ZNF622

gene
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Also known as MGC2485MGC17552ZPR9

Summary

ZNF622 (zinc finger protein 622, HGNC:30958) is a protein-coding gene on chromosome 5p15.1, encoding Cytoplasmic 60S subunit biogenesis factor ZNF622 (Q969S3). Pre-60S-associated cytoplasmic factor involved in the cytoplasmic maturation of the 60S subunit. It is a selective cancer dependency (DepMap: 14.9% of cell lines).

Enables preribosome binding activity. Involved in several processes, including intrinsic apoptotic signaling pathway in response to oxidative stress; positive regulation of JNK cascade; and positive regulation of kinase activity. Located in Golgi apparatus; cytosol; and nuclear lumen.

Source: NCBI Gene 90441 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 77 total
  • Cancer dependency (DepMap): dependent in 14.9% of screened cell lines
  • MANE Select transcript: NM_033414

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30958
Approved symbolZNF622
Namezinc finger protein 622
Location5p15.1
Locus typegene with protein product
StatusApproved
AliasesMGC2485, MGC17552, ZPR9
Ensembl geneENSG00000173545
Ensembl biotypeprotein_coding
OMIM608694
Entrez90441

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 protein_coding

ENST00000308683, ENST00000933612, ENST00000933613, ENST00000933614, ENST00000933615, ENST00000933616

RefSeq mRNA: 1 — MANE Select: NM_033414 NM_033414

CCDS: CCDS3886

Canonical transcript exons

ENST00000308683 — 6 exons

ExonStartEnd
ENSE000012085061645301316453156
ENSE000012085101645851716458629
ENSE000012085171646310816463270
ENSE000012085211646348216463742
ENSE000012085231645151916451784
ENSE000012085281646504116465800

Expression profiles

Bgee: expression breadth ubiquitous, 257 present calls, max score 98.53.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 31.8767 / max 251.8593, expressed in 1822 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
6099820.65651814
6099711.22011799

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
left ventricle myocardiumUBERON:000656698.53gold quality
cardiac muscle of right atriumUBERON:000337997.13gold quality
myocardiumUBERON:000234996.69gold quality
epithelial cell of pancreasCL:000008394.84gold quality
amniotic fluidUBERON:000017394.63gold quality
kidney epitheliumUBERON:000481994.54gold quality
heart right ventricleUBERON:000208094.45gold quality
apex of heartUBERON:000209894.39gold quality
heart left ventricleUBERON:000208493.85gold quality
cardiac ventricleUBERON:000208293.77gold quality
body of pancreasUBERON:000115093.71gold quality
pancreasUBERON:000126492.22gold quality
upper arm skinUBERON:000426392.16gold quality
heartUBERON:000094891.71gold quality
tendon of biceps brachiiUBERON:000818891.08gold quality
mucosa of sigmoid colonUBERON:000499391.01gold quality
gastrocnemiusUBERON:000138890.92gold quality
colonic mucosaUBERON:000031790.84gold quality
mucosa of transverse colonUBERON:000499190.75gold quality
islet of LangerhansUBERON:000000690.67gold quality
cardiac atriumUBERON:000208190.60gold quality
medial globus pallidusUBERON:000247790.45gold quality
right atrium auricular regionUBERON:000663190.40gold quality
muscle of legUBERON:000138390.32gold quality
endothelial cellCL:000011590.23gold quality
palpebral conjunctivaUBERON:000181290.10gold quality
tendonUBERON:000004389.92gold quality
cartilage tissueUBERON:000241889.92gold quality
parotid glandUBERON:000183189.85gold quality
globus pallidusUBERON:000187589.68gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-MTAB-7052yes683.01
E-GEOD-100618yes257.78
E-MTAB-6386no192.63
E-ANND-3no0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): MYBL2

miRNA regulators (miRDB)

25 targeting ZNF622, 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-545-3P99.9570.742783
HSA-MIR-6845-3P99.9466.881439
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-497-5P99.9271.832674
HSA-MIR-589-3P99.9169.622088
HSA-MIR-15A-5P99.9072.802787
HSA-MIR-15B-5P99.9072.782798
HSA-MIR-16-5P99.9072.802780
HSA-MIR-195-5P99.9072.812805
HSA-MIR-424-5P99.8971.902641
HSA-MIR-6838-5P99.8971.942690
HSA-MIR-10393-3P99.7266.56961
HSA-MIR-6801-5P99.7266.50981
HSA-MIR-64699.6867.841645
HSA-MIR-4524A-5P99.5771.731193
HSA-MIR-4524B-5P99.5771.681195
HSA-MIR-182-3P99.5767.57825
HSA-MIR-766-5P99.4767.912225
HSA-MIR-6830-3P98.6268.071760
HSA-MIR-4768-3P98.1666.022330
HSA-MIR-1212698.0964.82637
HSA-MIR-503-5P97.8766.83575
HSA-MIR-56297.6665.63698
HSA-MIR-597-3P96.4668.031035

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 14.9% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 3)

  • ZPR9 plays an important role in modulation of the transactivation by B-MYB and cellular growth of neuroblastoma cells (PMID:12645566)
  • ZPR9 was found to physically interact with ASK1 through a disulfide linkage;ZPR9 functions as a novel positive regulator of ASK1. (PMID:21771788)
  • Results from a study on gene expression variability markers in early-stage human embryos shows that ZNF622 is a putative expression variability marker for the 3-day, 8-cell embryo stage. (PMID:26288249)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_rerioznf622ENSDARG00000014692
mus_musculusZfp622ENSMUSG00000052253
rattus_norvegicusZfp622l1ENSRNOG00000010589
rattus_norvegicusENSRNOG00000065109
drosophila_melanogasterCG6769FBGN0030878
caenorhabditis_elegansWBGENE00015809

Protein

Protein identifiers

Cytoplasmic 60S subunit biogenesis factor ZNF622Q969S3 (reviewed: Q969S3)

Alternative names: Zinc finger protein 622, Zinc finger-like protein 9

All UniProt accessions (1): Q969S3

UniProt curated annotations — full annotation on UniProt →

Function. Pre-60S-associated cytoplasmic factor involved in the cytoplasmic maturation of the 60S subunit.

Subunit / interactions. Homo- and heterodimer. Associates with pre-60S ribosomal particles. Interacts with MELK and MYBL2. Interacts with DNAJC21.

Subcellular location. Cytoplasm. Nucleus.

Tissue specificity. Expressed in lung, kidney, spleen, liver and brain with lowest expression in kidney.

Post-translational modifications. Phosphorylated by MELK. The phosphorylation may redirect the protein to the nucleus. Ubiquitinated by HECTD1, leading to its degradation.

Similarity. Belongs to the REI1 family.

RefSeq proteins (1): NP_219482* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003604Matrin/U1-like-C_Znf_C2H2Domain
IPR013087Znf_C2H2_typeDomain
IPR022755Znf_C2H2_jazDomain
IPR036236Znf_C2H2_sfHomologous_superfamily
IPR040025Znf622/Rei1/Reh1Family
IPR041661ZN622/Rei1/Reh1_Znf-C2H2Domain

Pfam: PF12171, PF12756

UniProt features (9 total): zinc finger region 2, compositionally biased region 2, modified residue 2, initiator methionine 1, chain 1, region of interest 1

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
9GMOELECTRON MICROSCOPY2.59
6LQMELECTRON MICROSCOPY3.09
6LSRELECTRON MICROSCOPY3.13

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q969S3-F173.050.27

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 (2): 2, 276

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 131 (showing top): SHEPARD_BMYB_MORPHOLINO_UP, GOBP_RIBOSOME_BIOGENESIS, GOBP_REGULATION_OF_PHOSPHORYLATION, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, SHEPARD_CRASH_AND_BURN_MUTANT_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GOBP_POSITIVE_REGULATION_OF_MAPK_CASCADE, GOBP_REGULATION_OF_TRANSFERASE_ACTIVITY, GOBP_POSITIVE_REGULATION_OF_CATALYTIC_ACTIVITY, GOBP_POSITIVE_REGULATION_OF_MOLECULAR_FUNCTION, GOBP_APOPTOTIC_SIGNALING_PATHWAY, WANG_LMO4_TARGETS_DN, GOBP_POSITIVE_REGULATION_OF_PHOSPHORUS_METABOLIC_PROCESS, GOBP_JNK_CASCADE, MARTIN_VIRAL_GPCR_SIGNALING_DN

GO Biological Process (7): intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631), positive regulation of kinase activity (GO:0033674), ribosomal large subunit biogenesis (GO:0042273), positive regulation of apoptotic process (GO:0043065), positive regulation of MAPK cascade (GO:0043410), positive regulation of JNK cascade (GO:0046330), ribosome biogenesis (GO:0042254)

GO Molecular Function (6): RNA binding (GO:0003723), zinc ion binding (GO:0008270), preribosome binding (GO:1990275), nucleic acid binding (GO:0003676), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (7): nucleoplasm (GO:0005654), nucleolus (GO:0005730), Golgi apparatus (GO:0005794), cytosol (GO:0005829), preribosome, large subunit precursor (GO:0030687), nucleus (GO:0005634), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
ribonucleoprotein complex biogenesis2
binding2
nuclear lumen2
cytoplasm2
intracellular membrane-bounded organelle2
intrinsic apoptotic signaling pathway1
kinase activity1
positive regulation of phosphorylation1
positive regulation of catalytic activity1
regulation of kinase activity1
ribosome biogenesis1
apoptotic process1
regulation of apoptotic process1
positive regulation of programmed cell death1
MAPK cascade1
regulation of MAPK cascade1
positive regulation of intracellular signal transduction1
JNK cascade1
positive regulation of MAPK cascade1
regulation of JNK cascade1
nucleic acid binding1
transition metal ion binding1
ribonucleoprotein complex binding1
cation binding1
intracellular membraneless organelle1
endomembrane system1
preribosome1
intracellular anatomical structure1

Protein interactions and networks

STRING

1812 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZNF622MELKQ14680958
ZNF622MYBL2P10244914
ZNF622PA2G4Q9UQ80641
ZNF622RSL24D1Q9UHA3487
ZNF622ZNF593O00488483
ZNF622NMD3Q96D46478
ZNF622LSG1Q9H089473
ZNF622CRLS1Q9UJA2468
ZNF622MRTO4Q9UKD2468
ZNF622HSPA8P11142449
ZNF622EIF6P56537449
ZNF622DNAJC21Q5F1R6449
ZNF622SAFB2Q14151445
ZNF622TXNP10599439
ZNF622LY6HO94772438

IntAct

110 interactions, top by confidence:

ABTypeScore
MAP3K5MAP2K3psi-mi:“MI:0914”(association)0.760
MAP3K5YWHABpsi-mi:“MI:0914”(association)0.720
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
MAP3K5TXNpsi-mi:“MI:0914”(association)0.680
MAP3K5ZNF622psi-mi:“MI:0915”(physical association)0.660
ZNF622MAP3K5psi-mi:“MI:0915”(physical association)0.660
MAP3K5ZNF622psi-mi:“MI:0407”(direct interaction)0.660
ZNF622MAP3K5psi-mi:“MI:0407”(direct interaction)0.660
ZNF622MAP3K5psi-mi:“MI:0217”(phosphorylation reaction)0.660
YAF2E2F6psi-mi:“MI:0914”(association)0.640
PRPF31PRPF4psi-mi:“MI:0914”(association)0.640
BEND7ZNF622psi-mi:“MI:0915”(physical association)0.560
MACROH2A1ZNF622psi-mi:“MI:0915”(physical association)0.560
CAVIN1ZZEF1psi-mi:“MI:0914”(association)0.530
EZRBCRpsi-mi:“MI:0914”(association)0.480
ZNF622Dlg4psi-mi:“MI:0407”(direct interaction)0.440
HMGB2ZNF622psi-mi:“MI:0915”(physical association)0.370
ZNF622psi-mi:“MI:0915”(physical association)0.370

BioGRID (176): MRTO4 (Co-fractionation), ZNF622 (Co-fractionation), ZNF622 (Reconstituted Complex), ZNF622 (Proximity Label-MS), ZNF622 (Proximity Label-MS), ZNF622 (Proximity Label-MS), ZNF622 (Proximity Label-MS), ZNF622 (Affinity Capture-MS), ZNF622 (Affinity Capture-MS), ZNF622 (Affinity Capture-MS), ZNF622 (Affinity Capture-MS), ZNF622 (Affinity Capture-MS), ZNF622 (Affinity Capture-MS), ZNF622 (Affinity Capture-MS), ZNF622 (Affinity Capture-MS)

ESM2 similar proteins: A1CFJ6, A1CYJ1, A2QGZ1, A3LU29, A4R9U5, A5DFT1, A5DYR5, A6RC73, A6RNR4, A6RVU0, A6SK81, A6ZQU8, A7E664, A7EGB5, A7EPT0, A7TP28, B8MSM6, C5P263, P0CP24, P0CP25, P0CS78, P0CS79, P40007, Q0CDP3, Q0UBQ5, Q1DLJ4, Q1EBC4, Q4IPB3, Q4PII9, Q4SQ06, Q4W9V0, Q4WIK9, Q4WNY4, Q59YD8, Q5AVK6, Q5AWM5, Q5B4T5, Q5BEG5, Q6BWR0, Q6CE60

Diamond homologs: G0S920, O59811, Q58CQ5, Q7TM96, Q80UU1, Q90Y35, Q91VY9, Q969S3, Q9H8Y5, Q9HET8, O74977, P38344, Q66H85, Q04311, Q06709, Q8H1G5, Q9ZQ18

SIGNOR signaling

2 interactions.

AEffectBMechanism
MAP3K5up-regulatesZNF622phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 117 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
Eukaryotic Translation Initiation519.8×1e-04
Cap-dependent Translation Initiation519.8×1e-04
SARS-CoV-1 modulates host translation machinery519.8×1e-04
Eukaryotic Translation Elongation517.9×2e-04
Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S517.4×2e-04
Influenza Viral RNA Transcription and Replication616.6×5e-05
SARS-CoV-1-host interactions715.8×1e-05
SRP-dependent cotranslational protein targeting to membrane1215.4×7e-09

GO biological processes:

GO termPartnersFoldFDR
cytoplasmic translation1018.7×1e-07
regulation of alternative mRNA splicing, via spliceosome512.3×7e-03
translation88.3×2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance60
Likely benign6
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

618 predictions. Top by Δscore:

VariantEffectΔscore
5:16453008:TGTAC:Tdonor_loss1.0000
5:16453009:GTACC:Gdonor_loss1.0000
5:16453010:TACCT:Tdonor_loss1.0000
5:16453011:A:Cdonor_loss1.0000
5:16453012:C:CTdonor_loss1.0000
5:16453154:CAC:Cacceptor_gain1.0000
5:16453157:C:CAacceptor_loss1.0000
5:16453157:C:CCacceptor_gain1.0000
5:16453158:T:Aacceptor_loss1.0000
5:16458510:CACTT:Cdonor_loss1.0000
5:16458511:ACTTA:Adonor_loss1.0000
5:16458512:CTTAC:Cdonor_loss1.0000
5:16458513:TTA:Tdonor_loss1.0000
5:16458514:TACC:Tdonor_loss1.0000
5:16458515:A:ACdonor_gain1.0000
5:16458515:ACCAG:Adonor_loss1.0000
5:16458516:C:CCdonor_gain1.0000
5:16458516:C:Gdonor_loss1.0000
5:16458625:TACTC:Tacceptor_gain1.0000
5:16458627:CTC:Cacceptor_gain1.0000
5:16458629:CCTA:Cacceptor_loss1.0000
5:16458630:C:CCacceptor_gain1.0000
5:16458630:CTAT:Cacceptor_loss1.0000
5:16463102:GCTTA:Gdonor_loss1.0000
5:16463103:CTTAC:Cdonor_loss1.0000
5:16463104:TTACC:Tdonor_loss1.0000
5:16463105:TACC:Tdonor_loss1.0000
5:16463106:A:ACdonor_gain1.0000
5:16463106:ACCTA:Adonor_loss1.0000
5:16463107:C:CCdonor_gain1.0000

AlphaMissense

3185 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:16463244:A:GC305R0.998
5:16465525:G:CF47L0.998
5:16465525:G:TF47L0.998
5:16465526:A:GF47S0.998
5:16465527:A:GF47L0.998
5:16465571:A:GL32P0.998
5:16465573:G:CN31K0.998
5:16465573:G:TN31K0.998
5:16465587:A:GW27R0.998
5:16465587:A:TW27R0.998
5:16465641:A:GC9R0.998
5:16463187:G:CH324D0.997
5:16463234:C:GC308S0.997
5:16463235:A:TC308S0.997
5:16463242:G:CC305W0.997
5:16465640:C:TC9Y0.997
5:16465650:A:GC6R0.997
5:16463167:G:CH330Q0.996
5:16463167:G:TH330Q0.996
5:16463185:A:CH324Q0.996
5:16463185:A:TH324Q0.996
5:16463235:A:GC308R0.996
5:16463243:C:TC305Y0.996
5:16465565:C:GR34P0.996
5:16465584:G:CH28D0.996
5:16465585:C:AW27C0.996
5:16465585:C:GW27C0.996
5:16465639:G:CC9W0.996
5:16465640:C:AC9F0.996
5:16465648:G:CC6W0.996

dbSNP variants (sampled 300 via entrez): RS1000081874 (5:16456032 G>A), RS1000254191 (5:16454157 A>G), RS1000909423 (5:16461826 G>C), RS1000950932 (5:16455011 A>T), RS1001085413 (5:16454765 T>C), RS1001167717 (5:16456751 G>A), RS1001305412 (5:16456510 A>C), RS1002077343 (5:16462268 A>C), RS1002165238 (5:16455290 G>A), RS1002281554 (5:16459952 G>A), RS1002314056 (5:16459516 T>C,G), RS1002797209 (5:16465349 A>C), RS1002840167 (5:16458657 T>C), RS1002988725 (5:16462869 C>A), RS1003107031 (5:16451970 C>T)

Disease associations

OMIM: gene MIM:608694 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST003025_12Attention function in attention deficit hyperactive disorder3.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0007636attention function measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, increases activity, increases expression3
Valproic Acidaffects cotreatment, increases expression3
Tobacco Smoke Pollutionincreases expression2
Cyclosporineincreases expression2
Particulate Matterdecreases expression, increases abundance, increases expression2
aristolochic acid Iincreases expression1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
GSK-J4increases expression1
FR900359affects phosphorylation1
triphenyl phosphateaffects expression1
pirinixic acidaffects binding, decreases expression, increases activity1
bisphenol Aaffects cotreatment, increases methylation1
2-methyl-4-isothiazolin-3-oneincreases expression1
butyraldehydeincreases expression1
potassium chromate(VI)affects cotreatment, increases expression1
epigallocatechin gallateaffects cotreatment, increases expression1
CGP 52608affects binding, increases reaction1
abrineincreases expression1
licochalcone Bincreases expression1
PCI 5002increases expression, affects cotreatment1
Resveratrolincreases expression, affects cotreatment1
Fulvestrantaffects cotreatment, increases methylation1
Air Pollutantsdecreases expression, increases abundance1
Copperaffects binding, decreases expression1
Disulfiramdecreases expression, affects binding1
Hydralazineaffects cotreatment, increases expression1
Methyl Methanesulfonateincreases expression1
Phenobarbitalaffects expression1
Plant Extractsaffects cotreatment, increases expression1
Ribonucleotidesaffects binding1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

CellosaurusNameCategorySex
CVCL_B2LWAbcam HeLa ZNF622 KOCancer cell lineFemale

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.