ZNF830

gene
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Also known as MGC20398OMCG1

Summary

ZNF830 (zinc finger protein 830, HGNC:28291) is a protein-coding gene on chromosome 17q12, encoding Zinc finger protein 830 (Q96NB3). May play a role in pre-mRNA splicing as component of the spliceosome. It is a common-essential gene (DepMap: required in 99.4% of cancer cell lines).

Predicted to enable nucleic acid binding activity and zinc ion binding activity. Predicted to be involved in several processes, including mitotic DNA integrity checkpoint signaling; nuclear DNA replication; and preantral ovarian follicle growth. Predicted to act upstream of or within several processes, including blastocyst growth; chromosome organization; and intestinal epithelial structure maintenance. Predicted to be located in nucleoplasm. Predicted to be part of spliceosomal complex. Predicted to be active in nucleus.

Source: NCBI Gene 91603 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 39 total
  • Cancer dependency (DepMap): dependent in 99.4% of screened cell lines (common-essential)
  • MANE Select transcript: NM_052857

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28291
Approved symbolZNF830
Namezinc finger protein 830
Location17q12
Locus typegene with protein product
StatusApproved
AliasesMGC20398, OMCG1
Ensembl geneENSG00000198783
Ensembl biotypeprotein_coding
Entrez91603

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 nonsense_mediated_decay

ENST00000361952, ENST00000578339

RefSeq mRNA: 1 — MANE Select: NM_052857 NM_052857

CCDS: CCDS32618

Canonical transcript exons

ENST00000361952 — 1 exons

ExonStartEnd
ENSE000011060403496154034963777

Expression profiles

Bgee: expression breadth ubiquitous, 255 present calls, max score 95.81.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.1583 / max 139.9218, expressed in 1727 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1603247.15831727

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
tendon of biceps brachiiUBERON:000818895.81gold quality
kidney epitheliumUBERON:000481994.02gold quality
epithelial cell of pancreasCL:000008393.75gold quality
upper arm skinUBERON:000426392.76gold quality
left ventricle myocardiumUBERON:000656692.70gold quality
cardiac muscle of right atriumUBERON:000337992.59gold quality
epithelium of nasopharynxUBERON:000195192.43gold quality
parotid glandUBERON:000183191.83gold quality
thymusUBERON:000237091.82gold quality
medial globus pallidusUBERON:000247791.06gold quality
germinal epithelium of ovaryUBERON:000130490.69gold quality
tendonUBERON:000004390.58gold quality
pylorusUBERON:000116689.88gold quality
globus pallidusUBERON:000187589.77gold quality
cerebellar vermisUBERON:000472089.65gold quality
cardia of stomachUBERON:000116289.30gold quality
amniotic fluidUBERON:000017388.77gold quality
palpebral conjunctivaUBERON:000181288.75gold quality
tibialis anteriorUBERON:000138588.64gold quality
pericardiumUBERON:000240788.64gold quality
calcaneal tendonUBERON:000370188.60gold quality
layer of synovial tissueUBERON:000761688.25gold quality
mammalian vulvaUBERON:000099787.87gold quality
urethraUBERON:000005787.79gold quality
deciduaUBERON:000245087.76gold quality
deltoidUBERON:000147687.74gold quality
trabecular bone tissueUBERON:000248387.67gold quality
ileal mucosaUBERON:000033187.60gold quality
dorsal root ganglionUBERON:000004487.13gold quality
granulocyteCL:000009487.07gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes3.78
E-GEOD-110499no397.63
E-CURD-10no246.14

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

41 targeting ZNF830, 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-3613-3P100.0076.367965
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-338-5P99.9272.342951
HSA-MIR-130599.9171.433443
HSA-MIR-10523-5P99.9169.222038
HSA-MIR-548D-3P99.8770.674362
HSA-MIR-548BB-3P99.8670.584354
HSA-MIR-383-3P99.8565.841359
HSA-MIR-548AC99.8470.774351
HSA-MIR-548H-3P99.8470.804349
HSA-MIR-548Z99.8470.804349
HSA-MIR-132399.8369.892471
HSA-MIR-4766-5P99.7569.232662
HSA-MIR-425599.7267.701541
HSA-MIR-4699-3P99.7170.153142
HSA-MIR-117999.7168.701040
HSA-MIR-509399.6769.262291
HSA-MIR-3616-5P99.5567.02989
HSA-MIR-57399.5567.44955
HSA-MIR-568399.3668.592083

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.4% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 1)

  • ZNF830 mediates cancer chemoresistance through promoting homologous recombination repair. (PMID:29244158)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
mus_musculusZfp830ENSMUSG00000046010
rattus_norvegicusZfp830ENSRNOG00000073735
drosophila_melanogasterCG11839FBGN0039271
caenorhabditis_elegansWBGENE00011411

Protein

Protein identifiers

Zinc finger protein 830Q96NB3 (reviewed: Q96NB3)

Alternative names: Coiled-coil domain-containing protein 16

All UniProt accessions (2): Q96NB3, J3QQQ3

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in pre-mRNA splicing as component of the spliceosome. Acts as an important regulator of the cell cycle that participates in the maintenance of genome integrity. During cell cycle progression in embryonic fibroblast, prevents replication fork collapse, double-strand break formation and cell cycle checkpoint activation. Controls mitotic cell cycle progression and cell survival in rapidly proliferating intestinal epithelium and embryonic stem cells. During the embryo preimplantation, controls different aspects of M phase. During early oocyte growth, plays a role in oocyte survival by preventing chromosomal breaks formation, activation of TP63 and reduction of transcription.

Subunit / interactions. Component of the XAB2 complex, a multimeric protein complex composed of XAB2, PRPF19, AQR, ZNF830, ISY1, and PPIE; this complex binds preferentially to RNA. Interacts with XAB2. Identified in a pentameric intron-binding (IB) complex composed of AQR, XAB2, ISY1, ZNF830 and PPIE that is incorporated into the spliceosome as a preassembled complex. The IB complex does not contain PRPF19.

Subcellular location. Nucleus. Chromosome. Nucleus speckle.

Post-translational modifications. Phosphorylated in response to DNA damage by the cell cycle checkpoint kinases ATR/ATM.

RefSeq proteins (1): NP_443089* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003604Matrin/U1-like-C_Znf_C2H2Domain
IPR013087Znf_C2H2_typeDomain
IPR036236Znf_C2H2_sfHomologous_superfamily
IPR040050ZNF830-likeFamily
IPR059039ZNF380_CCDomain

Pfam: PF12874, PF23406

UniProt features (19 total): sequence variant 5, modified residue 4, compositionally biased region 4, region of interest 2, initiator methionine 1, chain 1, zinc finger region 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96NB3-F166.500.19

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 (4): 2, 225, 351, 362

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

IDPathway
R-HSA-6781823Formation of TC-NER Pre-Incision Complex
R-HSA-6781827Transcription-Coupled Nucleotide Excision Repair (TC-NER)
R-HSA-6782135Dual incision in TC-NER
R-HSA-6782210Gap-filling DNA repair synthesis and ligation in TC-NER
R-HSA-72163mRNA Splicing - Major Pathway

MSigDB gene sets: 155 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_UP, GOBP_CELL_CYCLE_DNA_REPLICATION, GOBP_CELL_CYCLE_PHASE_TRANSITION, GOBP_GROWTH, GOBP_OOGENESIS, DARWICHE_SKIN_TUMOR_PROMOTER_DN, DARWICHE_PAPILLOMA_RISK_LOW_DN, DARWICHE_PAPILLOMA_RISK_HIGH_DN, DARWICHE_SQUAMOUS_CELL_CARCINOMA_DN, GOBP_MITOTIC_G2_M_TRANSITION_CHECKPOINT, GOBP_REGULATION_OF_CELL_CYCLE_G2_M_PHASE_TRANSITION, GOBP_OVARIAN_FOLLICLE_DEVELOPMENT, GOBP_NEGATIVE_REGULATION_OF_CELL_CYCLE_PROCESS, GOBP_REPRODUCTIVE_SYSTEM_DEVELOPMENT, GOBP_NEGATIVE_REGULATION_OF_CELL_CYCLE

GO Biological Process (14): ovarian follicle development (GO:0001541), preantral ovarian follicle growth (GO:0001546), blastocyst growth (GO:0001832), RNA processing (GO:0006396), mRNA processing (GO:0006397), RNA splicing (GO:0008380), nuclear DNA replication (GO:0033260), mitotic DNA replication checkpoint signaling (GO:0033314), negative regulation of apoptotic process (GO:0043066), mitotic DNA damage checkpoint signaling (GO:0044773), chromosome organization (GO:0051276), cell division (GO:0051301), intestinal epithelial structure maintenance (GO:0060729), mitotic cell cycle (GO:0000278)

GO Molecular Function (4): nucleic acid binding (GO:0003676), zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (5): nucleus (GO:0005634), nucleoplasm (GO:0005654), spliceosomal complex (GO:0005681), chromosome (GO:0005694), nuclear speck (GO:0016607)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Transcription-Coupled Nucleotide Excision Repair (TC-NER)3
Nucleotide Excision Repair1
mRNA Splicing1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
developmental growth2
RNA processing2
cell cycle2
mitotic cell cycle2
mitotic DNA integrity checkpoint signaling2
binding2
female gonad development1
anatomical structure development1
ovarian follicle development1
ovulation cycle process1
multi-layer follicle stage1
blastocyst development1
gene expression1
RNA biosynthetic process1
primary metabolic process1
mRNA metabolic process1
nucleus1
cell cycle DNA replication1
DNA replication checkpoint signaling1
mitotic G2/M transition checkpoint1
apoptotic process1
regulation of apoptotic process1
negative regulation of programmed cell death1
DNA damage checkpoint signaling1
organelle organization1
cellular process1
maintenance of gastrointestinal epithelium1
mitotic nuclear division1
transition metal ion binding1
cation binding1
intracellular membrane-bounded organelle1
nuclear lumen1
cellular anatomical structure1
nuclear protein-containing complex1
ribonucleoprotein complex1
intracellular membraneless organelle1
nuclear ribonucleoprotein granule1

Protein interactions and networks

STRING

704 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZNF830PPIEQ9UNP9926
ZNF830PRPF19Q9UMS4874
ZNF830CRNKL1Q9BZJ0792
ZNF830XAB2Q9HCS7785
ZNF830AQRO60306753
ZNF830PRCCQ92733696
ZNF830KANSL2Q9H9L4665
ZNF830PIM2Q9P1W9646
ZNF830CDC5LQ99459593
ZNF830SNW1Q13573498
ZNF830RBBP8Q99708494
ZNF830ZNF281Q9Y2X9478
ZNF830ASCC2Q9H1I8474
ZNF830CFAP221Q4G0U5471
ZNF830FKBP6O75344465

IntAct

69 interactions, top by confidence:

ABTypeScore
BCL2L1BCL2L11psi-mi:“MI:0914”(association)0.870
CDK8MED19psi-mi:“MI:2364”(proximity)0.850
PPIEAQRpsi-mi:“MI:0914”(association)0.810
PRPF19PLRG1psi-mi:“MI:0914”(association)0.770
AQRZNF830psi-mi:“MI:0407”(direct interaction)0.760
AQRZNF830psi-mi:“MI:0915”(physical association)0.760
AQRZNF830psi-mi:“MI:0914”(association)0.760
ISY1AQRpsi-mi:“MI:0914”(association)0.740
SNW1AQRpsi-mi:“MI:0914”(association)0.650
SNW1ZNF830psi-mi:“MI:0915”(physical association)0.630
ZNF830PPIL2psi-mi:“MI:0915”(physical association)0.630
ZNF830SNW1psi-mi:“MI:0915”(physical association)0.630
PPIL2ZNF830psi-mi:“MI:0915”(physical association)0.630
APPL1ZNF830psi-mi:“MI:0915”(physical association)0.590
SESTD1ZNF830psi-mi:“MI:0915”(physical association)0.560
SNRPEPRMT5psi-mi:“MI:0914”(association)0.530
PRPF19STRNpsi-mi:“MI:0914”(association)0.530
SNRPESNRPGP15psi-mi:“MI:0914”(association)0.530
PRPF8ZNF830psi-mi:“MI:0915”(physical association)0.510

BioGRID (131): ZNF830 (Affinity Capture-MS), ZNF830 (Co-fractionation), ZNF830 (Co-fractionation), ZNF830 (Co-fractionation), ZNF830 (Affinity Capture-MS), ZNF830 (Affinity Capture-MS), AQR (Affinity Capture-MS), XAB2 (Affinity Capture-MS), ISY1 (Affinity Capture-MS), PPIE (Affinity Capture-MS), PPIL2 (Affinity Capture-MS), ZNF830 (Affinity Capture-MS), ZNF830 (Affinity Capture-MS), ZNF830 (Affinity Capture-MS), ZNF830 (Affinity Capture-MS)

ESM2 similar proteins: A4PB26, D3ZTQ1, G1SW77, O16053, O88271, Q12872, Q32LE2, Q3MHS2, Q3U155, Q3USH5, Q4ADK4, Q4ADK7, Q4VAA2, Q5M8L3, Q5PQP2, Q5PQS7, Q5RKH3, Q5VSY0, Q5XHI2, Q5XIG5, Q5XIM5, Q5ZLH9, Q60FC2, Q63ZM9, Q6AXS5, Q6DIS2, Q6DJ13, Q6GNQ4, Q6NWC9, Q6PFK1, Q75UQ2, Q7T370, Q7ZYA6, Q8HXY9, Q8K039, Q8MMC4, Q8NC51, Q8R1N0, Q92733, Q96NB3

Diamond homologs: Q3MHS2, Q63ZM9, Q6DJ13, Q6P0I6, Q8R1N0, Q96NB3, Q9M8S7

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 55 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
mRNA Splicing - Minor Pathway629.9×1e-06
mRNA Splicing - Major Pathway2125.5×8e-23
mRNA Splicing1024.4×4e-10
Processing of Capped Intron-Containing Pre-mRNA1323.7×4e-13
mRNA Polyadenylation1019.5×3e-09
CHD1 and CHD2 subfamily819.3×3e-07
Dengue Virus-Host Interactions1818.3×1e-16
Metabolism of RNA1211.1×2e-08

GO biological processes:

GO termPartnersFoldFDR
U2-type prespliceosome assembly676.4×2e-08
mRNA splicing, via spliceosome2241.1×3e-28
RNA splicing712.6×1e-04
mRNA processing711.2×2e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance38
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

51 predictions. Top by Δscore:

VariantEffectΔscore
17:34962599:G:GTdonor_gain0.8800
17:34962629:G:GTdonor_gain0.7200
17:34962641:G:GTdonor_gain0.7000
17:34962656:G:GTdonor_gain0.5300
17:34962211:CAAGG:Cacceptor_gain0.5100
17:34962666:TGA:Tdonor_gain0.4400
17:34962210:CCAAG:Cacceptor_gain0.4300
17:34962632:G:Tdonor_gain0.4300
17:34962212:AAGGC:Aacceptor_gain0.4100
17:34961938:AC:Adonor_gain0.3800
17:34962133:C:Tdonor_gain0.3800
17:34962209:CCCAA:Cacceptor_gain0.3800
17:34962161:G:GTdonor_gain0.3600
17:34962204:ATCCT:Aacceptor_gain0.3500
17:34962213:AGG:Aacceptor_gain0.3500
17:34962624:A:Gdonor_gain0.3400
17:34962161:G:Tdonor_gain0.3200
17:34962208:TCCCA:Tacceptor_gain0.3200
17:34962632:G:GTdonor_gain0.3100
17:34961983:A:Tdonor_gain0.3000
17:34962205:TCCTC:Tacceptor_gain0.3000
17:34962206:CCTCC:Cacceptor_gain0.3000
17:34962207:CTCCC:Cacceptor_gain0.3000
17:34962668:A:AGdonor_gain0.2700
17:34961931:CTCAG:Cdonor_loss0.2600
17:34961932:TCAG:Tdonor_loss0.2600
17:34961933:CAGGT:Cdonor_loss0.2600
17:34961934:AG:Adonor_loss0.2600
17:34961935:GGT:Gdonor_loss0.2600
17:34961936:GTACA:Gdonor_loss0.2600

AlphaMissense

2445 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:34962314:T:CF250L1.000
17:34962316:T:AF250L1.000
17:34962316:T:GF250L1.000
17:34962395:T:CF277L1.000
17:34962396:T:CF277S1.000
17:34962397:C:AF277L1.000
17:34962397:C:GF277L1.000
17:34962498:A:CQ311P1.000
17:34962661:G:CW365C1.000
17:34962661:G:TW365C1.000
17:34961723:T:CC53R0.999
17:34961745:T:AV60D0.999
17:34961762:T:AW66R0.999
17:34961762:T:CW66R0.999
17:34961764:G:CW66C0.999
17:34961764:G:TW66C0.999
17:34962303:T:CL246S0.999
17:34962315:T:CF250S0.999
17:34962317:T:CF251L0.999
17:34962318:T:GF251C0.999
17:34962319:T:AF251L0.999
17:34962319:T:GF251L0.999
17:34962386:T:AW274R0.999
17:34962386:T:CW274R0.999
17:34962388:G:CW274C0.999
17:34962388:G:TW274C0.999
17:34962396:T:GF277C0.999
17:34962404:G:CA280P0.999
17:34962434:G:CA290P0.999
17:34962443:G:CA293P0.999

dbSNP variants (sampled 300 via entrez): RS1001361386 (17:34963770 T>C), RS1002989528 (17:34962284 G>A), RS1003114732 (17:34962842 G>A,T), RS1003321442 (17:34961173 C>A,T), RS1003378809 (17:34960984 C>G), RS1005432992 (17:34961452 C>G,T), RS1005539603 (17:34963444 T>C), RS1005801525 (17:34961510 G>A,T), RS1007066420 (17:34960348 C>A,T), RS1007163112 (17:34959939 A>C), RS1007521674 (17:34960161 C>A,T), RS1008948409 (17:34963078 T>C), RS1009877886 (17:34964053 C>T), RS1010059103 (17:34963160 A>G), RS1011345508 (17:34961926 G>C,T)

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

2 associations (top):

StudyTraitp-value
GCST003542_132Night sleep phenotypes2.000000e-07
GCST003542_133Night sleep phenotypes4.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
FR900359increases phosphorylation1
sodium arseniteaffects cotreatment, increases abundance, increases expression1
manganese chlorideincreases abundance, increases expression, affects cotreatment1
potassium chromate(VI)increases expression, affects cotreatment1
beta-methylcholineaffects expression1
epigallocatechin gallateaffects cotreatment, increases expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic acidincreases expression1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)increases expression1
Arsenicaffects cotreatment, increases abundance, increases expression1
Benzo(a)pyrenedecreases methylation, increases methylation1
Doxorubicindecreases phosphorylation, affects phosphorylation, affects response to substance1
Manganeseincreases abundance, increases expression, affects cotreatment1
Potassium Dichromateincreases expression1
Smokedecreases expression1
Tobacco Smoke Pollutionincreases expression1
Urethanedecreases expression1
Vincristinedecreases expression1
Copper Sulfatedecreases expression1
Lactic Aciddecreases expression1
Vitamin K 3affects expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.