800
12:124011441:GG:Gdonor_loss0.9800
12:124011442:G:Tdonor_loss0.9800
12:124011443:T:Gdonor_loss0.9800
12:123973399:G:GTdonor_gain0.9700
12:123973400:G:Tdonor_gain0.9700

AlphaMissense

1787 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:124012514:T:CF124L0.998
12:124012516:T:AF124L0.998
12:124012516:T:GF124L0.998
12:124012598:T:CF152L0.998
12:124012600:C:AF152L0.998
12:124012600:C:GF152L0.998
12:124012682:T:CF180L0.998
12:124012684:C:AF180L0.998
12:124012684:C:GF180L0.998
12:124012766:T:CF208L0.997
12:124012768:C:AF208L0.997
12:124012768:C:GF208L0.997
12:124012430:T:CF96L0.996
12:124012432:C:AF96L0.996
12:124012432:C:GF96L0.996
12:124012850:T:CF236L0.996
12:124012852:C:AF236L0.996
12:124012852:C:GF236L0.996
12:124012709:C:GH189D0.993
12:124012449:T:CL102P0.992
12:124012515:T:CF124S0.992
12:124012533:T:CL130P0.992
12:124012701:T:CL186P0.992
12:124012711:C:AH189Q0.992
12:124012711:C:GH189Q0.992
12:124012683:T:CF180S0.991
12:124012543:T:AH133Q0.990
12:124012543:T:GH133Q0.990
12:124012599:T:CF152S0.990
12:124012617:T:CL158P0.990

dbSNP variants (sampled 300 via entrez): RS1000005912 (12:123978645 C>G), RS1000106696 (12:123978301 T>C), RS1000145084 (12:124013947 A>C,G), RS1000227671 (12:123990088 A>G,T), RS1000317136 (12:123977860 A>G), RS1000351428 (12:123973221 TC>T,TCC), RS1000491757 (12:124007879 G>A), RS1000508148 (12:123982925 C>T), RS1000515484 (12:123989140 A>G), RS1000582197 (12:123990520 C>T), RS1000604963 (12:123995163 C>T), RS1000642259 (12:123988936 C>T), RS1000686141 (12:123982776 A>G), RS1000693148 (12:123989245 C>T), RS1000741109 (12:123982629 G>A)

Disease associations

OMIM: gene MIM:617890 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

67 associations (top):

StudyTraitp-value
GCST000755_47HDL cholesterol3.000000e-10
GCST000758_20Triglycerides1.000000e-08
GCST001523_44Visceral adipose tissue adjusted for BMI9.000000e-06
GCST001524_26Visceral adipose tissue/subcutaneous adipose tissue ratio7.000000e-06
GCST002216_10Triglycerides2.000000e-08
GCST002223_66HDL cholesterol8.000000e-10
GCST002233_8Adiponectin levels2.000000e-07
GCST002399_1Clubfoot2.000000e-07
GCST002782_127Waist-to-hip ratio adjusted for body mass index7.000000e-15
GCST002782_128Waist-to-hip ratio adjusted for body mass index7.000000e-14
GCST002782_129Waist-to-hip ratio adjusted for body mass index6.000000e-14
GCST002782_130Waist-to-hip ratio adjusted for body mass index2.000000e-13
GCST004064_51Waist-hip ratio1.000000e-09
GCST004064_73Waist-hip ratio2.000000e-06
GCST004232_10HDL cholesterol levels1.000000e-34
GCST004234_12HDL cholesterol levels6.000000e-10
GCST004237_10Triglyceride levels2.000000e-11
GCST004505_3Waist-to-hip ratio adjusted for BMI (adjusted for smoking behaviour)3.000000e-08
GCST004505_4Waist-to-hip ratio adjusted for BMI (adjusted for smoking behaviour)3.000000e-09
GCST005956_10Waist-to-hip ratio adjusted for BMI6.000000e-08
GCST005958_11Waist-to-hip ratio adjusted for BMI (age >50)4.000000e-07
GCST005962_22Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)1.000000e-08
GCST009107_2Body mass index variance1.000000e-10
GCST009380_5Type 2 diabetes (adjusted for BMI)2.000000e-08
GCST009380_6Type 2 diabetes (adjusted for BMI)2.000000e-06
GCST009404_21Optic cup area1.000000e-10
GCST009602_23Metabolic syndrome4.000000e-10
GCST009723_71Vertical cup-disc ratio (adjusted for vertical disc diameter)2.000000e-09
GCST009724_100Vertical cup-disc ratio (multi-trait analysis)2.000000e-14
GCST010002_177Refractive error4.000000e-08

EFO canonical traits (15, from GWAS)

EFO IDTrait name
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0004530triglyceride measurement
EFO:0004340body mass index
EFO:0004767visceral:subcutaneous adipose tissue ratio
EFO:0004502adiponectin measurement
EFO:0007788BMI-adjusted waist-hip ratio
EFO:0004343waist-hip ratio
EFO:0004318smoking behavior
EFO:0008007age at assessment
EFO:0008343sex interaction measurement
EFO:0000195metabolic syndrome
EFO:0006939cup-to-disc ratio measurement
EFO:0004995lean body mass
EFO:0007789BMI-adjusted waist circumference
EFO:0008039BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arseniteincreases abundance, increases expression, decreases expression3
entinostatdecreases expression, affects cotreatment2
Valproic Aciddecreases expression, decreases methylation2
Cyclosporineincreases expression, increases methylation2
Cadmium Chloridedecreases expression, increases expression2
aristolochic acid Idecreases expression1
TAK-243increases sumoylation1
triphenyl phosphateaffects expression1
cobaltous chloridedecreases expression1
manganese chlorideincreases abundance, increases expression1
CGP 52608affects binding, increases reaction1
K 7174increases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
ICG 001increases expression1
dorsomorphinaffects cotreatment, decreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acidincreases expression1
Sunitinibincreases expression1
Arsenicincreases abundance, increases expression1
Atrazinedecreases expression1
Benzo(a)pyrenedecreases methylation1
Diethylstilbestroldecreases expression1
Doxorubicindecreases expression1
Manganeseincreases abundance, increases expression1
Tretinoindecreases expression1
Triiodothyronineincreases expression1
Antirheumatic Agentsincreases expression1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

CellosaurusNameCategorySex
CVCL_HD38HEK293 eGFP-ZNF664Transformed cell lineFemale

Clinical trials (associated diseases)

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