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ZNF616

gene
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Also known as MGC45556

Summary

ZNF616 (zinc finger protein 616, HGNC:28062) is a protein-coding gene on chromosome 19q13.41, encoding Zinc finger protein 616 (Q08AN1). 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 90317 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 146 total
  • MANE Select transcript: NM_178523

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28062
Approved symbolZNF616
Namezinc finger protein 616
Location19q13.41
Locus typegene with protein product
StatusApproved
AliasesMGC45556
Ensembl geneENSG00000204611
Ensembl biotypeprotein_coding
Entrez90317

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 8 protein_coding

ENST00000330123, ENST00000596290, ENST00000597013, ENST00000600228, ENST00000600282, ENST00000885299, ENST00000918015, ENST00000947372

RefSeq mRNA: 1 — MANE Select: NM_178523 NM_178523

CCDS: CCDS33090

Canonical transcript exons

ENST00000600228 — 4 exons

ExonStartEnd
ENSE000014714215213050152130588
ENSE000025103165212392352124049
ENSE000030156995213973252139938
ENSE000030967935211309152117024

Expression profiles

Bgee: expression breadth ubiquitous, 194 present calls, max score 89.58.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.1106 / max 143.1427, expressed in 1656 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1825176.11061656

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
sural nerveUBERON:001548889.58gold quality
adrenal tissueUBERON:001830388.56gold quality
cortical plateUBERON:000534384.18gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047383.87gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099182.99gold quality
ganglionic eminenceUBERON:000402381.88gold quality
calcaneal tendonUBERON:000370181.15gold quality
islet of LangerhansUBERON:000000680.72gold quality
left adrenal gland cortexUBERON:003582580.58gold quality
right adrenal gland cortexUBERON:003582780.25gold quality
adrenal glandUBERON:000236980.17gold quality
right adrenal glandUBERON:000123380.14gold quality
left adrenal glandUBERON:000123480.05gold quality
stromal cell of endometriumCL:000225579.71gold quality
left ovaryUBERON:000211979.40gold quality
buccal mucosa cellCL:000233679.03gold quality
adrenal cortexUBERON:000123578.92gold quality
ventricular zoneUBERON:000305378.23gold quality
smooth muscle tissueUBERON:000113577.93gold quality
ovaryUBERON:000099277.64gold quality
right ovaryUBERON:000211877.34gold quality
pancreasUBERON:000126476.95gold quality
body of pancreasUBERON:000115076.38gold quality
rectumUBERON:000105276.35gold quality
body of uterusUBERON:000985376.02gold quality
colonic epitheliumUBERON:000039775.86gold quality
lower esophagus mucosaUBERON:003583475.75gold quality
ectocervixUBERON:001224974.94gold quality
leukocyteCL:000073874.49gold quality
monocyteCL:000057674.38gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no3.76

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): E2F1

miRNA regulators (miRDB)

87 targeting ZNF616, 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-3064-3P100.0070.091254
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-340-5P100.0072.504437
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-511-3P99.9968.851467
HSA-MIR-453199.9969.703181
HSA-MIR-56899.9869.862084
HSA-MIR-60799.9773.625593
HSA-MIR-381-3P99.9371.872854
HSA-MIR-30099.9271.762856
HSA-MIR-450B-5P99.9271.483175
HSA-MIR-7-1-3P99.9171.534384
HSA-MIR-7-2-3P99.9171.404394
HSA-MIR-368699.9070.532432
HSA-MIR-990299.8969.152250
HSA-MIR-380-3P99.8970.181978
HSA-MIR-153-5P99.8973.866317
HSA-MIR-548D-3P99.8770.674362
HSA-MIR-5582-3P99.8672.484221
HSA-MIR-548BB-3P99.8670.584354
HSA-MIR-548AR-3P99.8571.263889
HSA-MIR-548AC99.8470.774351
HSA-MIR-548H-3P99.8470.804349
HSA-MIR-548Z99.8470.804349
HSA-MIR-548AZ-3P99.8270.563549
HSA-MIR-548BC99.8270.613524
HSA-MIR-548E-3P99.8270.593514
HSA-MIR-548F-3P99.8270.593540
HSA-MIR-5002-5P99.7670.841763

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 616 — Q08AN1 (reviewed: Q08AN1)

All UniProt accessions (4): Q08AN1, M0QXF0, M0QYU5, M0R0C2

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 (1): NP_848618* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001909KRABDomain
IPR013087Znf_C2H2_typeDomain
IPR036051KRAB_dom_sfHomologous_superfamily
IPR036236Znf_C2H2_sfHomologous_superfamily
IPR050329GLI_C2H2-zinc-fingerFamily

Pfam: PF00096, PF01352

UniProt features (26 total): zinc finger region 21, sequence variant 2, chain 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q08AN1-F171.020.03

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-212436Generic Transcription Pathway

MSigDB gene sets: 50 (showing top): RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, XU_GH1_EXOGENOUS_TARGETS_DN, GOCC_NUCLEOLUS, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, LU_EZH2_TARGETS_UP, GOBP_POSITIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, CREB3L4_TARGET_GENES, GLI4_TARGET_GENES, ID2_TARGET_GENES, SALL4_TARGET_GENES, ZNF350_TARGET_GENES, MIR300, MIR381_3P, MIR4778_5P

GO Biological Process (4): regulation of transcription by RNA polymerase II (GO:0006357), positive regulation of transcription by RNA polymerase II (GO:0045944), regulation of DNA-templated transcription (GO:0006355), negative regulation of macromolecule biosynthetic process (GO:0010558)

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), transcription cis-regulatory region binding (GO:0000976), DNA binding (GO:0003677), metal ion binding (GO:0046872)

GO Cellular Component (3): nucleus (GO:0005634), nucleolus (GO:0005730), microtubule cytoskeleton (GO:0015630)

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
transcription by RNA polymerase II2
regulation of transcription by RNA polymerase II2
RNA polymerase II transcription regulatory region sequence-specific DNA binding2
regulation of DNA-templated transcription1
positive regulation of DNA-templated transcription1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
macromolecule biosynthetic process1
negative regulation of biosynthetic process1
regulation of macromolecule biosynthetic process1
negative regulation of macromolecule metabolic process1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
transition metal ion binding1
transcription regulatory region nucleic acid binding1
sequence-specific double-stranded DNA binding1
nucleic acid binding1
cation binding1
intracellular membrane-bounded organelle1
nuclear lumen1
intracellular membraneless organelle1
cytoskeleton1

Protein interactions and networks

STRING

688 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZNF616OR5AP2Q8NGF4506
ZNF616OR5I1Q13606490
ZNF616FOXD4L6Q3SYB3478
ZNF616OR1L8Q8NGR8475
ZNF616OR8B4Q96RC9448
ZNF616C11orf24Q96F05432
ZNF616SYNDIG1Q9H7V2426
ZNF616FBXO48Q5FWF7418
ZNF616OR2I1Q8NGU4417
ZNF616NUP62CLQ9H1M0396
ZNF616OR4D10Q8NGI6393
ZNF616SH3RF2Q8TEC5370
ZNF616DPY19L1Q2PZI1360
ZNF616BHLHA9Q7RTU4352
ZNF616PCNX3Q9H6A9348
ZNF616CDC14BO60729348

IntAct

19 interactions, top by confidence:

ABTypeScore
CUL9TP53psi-mi:“MI:0914”(association)0.920
TRIM28ZNF320psi-mi:“MI:0914”(association)0.530
ZNF616bipApsi-mi:“MI:0915”(physical association)0.370
Nrip3ILVBLpsi-mi:“MI:0914”(association)0.350
ZSCAN5AMRPS12psi-mi:“MI:0914”(association)0.350
Pafah1b1ATXN3psi-mi:“MI:0914”(association)0.350
ImmtGOSR1psi-mi:“MI:0914”(association)0.350
TRIM28ZNF320psi-mi:“MI:0914”(association)0.350
Mpsi-mi:“MI:0914”(association)0.350
PURGZNF320psi-mi:“MI:0914”(association)0.350
RPL36GTPBP10psi-mi:“MI:0914”(association)0.350
OASLZNF316psi-mi:“MI:0914”(association)0.350
RPL17psi-mi:“MI:0914”(association)0.350
KRR1PES1psi-mi:“MI:0914”(association)0.350
RPL23AMPHOSPH10psi-mi:“MI:0914”(association)0.350
ZBTB47MPHOSPH10psi-mi:“MI:0914”(association)0.350
CUL9NVLpsi-mi:“MI:0914”(association)0.350

BioGRID (19): ZNF616 (Biochemical Activity), ZNF616 (Affinity Capture-MS), ZNF616 (Affinity Capture-MS), ZNF616 (Affinity Capture-MS), ZNF616 (Affinity Capture-MS), ZNF616 (Affinity Capture-MS), ZNF616 (Affinity Capture-MS), ZNF616 (Affinity Capture-MS), ZNF616 (Affinity Capture-MS), ZNF616 (Affinity Capture-MS), ZNF616 (Affinity Capture-MS), ZNF616 (Affinity Capture-MS), ZNF616 (Affinity Capture-MS), ZNF616 (Affinity Capture-MS), ZNF616 (Affinity Capture-MS)

ESM2 similar proteins: A2VDQ7, A6NNF4, A8MQ14, A8MTY0, E9QAG8, O75290, O75373, P08043, P0CJ79, P10751, P17017, P17027, P17039, P35789, P51522, P51523, Q08AN1, Q14585, Q14587, Q3SYV7, Q3ZCX4, Q4R4C7, Q52M93, Q5MCW4, Q5R5U3, Q5R8X1, Q5R9F0, Q5SXM1, Q6ECI4, Q6JLC9, Q6P3V2, Q6P5C7, Q6ZN57, Q86UE3, Q86XN6, Q86YE8, Q8C827, Q8IYB9, Q8N4W9, Q8N7M2

Diamond homologs: A0A1W2PQL4, A2RRD8, A2VDQ7, A6NHJ4, A6NK75, A6NN14, A6NNF4, A6NP11, B4DX44, B4DXR9, E9PW05, O14628, O43345, O75290, O75346, O75373, O75820, P0CB33, P0CJ79, P0DKX0, P10755, P17032, P17035, P52738, Q02386, Q03923, Q03936, Q05481, Q08AN1, Q09FC8, Q0VGE8, Q14586, Q14593, Q147U1, Q15928, Q3MIS6, Q3SXZ3, Q494X3, Q4R6C2, Q5HY98

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 26 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
Major pathway of rRNA processing in the nucleolus and cytosol626.5×4e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance134
Likely benign10
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

758 predictions. Top by Δscore:

VariantEffectΔscore
19:52117024:CCTG:Cacceptor_loss1.0000
19:52117025:C:Tacceptor_loss1.0000
19:52123920:CA:Cdonor_loss1.0000
19:52123921:A:ACdonor_gain1.0000
19:52123921:AC:Adonor_gain1.0000
19:52123921:ACC:Adonor_loss1.0000
19:52123922:C:CGdonor_gain1.0000
19:52123922:CC:Cdonor_gain1.0000
19:52123922:CCT:Cdonor_gain1.0000
19:52123922:CCTA:Cdonor_gain1.0000
19:52123922:CCTAG:Cdonor_gain1.0000
19:52124045:TGCCC:Tacceptor_gain1.0000
19:52124046:GCCC:Gacceptor_gain1.0000
19:52124047:CCC:Cacceptor_gain1.0000
19:52124047:CCCC:Cacceptor_gain1.0000
19:52124048:CC:Cacceptor_gain1.0000
19:52124048:CCC:Cacceptor_gain1.0000
19:52124049:CC:Cacceptor_gain1.0000
19:52124050:C:CCacceptor_gain1.0000
19:52124050:C:Tacceptor_gain1.0000
19:52124051:T:Aacceptor_loss1.0000
19:52124055:A:ACacceptor_gain1.0000
19:52130586:AACC:Aacceptor_loss1.0000
19:52130587:ACC:Aacceptor_loss1.0000
19:52130588:CCTGA:Cacceptor_loss1.0000
19:52130589:C:CAacceptor_loss1.0000
19:52130590:T:Aacceptor_loss1.0000
19:52139730:A:ACdonor_gain1.0000
19:52139731:C:CCdonor_gain1.0000
19:52117020:GATAC:Gacceptor_gain0.9900

AlphaMissense

5210 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:52115322:A:CF614L0.997
19:52115322:A:TF614L0.997
19:52115324:A:GF614L0.997
19:52116078:G:CF362L0.994
19:52116078:G:TF362L0.994
19:52116080:A:GF362L0.994
19:52115658:G:CF502L0.993
19:52115658:G:TF502L0.993
19:52115660:A:GF502L0.993
19:52116330:A:CF278L0.993
19:52116330:A:TF278L0.993
19:52116332:A:GF278L0.993
19:52115238:A:CF642L0.992
19:52115238:A:TF642L0.992
19:52115240:A:GF642L0.992
19:52115490:G:CF558L0.992
19:52115490:G:TF558L0.992
19:52115492:A:GF558L0.992
19:52116162:A:CF334L0.992
19:52116162:A:TF334L0.992
19:52116164:A:GF334L0.992
19:52116246:A:CF306L0.992
19:52116246:A:TF306L0.992
19:52116248:A:GF306L0.992
19:52116498:A:CF222L0.992
19:52116498:A:TF222L0.992
19:52116500:A:GF222L0.992
19:52115154:A:CF670L0.991
19:52115154:A:TF670L0.991
19:52115156:A:GF670L0.991

dbSNP variants (sampled 300 via entrez): RS1000071561 (19:52125835 G>A), RS1000112946 (19:52121005 A>C), RS1000136707 (19:52137078 G>C), RS1000259765 (19:52124442 C>A,G,T), RS1000374673 (19:52118316 G>A), RS1000569739 (19:52132564 T>A,C), RS1000675885 (19:52127307 G>A,C), RS1000708775 (19:52119694 A>T), RS1001204509 (19:52137190 G>A,C), RS1001247629 (19:52135860 G>A), RS1001274637 (19:52134476 A>C), RS1001423502 (19:52132072 A>C), RS1001540189 (19:52138507 G>A), RS1001594077 (19:52136093 G>C), RS1001700860 (19:52130948 T>C)

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

4 associations (top):

StudyTraitp-value
GCST005566_28Insomnia3.000000e-07
GCST007277_24Tourette syndrome9.000000e-07
GCST007680_5Triiodothyronine levels and thyroxine levels1.000000e-06
GCST009391_350Metabolite levels5.000000e-06

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0008392triiodothyronine measurement
EFO:0010432triacylglycerol 56:5 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arseniteincreases expression, decreases expression3
bisphenol Aincreases expression, affects cotreatment, decreases methylation2
Acetaminophendecreases expression, increases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
propionaldehydeincreases expression1
arseniteaffects binding, decreases reaction1
butyraldehydeincreases expression1
potassium chromate(VI)decreases expression1
ferrous chloridedecreases expression1
aflatoxin B2increases methylation1
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
torcetrapibincreases expression1
dorsomorphinaffects cotreatment, decreases expression1
jinfukangaffects cotreatment, decreases expression1
mono(carboxy-isooctyl)phthalateaffects expression1
Resveratrolaffects cotreatment, increases expression1
Temozolomideincreases expression1
Fulvestrantaffects cotreatment, decreases methylation1
Air Pollutants, Occupationaldecreases expression1
Benzo(a)pyreneaffects methylation1
Cisplatinaffects cotreatment, decreases expression1
Endosulfandecreases expression1
Estradiolaffects expression1
Nickeldecreases expression1
Plant Extractsaffects cotreatment, increases expression1
Tretinoindecreases expression1

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): insomnia

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.2
BioBTree
v2.0.2

Sources 75

This page pulls from 75 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomereactomeparentrefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot