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ZNRF1 zinc and ring finger 1 [ Homo sapiens (human) ]

Gene ID: 84937, updated on 7-Apr-2024

Summary

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Official Symbol
ZNRF1provided by HGNC
Official Full Name
zinc and ring finger 1provided by HGNC
Primary source
HGNC:HGNC:18452
See related
Ensembl:ENSG00000186187 MIM:612060; AllianceGenome:HGNC:18452
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NIN283
Summary
This gene encodes an E3 ubiquitin-protein ligase that plays a role in neural-cell differentiation. Overexpression of this gene causes neurite-like elongation. The encoded protein contains both a zinc finger and a RING finger motif and is localized in the endosome/lysosome compartment, indicating that it may be involved in ubiquitin-mediated protein modification, and in synaptic vessicle membranes in neurons. [provided by RefSeq, Feb 2012]
Expression
Ubiquitous expression in testis (RPKM 4.3), thyroid (RPKM 4.3) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
16q23.1
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (74999024..75110994)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (81045795..81157694)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (75032922..75144892)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371343 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11111 Neighboring gene Sharpr-MPRA regulatory region 8667 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:74905369-74905917 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:74908123-74908848 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:74909577-74910302 Neighboring gene WD repeat domain 59 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:74997467-74997687 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7704 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11112 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:75020112-75020312 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7705 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7706 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11113 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11115 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11116 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:75095860-75097059 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11117 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:75108734-75109234 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:75109235-75109735 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:75113000-75113201 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75113937-75114482 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:75121619-75122275 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:75127186-75127378 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75129219-75129949 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75129950-75130679 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11119 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7707 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7708 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:75136275-75136776 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_44438 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11121 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11122 Neighboring gene Sharpr-MPRA regulatory region 12749 Neighboring gene lactate dehydrogenase D Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11123 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7709 Neighboring gene ZFP1 zinc finger protein

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Identification of genes induced in peripheral nerve after injury. Expression profiling and novel gene discovery. Araki T, et al. J Biol Chem, 2001 Sep 7. PMID 11427537
  2. LZTFL1 inhibits kidney tumor cell growth by destabilizing AKT through ZNRF1-mediated ubiquitin proteosome pathway. Lu J, et al. Oncogene, 2023 May. PMID 36966254, Free PMC Article
  3. Proteasomal degradation of glutamine synthetase regulates schwann cell differentiation. Saitoh F, et al. J Neurosci, 2010 Jan 27. PMID 20107048, Free PMC Article
  4. Common variants in or near ZNRF1, COLEC12, SCYL1BP1 and API5 are associated with diabetic retinopathy in Chinese patients with type 2 diabetes. Peng D, et al. Diabetologia, 2015 Jun. PMID 25819896
  5. ZNRF proteins constitute a family of presynaptic E3 ubiquitin ligases. Araki T, et al. J Neurosci, 2003 Oct 15. PMID 14561866, Free PMC Article

See all (29) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. LZTFL1 inhibits kidney tumor cell growth by destabilizing AKT through ZNRF1-mediated ubiquitin proteosome pathway.
    Title: LZTFL1 inhibits kidney tumor cell growth by destabilizing AKT through ZNRF1-mediated ubiquitin proteosome pathway.
  2. as a consequence of its high E2 affinity, an excess of ZNRF1 inhibits Ube2N-mediated ubiquitination at concentrations >/=500 nM instead of showing enhanced ubiquitination
    Title: Structural insights into the nanomolar affinity of RING E3 ligase ZNRF1 for Ube2N and its functional implications.
  3. rs17684886 (ZNRF1) and rs599019 (COLEC12) are associated with diabetic retinopathy and rs6427247 (SCYL1BP1) and rs899036 (API5) are associated with severe diabetic retinopathy in Chinese patients with type 2 diabetes
    Title: Common variants in or near ZNRF1, COLEC12, SCYL1BP1 and API5 are associated with diabetic retinopathy in Chinese patients with type 2 diabetes.
  4. ZNRF1 and ZNRF2 are new players in regulation of the ubiquitous Na(+)/K(+)ATPase that is tuned to changing demands in many physiological contexts.
    Title: ZNRF2 is released from membranes by growth factors and, together with ZNRF1, regulates the Na+/K+ATPase.
  5. Observational study of gene-disease association. (HuGE Navigator)
    Title: Fine mapping and association studies of a high-density lipoprotein cholesterol linkage region on chromosome 16 in French-Canadian subjects.
  6. These results suggest that ZNRF1 mediates regulation of neuritogenesis via interaction with tubulin.
    Title: ZNRF1 interacts with tubulin and regulates cell morphogenesis.
  7. data suggest that ZNRF proteins play a role in the establishment and maintenance of neuronal transmission and plasticity via their ubiquitin ligase activity
    Title: ZNRF proteins constitute a family of presynaptic E3 ubiquitin ligases.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Multidimensional prognostic risk assessment identifies association between IL12B variation and surgery in Crohn's disease.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ14846, FLJ46491, MGC15430, DKFZp434E229

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ubiquitin protein ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ubiquitin protein ligase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables ubiquitin-protein transferase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in positive regulation of toll-like receptor 4 signaling pathway IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in protein K48-linked ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein K48-linked ubiquitination ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in endosome IDA
Inferred from Direct Assay
more info
  
is_active_in intracellular membrane-bounded organelle IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in lysosome IEA
Inferred from Electronic Annotation
more info
  
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in membrane IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in plasma membrane IC
Inferred by Curator
more info
 PubMed 
located_in synaptic vesicle membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
E3 ubiquitin-protein ligase ZNRF1
Names
RING-type E3 ubiquitin transferase ZNRF1
nerve injury gene 283
nerve injury-induced gene 283 protein
zinc and ring finger 1, E3 ubiquitin protein ligase
zinc and ring finger protein 1
zinc/RING finger protein 1
NP_115644.1
XP_011521694.1
XP_016879282.1
XP_016879283.1
XP_054170185.1
XP_054170186.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_032268.5 → NP_115644.1  E3 ubiquitin-protein ligase ZNRF1

    See identical proteins and their annotated locations for NP_115644.1

    Status: REVIEWED

    Source sequence(s)
    AC092383, AC099508, AF378524
    Consensus CDS
    CCDS10912.1
    UniProtKB/Swiss-Prot
    D3DUJ9, Q8ND25, Q9H083
    UniProtKB/TrEMBL
    H3BRB6
    Related
    ENSP00000335091.4, ENST00000335325.9
    Conserved Domains (1) summary
    cd16694
    Location:182 → 227
    mRING-CH-C4HC2H_ZNRF1; Modified RING-CH finger, H2 subclass (C4HC2H-type), found in zinc/RING finger protein 1 (ZNRF1) and similar proteins

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    74999024..75110994
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017023793.2 → XP_016879282.1  E3 ubiquitin-protein ligase ZNRF1 isoform X1

    UniProtKB/Swiss-Prot
    D3DUJ9, Q8ND25, Q9H083
    UniProtKB/TrEMBL
    H3BRB6
    Related
    ENSP00000456168.1, ENST00000566250.5
    Conserved Domains (1) summary
    cd16694
    Location:182 → 227
    mRING-CH-C4HC2H_ZNRF1; Modified RING-CH finger, H2 subclass (C4HC2H-type), found in zinc/RING finger protein 1 (ZNRF1) and similar proteins

  2. XM_011523392.2 → XP_011521694.1  E3 ubiquitin-protein ligase ZNRF1 isoform X3

  3. XM_017023794.2 → XP_016879283.1  E3 ubiquitin-protein ligase ZNRF1 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    81045795..81157694
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054314210.1 → XP_054170185.1  E3 ubiquitin-protein ligase ZNRF1 isoform X1

    UniProtKB/Swiss-Prot
    D3DUJ9, Q8ND25, Q9H083

  2. XM_054314211.1 → XP_054170186.1  E3 ubiquitin-protein ligase ZNRF1 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8ND25.2 GenPept UniProtKB/Swiss-Prot:Q8ND25

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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