ZNRF2

gene
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Also known as RNF202

Summary

ZNRF2 (zinc and ring finger 2, HGNC:22316) is a protein-coding gene on chromosome 7p14.3, encoding E3 ubiquitin-protein ligase ZNRF2 (Q8NHG8). E3 ubiquitin-protein ligase that plays a role in the establishment and maintenance of neuronal transmission and plasticity.

Enables ubiquitin protein ligase activity. Involved in positive regulation of autophagosome-lysosome fusion. Located in cytoplasmic vesicle membrane; nuclear lumen; and plasma membrane. Part of protein-containing complex. Is active in intracellular membrane-bounded organelle.

Source: NCBI Gene 223082 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 12 total
  • MANE Select transcript: NM_147128

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:22316
Approved symbolZNRF2
Namezinc and ring finger 2
Location7p14.3
Locus typegene with protein product
StatusApproved
AliasesRNF202
Ensembl geneENSG00000180233
Ensembl biotypeprotein_coding
OMIM612061
Entrez223082

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000323037, ENST00000459998, ENST00000937786, ENST00000953272, ENST00000953273

RefSeq mRNA: 1 — MANE Select: NM_147128 NM_147128

CCDS: CCDS5426

Canonical transcript exons

ENST00000323037 — 5 exons

ExonStartEnd
ENSE000012202503035572830355833
ENSE000012644453032364230323737
ENSE000012644553036237730362456
ENSE000013752653028459730285826
ENSE000018196863036603530367689

Expression profiles

Bgee: expression breadth ubiquitous, 216 present calls, max score 89.32.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.5695 / max 154.1745, expressed in 1647 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter IDTPM avgSamples expressed
779783.52251271
779812.84351095
779801.2274740
779790.5525340
779770.5178259
779830.4544264
779820.4512250

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099189.32gold quality
buccal mucosa cellCL:000233688.47silver quality
monocyteCL:000057687.58gold quality
calcaneal tendonUBERON:000370187.55gold quality
leukocyteCL:000073887.36gold quality
rectumUBERON:000105286.72gold quality
islet of LangerhansUBERON:000000685.91gold quality
mucosa of transverse colonUBERON:000499184.72gold quality
secondary oocyteCL:000065584.12gold quality
right lobe of liverUBERON:000111483.96gold quality
jejunal mucosaUBERON:000039982.92gold quality
cortical plateUBERON:000534382.71gold quality
colonic mucosaUBERON:000031782.58gold quality
smooth muscle tissueUBERON:000113582.26gold quality
vermiform appendixUBERON:000115481.99gold quality
mucosa of sigmoid colonUBERON:000499381.32gold quality
epithelial cell of pancreasCL:000008381.29silver quality
testisUBERON:000047381.06gold quality
duodenumUBERON:000211480.97gold quality
right testisUBERON:000453480.87gold quality
adult mammalian kidneyUBERON:000008280.69gold quality
left testisUBERON:000453380.56gold quality
liverUBERON:000210780.42gold quality
granulocyteCL:000009480.39gold quality
pancreasUBERON:000126480.28gold quality
spermCL:000001980.22gold quality
gall bladderUBERON:000211080.18gold quality
lymph nodeUBERON:000002980.00gold quality
tendonUBERON:000004379.82gold quality
oral cavityUBERON:000016779.69gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes3.93

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): TP63

miRNA regulators (miRDB)

188 targeting ZNRF2, 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-3163100.0077.238605
HSA-MIR-4262100.0073.263931
HSA-MIR-8485100.0077.574731
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-3162-3P100.0065.37363
HSA-MIR-3924100.0072.092394
HSA-MIR-9-5P100.0072.282361
HSA-MIR-5692A100.0074.406850
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-6870-5P99.9968.552115
HSA-MIR-428299.9975.366408
HSA-MIR-480399.9871.993117
HSA-MIR-103A-3P99.9869.141595
HSA-MIR-10799.9869.141595
HSA-MIR-1213699.9872.815713
HSA-MIR-548N99.9871.944170
HSA-MIR-499A-5P99.9870.791323
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-314899.9775.066478
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345

Literature-anchored findings (GeneRIF, showing 6)

  • identification of ZNRF2; data suggest that ZNRF proteins play a role in the establishment and maintenance of neuronal transmission and plasticity via their ubiquitin ligase activity [ZNRF2] (PMID:14561866)
  • ZNRF1 and ZNRF2 are new players in regulation of the ubiquitous Na(+)/K(+)ATPase that is tuned to changing demands in many physiological contexts. (PMID:22797923)
  • These findings uncover ZNRF2 as a component of the amino acid sensing machinery that acts upstream of Rag-GTPases and the V-ATPase to activate mTORC1. (PMID:27244671)
  • Results detected significantly higher levels of ZNRF2 in osteosarcoma cells (OS) and provide evidence that ZNRF2 enhances OS cell growth and improves survival against doxorubicin. (PMID:28416774)
  • The findings obtained in the present study indicate that TTN-AS1 facilitated PTC progression by regulating the miR-153-3p/ZNRF2 axis and activating the PI3K/Akt/mTOR pathway. (PMID:30811764)
  • A pancancer analysis of the oncogenic role of ZNRF2 in human tumours. (PMID:37551845)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioznrf2bENSDARG00000098792
mus_musculusZnrf2ENSMUSG00000058446
rattus_norvegicusZnrf2ENSRNOG00000049057
drosophila_melanogasterCG14435FBGN0029911
caenorhabditis_elegansY71F9AL.10WBGENE00022115

Paralogs (2): RNF11 (ENSG00000123091), ZNRF1 (ENSG00000186187)

Protein

Protein identifiers

E3 ubiquitin-protein ligase ZNRF2Q8NHG8 (reviewed: Q8NHG8)

Alternative names: Protein Ells2, RING finger protein 202, RING-type E3 ubiquitin transferase ZNRF2, Zinc/RING finger protein 2

All UniProt accessions (2): Q8NHG8, A0A090N8Y8

UniProt curated annotations — full annotation on UniProt →

Function. E3 ubiquitin-protein ligase that plays a role in the establishment and maintenance of neuronal transmission and plasticity. Ubiquitinates the Na(+)/K(+) ATPase alpha-1 subunit/ATP1A1 and thereby influences its endocytosis and/or degradation. Acts also as a positive regulator of mTORC1 activation by amino acids, which functions upstream of the V-ATPase and of Rag-GTPases. In turn, phosphorylation by mTOR leads to its inhibition via targeting to the cytosol allowing a self-regulating feedback mechanism.

Subunit / interactions. Interacts with UBE2N. Interacts with ZNRF1. Interacts (when phosphorylated) with YWHAE.

Subcellular location. Endosome membrane. Lysosome membrane. Presynaptic cell membrane. Cytoplasm.

Tissue specificity. Highly expressed in the brain, with higher expression during development than in adult. Expressed also in mammary glands, testis, colon and kidney.

Post-translational modifications. Phosphorylated; leading to binding to YWHAE. Phosphorylated by MTOR at Ser-145 and dephosphorylated by PP6C. Ser-145 phosphorylation stimulates vesicle-to-cytosol translocation.

Domain organisation. The RING-type zinc finger domain is required for E3 ligase activity.

Pathway. Protein modification; protein ubiquitination.

RefSeq proteins (1): NP_667339* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001841Znf_RINGDomain
IPR013083Znf_RING/FYVE/PHDHomologous_superfamily
IPR051878ZNRF_ubiq-protein_ligaseFamily

Pfam: PF13639

UniProt features (24 total): modified residue 11, mutagenesis site 4, compositionally biased region 4, initiator methionine 1, chain 1, lipid moiety-binding region 1, zinc finger region 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8NHG8-F167.870.28

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 (12): 25, 82, 89, 113, 116, 135, 145, 151, 193, 2, 19, 21

Mutagenesis-validated functional residues (4):

PositionPhenotype
2complete loss of binding to atp1a1.
19counteracts the n-myristoyl-mediated targeting of znrf2 to membranes.
82partial decrease of ywhae binding upon igf1 stimulation.
145partial decrease of ywhae binding upon igf1 stimulation. more distinct membranal localization.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-983168Antigen processing: Ubiquitination & Proteasome degradation

MSigDB gene sets: 217 (showing top): SHEPARD_BMYB_MORPHOLINO_UP, GOBP_REGULATION_OF_VESICLE_FUSION, CCAWYNNGAAR_UNKNOWN, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION, GOCC_VACUOLAR_MEMBRANE, REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION, GOBP_VESICLE_ORGANIZATION, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GOBP_MEMBRANE_FUSION, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_POSITIVE_REGULATION_OF_ORGANELLE_ORGANIZATION, CTATGCA_MIR153

GO Biological Process (5): proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161), protein K48-linked ubiquitination (GO:0070936), positive regulation of autophagosome-lysosome fusion (GO:0160177), protein ubiquitination (GO:0016567), intracellular potassium ion homeostasis (GO:0030007)

GO Molecular Function (4): zinc ion binding (GO:0008270), ubiquitin protein ligase activity (GO:0061630), transferase activity (GO:0016740), metal ion binding (GO:0046872)

GO Cellular Component (15): fibrillar center (GO:0001650), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), lysosomal membrane (GO:0005765), cytosol (GO:0005829), plasma membrane (GO:0005886), endosome membrane (GO:0010008), membrane (GO:0016020), cytoplasmic vesicle membrane (GO:0030659), protein-containing complex (GO:0032991), presynaptic membrane (GO:0042734), lysosome (GO:0005764), endosome (GO:0005768), cell projection (GO:0042995), synapse (GO:0045202)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Class I MHC mediated antigen processing & presentation1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure6
cytoplasmic vesicle2
ubiquitin-dependent protein catabolic process1
proteasomal protein catabolic process1
protein polyubiquitination1
positive regulation of vesicle fusion1
autophagosome-lysosome fusion1
protein modification by small protein conjugation1
intracellular monoatomic cation homeostasis1
potassium ion homeostasis1
transition metal ion binding1
ubiquitin-protein transferase activity1
ubiquitin-like protein ligase activity1
catalytic activity1
cation binding1
nucleolus1
nuclear lumen1
intracellular anatomical structure1
lysosome1
lytic vacuole membrane1
cytoplasm1
membrane1
cell periphery1
endosome1
cytoplasmic vesicle membrane1
bounding membrane of organelle1
vesicle membrane1
cellular_component1
synaptic membrane1
presynapse1
lytic vacuole1
endomembrane system1
cell junction1

Protein interactions and networks

STRING

474 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZNRF2UBE2D2P51669786
ZNRF2A0A087WY85A0A087WY85693
ZNRF2UBE2SQ16763597
ZNRF2ZNRF4Q8WWF5595
ZNRF2RNF2Q99496547
ZNRF2CWC25Q9NXE8543
ZNRF2RSPRY1Q96DX4533
ZNRF2EAF1Q96JC9520
ZNRF2CLXNQ9HAE3498
ZNRF2GPATCH3Q96I76488
ZNRF2METTL6Q8TCB7451
ZNRF2ZNRF3Q9ULT6448
ZNRF2PLEKHA8Q96JA3446
ZNRF2RBM5P52756437
ZNRF2SNX20Q7Z614434

IntAct

20 interactions, top by confidence:

ABTypeScore
UBE2NUBA1psi-mi:“MI:0914”(association)0.640
YWHAGSHTN1psi-mi:“MI:0914”(association)0.560
WDR5BTCP1psi-mi:“MI:0914”(association)0.530
CHCHD4ENSApsi-mi:“MI:0914”(association)0.530
SLC37A4ZNRF2psi-mi:“MI:0915”(physical association)0.400
CGB1ZNRF2psi-mi:“MI:0915”(physical association)0.400
Xpo1IFT56psi-mi:“MI:0914”(association)0.350
YWHAHSHTN1psi-mi:“MI:0914”(association)0.350
ABCA2ABCD4psi-mi:“MI:0914”(association)0.350
NCKAP5KIF3Cpsi-mi:“MI:0914”(association)0.350
ZNRF2ANKRD28psi-mi:“MI:0914”(association)0.350
EEA1HSBP1psi-mi:“MI:0914”(association)0.350
MYH3MYH6psi-mi:“MI:0914”(association)0.350
WDR5BHSPA8psi-mi:“MI:0914”(association)0.350
ZNRF2BMH1psi-mi:“MI:0914”(association)0.350
UBE2NZNRF2psi-mi:“MI:0915”(physical association)0.000
ZNRF2ccapsi-mi:“MI:0915”(physical association)0.000

BioGRID (80): ZNRF2 (Affinity Capture-MS), ATP1A1 (Biochemical Activity), UBC (Biochemical Activity), UBE2N (Reconstituted Complex), ZNRF2 (Affinity Capture-MS), MTOR (Affinity Capture-Western), RPTOR (Affinity Capture-Western), MLST8 (Affinity Capture-Western), ZNRF2 (Biochemical Activity), PPP6C (Affinity Capture-Western), ANKRD28 (Affinity Capture-Western), PPP6R3 (Affinity Capture-Western), ZNRF2 (Biochemical Activity), ATP6V0A2 (Affinity Capture-Western), LAMTOR1 (Affinity Capture-Western)

ESM2 similar proteins: A1L020, A1L3F4, A7X8B3, A7X8B5, A7X8B7, A7X8B9, A7X8C2, A7X8C4, A7X8C7, A7X8C9, A7X8D2, A7X8D4, A7XW25, O97775, O97776, O97952, O97960, P06401, P10275, P84550, P84551, P89463, Q01JD1, Q05A36, Q0VDT2, Q3UE17, Q5PQQ7, Q5U5Q3, Q69Z36, Q6QT55, Q6ZK57, Q6ZN04, Q71FD5, Q7RTV3, Q7TSJ6, Q7XQN1, Q7XT42, Q84SL2, Q86XN8, Q8BQ89

Diamond homologs: A0A0D1E015, A0JMD2, A1CEK1, A1DFP5, A2QWA2, A4QTV1, A8QCE4, A8XJZ8, B0G126, B0WAQ0, B3MT31, B3P851, B4G2G5, B4IC49, B4JHI7, B4K982, B4M140, B4NFJ7, B4PRU6, D2H5P6, D3ZVP7, D4A8G9, E1BLZ4, F1MM41, F7EP40, O13821, O14964, O59722, O76902, O95405, O96838, P0CS26, P0CS27, P34756, P40343, Q05B78, Q08CN9, Q0CJV3, Q0P4S0, Q0U4Z8

SIGNOR signaling

1 interactions.

AEffectBMechanism
Ub:E2“up-regulates activity”ZNRF2ubiquitination

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance6
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1401 predictions. Top by Δscore:

VariantEffectΔscore
7:30323736:TGG:Tdonor_loss1.0000
7:30323737:GGT:Gdonor_loss1.0000
7:30323738:GTAA:Gdonor_loss1.0000
7:30323739:T:Gdonor_loss1.0000
7:30355832:GG:Gdonor_gain1.0000
7:30355833:GG:Gdonor_gain1.0000
7:30366052:A:Gacceptor_gain1.0000
7:30323636:TTTTA:Tacceptor_loss0.9900
7:30323637:TTTA:Tacceptor_loss0.9900
7:30323638:TTAG:Tacceptor_loss0.9900
7:30323639:TA:Tacceptor_loss0.9900
7:30323640:A:AGacceptor_gain0.9900
7:30323640:A:Cacceptor_loss0.9900
7:30323640:AG:Aacceptor_gain0.9900
7:30323641:G:Aacceptor_loss0.9900
7:30323641:G:GGacceptor_gain0.9900
7:30323641:GG:Gacceptor_gain0.9900
7:30323738:G:GGdonor_gain0.9900
7:30323740:AA:Adonor_loss0.9900
7:30342792:A:Gdonor_gain0.9900
7:30355216:T:Gdonor_gain0.9900
7:30355244:T:Gdonor_gain0.9900
7:30355726:A:AGacceptor_gain0.9900
7:30355726:AGAG:Aacceptor_gain0.9900
7:30355727:G:GGacceptor_gain0.9900
7:30355727:GA:Gacceptor_gain0.9900
7:30355727:GAGG:Gacceptor_gain0.9900
7:30366051:AAGAT:Aacceptor_gain0.9900
7:30284475:G:GGdonor_gain0.9800
7:30355834:G:GGdonor_gain0.9800

AlphaMissense

1555 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
7:30323650:T:AC160S1.000
7:30323650:T:CC160R1.000
7:30323651:G:AC160Y1.000
7:30323651:G:CC160S1.000
7:30323652:C:GC160W1.000
7:30323659:T:AC163S1.000
7:30323659:T:CC163R1.000
7:30323660:G:AC163Y1.000
7:30323660:G:CC163S1.000
7:30323661:C:GC163W1.000
7:30323695:C:GH175D1.000
7:30323707:T:AC179S1.000
7:30323707:T:CC179R1.000
7:30323708:G:AC179Y1.000
7:30323708:G:CC179S1.000
7:30323708:G:TC179F1.000
7:30323709:T:GC179W1.000
7:30323731:T:CY187H1.000
7:30323731:T:GY187D1.000
7:30355757:T:AC199S1.000
7:30355757:T:CC199R1.000
7:30355758:G:AC199Y1.000
7:30355758:G:CC199S1.000
7:30355758:G:TC199F1.000
7:30355759:T:GC199W1.000
7:30355764:T:AI201K1.000
7:30355764:T:CI201T1.000
7:30355764:T:GI201R1.000
7:30355766:T:AC202S1.000
7:30355766:T:CC202R1.000

dbSNP variants (sampled 300 via entrez): RS1000044239 (7:30304966 T>C), RS1000069194 (7:30338993 G>A), RS1000113953 (7:30283481 G>A), RS1000143331 (7:30352421 C>A,T), RS1000198576 (7:30364549 T>G), RS1000238009 (7:30358840 G>T), RS1000251574 (7:30339535 G>T), RS1000254714 (7:30321166 C>G,T), RS1000274692 (7:30283072 A>G), RS1000305971 (7:30289641 A>C), RS1000334819 (7:30309232 T>G), RS1000344918 (7:30345289 A>G), RS1000363929 (7:30333365 T>A), RS1000396511 (7:30333689 T>C,G), RS1000450291 (7:30352194 G>A,C,T)

Disease associations

OMIM: gene MIM:612061 | 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
GCST002936_26Cadmium levels1.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Aciddecreases methylation, increases expression2
FR900359affects phosphorylation1
bisphenol Faffects cotreatment, increases methylation1
urushiolincreases expression1
sodium arseniteaffects cotreatment, decreases expression, increases abundance1
butyraldehydedecreases expression1
manganese chloridedecreases expression, increases abundance, affects cotreatment1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
Bortezomibincreases expression1
Resveratrolaffects cotreatment, decreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Air Pollutantsaffects expression, increases abundance1
Arsenicaffects cotreatment, decreases expression, increases abundance1
Benzo(a)pyreneincreases methylation1
Caffeinedecreases phosphorylation1
Lipopolysaccharidesaffects cotreatment, decreases expression1
Manganeseaffects cotreatment, decreases expression, increases abundance1
Ozoneaffects expression, increases abundance1
Tretinoinincreases expression1
Vincristinedecreases expression1
Aflatoxin B1decreases methylation1
Asbestos, Serpentineincreases methylation1
Antirheumatic Agentsdecreases expression1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

CellosaurusNameCategorySex
CVCL_D8DKUbigene A-549 ZNRF2 KOCancer cell lineMale

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.