ZNF608

gene
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Also known as KIAA1281DKFZp434M098NY-REN-36

Summary

ZNF608 (zinc finger protein 608, HGNC:29238) is a protein-coding gene on chromosome 5q23.2, encoding Zinc finger protein 608 (Q9ULD9). Transcription factor, which represses ZNF609 transcription.

Predicted to enable zinc ion binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be active in nucleus.

Source: NCBI Gene 57507 — RefSeq curated summary.

At a glance

  • GWAS associations: 41
  • Clinical variants (ClinVar): 186 total
  • MANE Select transcript: NM_020747

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29238
Approved symbolZNF608
Namezinc finger protein 608
Location5q23.2
Locus typegene with protein product
StatusApproved
AliasesKIAA1281, DKFZp434M098, NY-REN-36
Ensembl geneENSG00000168916
Ensembl biotypeprotein_coding
OMIM620972
Entrez57507

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 4 protein_coding, 4 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000306315, ENST00000503896, ENST00000504926, ENST00000505686, ENST00000509799, ENST00000511308, ENST00000512940, ENST00000513985, ENST00000513986

RefSeq mRNA: 4 — MANE Select: NM_020747 NM_001385619, NM_001385620, NM_001385621, NM_020747

CCDS: CCDS34219

Canonical transcript exons

ENST00000513986 — 10 exons

ExonStartEnd
ENSE00002068555124746195124746639
ENSE00002075892124744084124745172
ENSE00003482666124701014124701269
ENSE00003490205124646679124649133
ENSE00003490382124649610124649697
ENSE00003508528124639133124639214
ENSE00003596018124641252124641405
ENSE00003643486124643511124643683
ENSE00003681967124644244124644661
ENSE00003916226124636915124637906

Expression profiles

Bgee: expression breadth ubiquitous, 241 present calls, max score 96.08.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.3863 / max 1727.4719, expressed in 1254 samples.

FANTOM5 promoters (16 alternative TSS)

Promoter IDTPM avgSamples expressed
631745.6205984
631834.9307887
631731.3510486
631791.1985380
631820.8769313
631680.7582401
631760.5934261
631720.5839238
631780.4610196
631710.2977167

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cardiac muscle of right atriumUBERON:000337996.08gold quality
embryoUBERON:000092294.57gold quality
ganglionic eminenceUBERON:000402394.57gold quality
ventricular zoneUBERON:000305394.29gold quality
corpus callosumUBERON:000233692.77gold quality
adrenal tissueUBERON:001830391.74gold quality
sural nerveUBERON:001548888.41gold quality
C1 segment of cervical spinal cordUBERON:000646987.95gold quality
spinal cordUBERON:000224087.70gold quality
cerebellar vermisUBERON:000472087.52gold quality
right adrenal gland cortexUBERON:003582786.71gold quality
left adrenal gland cortexUBERON:003582586.50gold quality
left adrenal glandUBERON:000123486.40gold quality
adrenal cortexUBERON:000123586.29gold quality
adrenal glandUBERON:000236986.24gold quality
mucosa of stomachUBERON:000119986.16gold quality
right adrenal glandUBERON:000123385.97gold quality
cortical plateUBERON:000534385.68gold quality
right uterine tubeUBERON:000130285.63gold quality
right lobe of thyroid glandUBERON:000111985.58gold quality
subthalamic nucleusUBERON:000190685.53gold quality
lateral globus pallidusUBERON:000247685.34gold quality
amygdalaUBERON:000187685.33gold quality
olfactory segment of nasal mucosaUBERON:000538685.29gold quality
right lungUBERON:000216785.12gold quality
cardiac atriumUBERON:000208185.01gold quality
upper lobe of left lungUBERON:000895284.79gold quality
duodenumUBERON:000211484.78gold quality
cerebellar cortexUBERON:000212984.62gold quality
right hemisphere of cerebellumUBERON:001489084.60gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-GEOD-93593yes14.67
E-ANND-3yes6.28
E-GEOD-83139yes5.05

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

184 targeting ZNF608, 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-190A-3P100.0080.355520
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-3163100.0077.238605
HSA-MIR-3924100.0072.092394
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-4692100.0067.322066
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-3646100.0073.565283
HSA-MIR-4673100.0066.641490
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-4481100.0066.421669
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-4776-3P100.0068.731340
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-186-5P99.9970.833707
HSA-MIR-451499.9967.101870
HSA-MIR-366299.9973.825684
HSA-MIR-548N99.9871.944170
HSA-MIR-1213699.9872.815713
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-4645-5P99.9865.811284
HSA-LET-7F-2-3P99.9870.982588

Literature-anchored findings (GeneRIF, showing 1)

  • Data indicate RNA Binding Protein with Multiple Splicing (RBPMS), Regulator of Chromosome Condensation and POZ Domain Containing Protein 1 (RCBTB1), and Zinc Finger protein 608 (ZNF608) as miR-21-3p target genes. (PMID:27166999)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
mus_musculusZfp608ENSMUSG00000052713
rattus_norvegicusZfp608ENSRNOG00000023197
drosophila_melanogastersbbFBGN0285917

Paralogs (1): ZNF609 (ENSG00000180357)

Protein

Protein identifiers

Zinc finger protein 608Q9ULD9 (reviewed: Q9ULD9)

Alternative names: Renal carcinoma antigen NY-REN-36

All UniProt accessions (4): A0A0C4DGB8, A2RRB2, B3KPE6, Q9ULD9

UniProt curated annotations — full annotation on UniProt →

Function. Transcription factor, which represses ZNF609 transcription.

Isoforms (2)

UniProt IDNamesCanonical?
Q9ULD9-11yes
Q9ULD9-22

RefSeq proteins (4): NP_001372548, NP_001372549, NP_001372550, NP_065798* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR013087Znf_C2H2_typeDomain
IPR040010ZN608/ZN609Family

UniProt features (62 total): compositionally biased region 22, region of interest 13, cross-link 12, modified residue 9, chain 1, zinc finger region 1, coiled-coil region 1, splice variant 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9ULD9-F144.800.03

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 (21): 421, 424, 481, 493, 627, 782, 895, 964, 1098, 283, 880, 1118, 1176, 1182, 1199, 1216, 1234, 1250, 1292, 1310 …

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 219 (showing top): MODULE_169, SARRIO_EPITHELIAL_MESENCHYMAL_TRANSITION_DN, GCGCTTT_MIR518B_MIR518C_MIR518D, BILD_HRAS_ONCOGENIC_SIGNATURE, AGCGCTT_MIR518F_MIR518E_MIR518A, CATTTCA_MIR203, AAACCAC_MIR140, ATTCTTT_MIR186, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, TGCCTTA_MIR124A, GAVIN_FOXP3_TARGETS_CLUSTER_P3, GAVIN_IL2_RESPONSIVE_FOXP3_TARGETS_UP, ZHENG_BOUND_BY_FOXP3, ZHENG_FOXP3_TARGETS_IN_T_LYMPHOCYTE_UP, ZHAN_MULTIPLE_MYELOMA_CD2_UP

GO Biological Process (2): negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (2): zinc ion binding (GO:0008270), metal ion binding (GO:0046872)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
transcription by RNA polymerase II2
regulation of transcription by RNA polymerase II1
negative regulation of DNA-templated transcription1
regulation of DNA-templated transcription1
transition metal ion binding1
cation binding1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

658 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZNF608TMEM160Q9NX00691
ZNF608DNAJC27Q9NZQ0606
ZNF608MTIF3Q9H2K0594
ZNF608NUDT3O95989583
ZNF608POC5Q8NA72575
ZNF608QPCTLQ9NXS2571
ZNF608GPRC5BQ9NZH0570
ZNF608V9GXZ4V9GXZ4570
ZNF608GRAMD2BQ96HH9546
ZNF608SEC16BQ96JE7544
ZNF608GNPDA2Q8TDQ7541
ZNF608TNNI3KQ59H18541
ZNF608ATN1P54259536
ZNF608LINGO2Q7L985517
ZNF608CADM2Q8N3J6507

IntAct

54 interactions, top by confidence:

ABTypeScore
HDAC1CDK2AP1psi-mi:“MI:0914”(association)0.840
HDAC1TNRC18psi-mi:“MI:0914”(association)0.790
MED23MED19psi-mi:“MI:2364”(proximity)0.770
DYNLL1BLTP3Bpsi-mi:“MI:0914”(association)0.730
HDAC1ZNF609psi-mi:“MI:0914”(association)0.730
NFICNFIBpsi-mi:“MI:2364”(proximity)0.690
DYNLL2BLTP3Bpsi-mi:“MI:0914”(association)0.640
EN1NFIBpsi-mi:“MI:2364”(proximity)0.470
ZNF608ATN1psi-mi:“MI:0407”(direct interaction)0.440
AUTS2ZNF609psi-mi:“MI:0914”(association)0.350
WDR5PHF20L1psi-mi:“MI:0914”(association)0.350
Mpsi-mi:“MI:0914”(association)0.350
SLC16A11ESYT2psi-mi:“MI:0914”(association)0.350
RAF1EIF3Fpsi-mi:“MI:0914”(association)0.350
ARMED6psi-mi:“MI:2364”(proximity)0.270
RAVER1KDM6Apsi-mi:“MI:2364”(proximity)0.270
SOX7NFIBpsi-mi:“MI:2364”(proximity)0.270
TBXTBCL9psi-mi:“MI:2364”(proximity)0.270
ERGBCL9psi-mi:“MI:2364”(proximity)0.270
FEVTAF4psi-mi:“MI:2364”(proximity)0.270
FOXI1BCL9psi-mi:“MI:2364”(proximity)0.270
FOXL1PGRMC1psi-mi:“MI:2364”(proximity)0.270
FOXQ1ZNF609psi-mi:“MI:2364”(proximity)0.270
GATA2BCL9psi-mi:“MI:2364”(proximity)0.270
HNF1BBCL9psi-mi:“MI:2364”(proximity)0.270
HNF4ATAF4psi-mi:“MI:2364”(proximity)0.270
IRF4ARID1Apsi-mi:“MI:2364”(proximity)0.270

BioGRID (99): ZNF608 (Affinity Capture-MS), ZNF608 (Proximity Label-MS), ZNF608 (Affinity Capture-MS), ZNF608 (Affinity Capture-RNA), ZNF608 (Affinity Capture-MS), ZNF608 (Affinity Capture-MS), ZNF608 (Proximity Label-MS), ZNF608 (Affinity Capture-MS), ZNF608 (Affinity Capture-MS), ZNF608 (Proximity Label-MS), ZNF608 (Proximity Label-MS), ZNF608 (Affinity Capture-MS), ZNF608 (Affinity Capture-MS), KANSL3 (Affinity Capture-MS), ZNF608 (Affinity Capture-MS)

ESM2 similar proteins: A2A935, A5GFT6, A5PK23, A5X7A0, A7MB40, A7XYH5, A7XYH9, A7XYI6, A7XYJ6, A7XYQ1, E1BE02, E2R9X2, E7F888, F1LMN3, F6NSX9, O15265, O95402, P78312, Q03989, Q04891, Q0P5V2, Q15911, Q3U108, Q56A10, Q58FA4, Q5ZJ69, Q5ZM88, Q61329, Q62255, Q68FE9, Q6PJG2, Q6ZSZ6, Q76L83, Q7YR76, Q86V15, Q8BZ32, Q8BZ47, Q8CGI1, Q8K4J6, Q8R4I1

Diamond homologs: O15014, Q56A10, Q8BZ47, Q9ULD9, Q9UTH8, P32432, Q5RDF5, Q80ZQ5, Q86VZ6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 65 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
Deactivation of the beta-catenin transactivating complex525.3×3e-04

GO biological processes:

GO termPartnersFoldFDR
positive regulation of transcription initiation by RNA polymerase II521.6×2e-04
somatic stem cell population maintenance519.7×3e-04
anatomical structure morphogenesis817.7×2e-06
transcription by RNA polymerase II1112.3×3e-07
gene expression78.9×4e-04
chromatin remodeling78.1×7e-04
positive regulation of gene expression95.5×9e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance172
Likely benign4
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1909 predictions. Top by Δscore:

VariantEffectΔscore
5:124639128:TTTA:Tdonor_loss1.0000
5:124639129:TTAC:Tdonor_loss1.0000
5:124639130:TA:Tdonor_loss1.0000
5:124639131:ACCT:Adonor_loss1.0000
5:124639132:C:CAdonor_loss1.0000
5:124639132:CCTT:Cdonor_gain1.0000
5:124641248:TGA:Tdonor_loss1.0000
5:124641249:GAC:Gdonor_loss1.0000
5:124641250:A:Tdonor_loss1.0000
5:124641251:C:CTdonor_loss1.0000
5:124641401:ACAGG:Aacceptor_gain1.0000
5:124641402:CAGG:Cacceptor_gain1.0000
5:124641402:CAGGC:Cacceptor_gain1.0000
5:124641403:AGG:Aacceptor_gain1.0000
5:124641404:GG:Gacceptor_gain1.0000
5:124641404:GGCT:Gacceptor_loss1.0000
5:124641406:C:CCacceptor_gain1.0000
5:124641406:CTGCA:Cacceptor_loss1.0000
5:124641407:T:Cacceptor_loss1.0000
5:124643505:GCTTA:Gdonor_loss1.0000
5:124643506:CTTAC:Cdonor_loss1.0000
5:124643508:TA:Tdonor_loss1.0000
5:124643509:A:ACdonor_gain1.0000
5:124643509:AC:Adonor_loss1.0000
5:124643509:ACAG:Adonor_gain1.0000
5:124643510:C:CTdonor_gain1.0000
5:124643510:CA:Cdonor_gain1.0000
5:124643510:CAG:Cdonor_gain1.0000
5:124643510:CAGC:Cdonor_gain1.0000
5:124643510:CAGCA:Cdonor_gain1.0000

AlphaMissense

4655 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:124648663:T:GQ574P1.000
5:124648667:G:CH573D1.000
5:124648670:A:CY572D1.000
5:124648670:A:GY572H1.000
5:124648675:A:GL570P1.000
5:124648675:A:TL570Q1.000
5:124648678:C:AG569V1.000
5:124648678:C:TG569D1.000
5:124648679:C:AG569C1.000
5:124648679:C:GG569R1.000
5:124648689:C:AK565N1.000
5:124648689:C:GK565N1.000
5:124648693:T:CY564C1.000
5:124648693:T:GY564S1.000
5:124648694:A:CY564D1.000
5:124648694:A:GY564H1.000
5:124648694:A:TY564N1.000
5:124648698:T:AK562N1.000
5:124648698:T:GK562N1.000
5:124648699:T:AK562I1.000
5:124648700:T:CK562E1.000
5:124648704:G:CC560W1.000
5:124648705:C:AC560F1.000
5:124648705:C:GC560S1.000
5:124648705:C:TC560Y1.000
5:124648706:A:CC560G1.000
5:124648706:A:GC560R1.000
5:124648706:A:TC560S1.000
5:124648719:A:CC555W1.000
5:124648720:C:AC555F1.000

dbSNP variants (sampled 300 via entrez): RS1000000396 (5:124745341 C>T), RS1000014558 (5:124689275 T>G), RS1000019869 (5:124700260 A>C), RS1000031178 (5:124715402 C>G,T), RS1000073354 (5:124699991 T>C), RS1000086213 (5:124651352 A>C), RS1000120564 (5:124665540 G>A), RS1000128118 (5:124709003 C>A,G), RS1000130255 (5:124748918 A>C), RS1000173083 (5:124650352 A>C,T), RS1000222691 (5:124706646 G>A), RS1000226098 (5:124658992 G>A), RS1000290327 (5:124702781 C>T), RS1000312462 (5:124670221 G>C), RS1000342179 (5:124669972 A>G)

Disease associations

OMIM: gene MIM:620972 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

41 associations (top):

StudyTraitp-value
GCST000824_6Erectile dysfunction and prostate cancer treatment4.000000e-06
GCST000830_20Body mass index2.000000e-09
GCST001521_30Subcutaneous adipose tissue7.000000e-07
GCST002021_10Body mass index5.000000e-06
GCST002339_2Type 2 diabetes (young onset) and obesity6.000000e-06
GCST002690_5Very long-chain saturated fatty acid levels (fatty acid 20:0)2.000000e-06
GCST002783_153Body mass index4.000000e-07
GCST002783_206Body mass index2.000000e-07
GCST003832_10Asthma (childhood onset)7.000000e-06
GCST003996_45Monobrow2.000000e-14
GCST004294_6Nicotine dependence2.000000e-06
GCST004485_45Survival in pancreatic cancer8.000000e-07
GCST004557_132Body mass index7.000000e-08
GCST004557_186Body mass index7.000000e-08
GCST004557_219Body mass index3.000000e-08
GCST004557_53Body mass index3.000000e-08
GCST004558_199Body mass index (joint analysis main effects and physical activity interaction)2.000000e-07
GCST004558_237Body mass index (joint analysis main effects and physical activity interaction)3.000000e-08
GCST004558_38Body mass index (joint analysis main effects and physical activity interaction)5.000000e-06
GCST004558_89Body mass index (joint analysis main effects and physical activity interaction)5.000000e-08
GCST004559_166Body mass index in physically active individuals2.000000e-08
GCST004559_188Body mass index in physically active individuals6.000000e-08
GCST004559_32Body mass index in physically active individuals2.000000e-06
GCST004559_83Body mass index in physically active individuals3.000000e-08
GCST004904_21Body mass index4.000000e-10
GCST004904_72Body mass index2.000000e-10
GCST007260_2B6 vitamer levels (multivariate analysis)8.000000e-07
GCST007324_5Adventurousness3.000000e-11
GCST007576_195Chronotype2.000000e-09
GCST008575_10IgM levels4.000000e-09

EFO canonical traits (13, from GWAS)

EFO IDTrait name
EFO:0004340body mass index
EFO:0006796very long-chain saturated fatty acid measurement
EFO:0007906synophrys measurement
EFO:0000638overall survival
EFO:0008002physical activity measurement
EFO:0004621vitamin B6 measurement
EFO:0008579risk-taking behaviour
EFO:0008328chronotype measurement
EFO:0010474cystathionine measurement
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0004462PR interval
EFO:0004980appendicular lean mass
EFO:0009749age at first sexual intercourse measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

60 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression4
trichostatin Aaffects cotreatment, decreases expression3
Air Pollutantsdecreases expression, affects cotreatment, increases abundance3
methylmercuric chloridedecreases expression, increases expression2
bisphenol Aaffects cotreatment, increases methylation, increases expression2
sodium arsenitedecreases expression2
Tetrachlorodibenzodioxinincreases expression2
Cyclosporinedecreases expression2
aristolochic acid Idecreases expression1
FR900359affects phosphorylation1
TAK-243increases sumoylation1
sotorasibaffects cotreatment, decreases expression1
alpha-pineneaffects cotreatment, decreases expression, increases abundance1
propionaldehydeincreases expression1
pirinixic acidincreases activity, affects binding, decreases expression1
tris(2-butoxyethyl) phosphateaffects expression1
beta-lapachonedecreases expression1
arseniteincreases methylation1
sulforaphanedecreases expression1
potassium chromate(VI)decreases expression1
nickel sulfatedecreases expression1
methacrylaldehydeaffects cotreatment, decreases expression, increases abundance1
S-(1,2-dichlorovinyl)cysteinedecreases expression1
di-n-butylphosphoric acidaffects expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
ICG 001increases expression1
abrineincreases expression1
Grape Seed Proanthocyanidinsdecreases expression, affects cotreatment1
dorsomorphinaffects cotreatment, decreases expression1
bisphenol Sincreases methylation1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): erectile dysfunction, nicotine dependence