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

Summary

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: mouse all
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Genomic context

Location:: 16q23.1

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (74999024..75110994)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (81045795..81157694)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (75032922..75144892)

Chromosome 16 - NC_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
These results suggest that ZNRF1 mediates regulation of neuritogenesis via interaction with tubulin.
Title: ZNRF1 interacts with tubulin and regulates cell morphogenesis.
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.

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Phenotypes

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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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-84608 (e-PCR)
- UniSTS:102936

RH64877 (e-PCR)
- UniSTS:92955

A004T26 (e-PCR)
- UniSTS:4931

RH102768 (e-PCR)
- UniSTS:97102

D16S3184 (e-PCR)
- UniSTS:79185

RH36321 (e-PCR)
- UniSTS:67431

D16S2877 (e-PCR)
- UniSTS:153447

ZNRF1__4725 (e-PCR)
- UniSTS:462973

G43020 (e-PCR)
- UniSTS:94877

SHGC-61187 (e-PCR)
- UniSTS:74147

RH68389 (e-PCR)
- UniSTS:59059

RH68472 (e-PCR)
- UniSTS:48828

G59919 (e-PCR)
- UniSTS:137200

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 autophagosome-lysosome fusion	IGI Inferred from Genetic Interaction more info	PubMed
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 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

EC 2.3.2.27

XP_011521694.1

EC 2.3.2.27

XP_016879282.1

EC 2.3.2.27

XP_016879283.1

EC 2.3.2.27

XP_054170185.1

EC 2.3.2.27

XP_054170186.1

EC 2.3.2.27

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)

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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

74999024..75110994

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
XM_011523392.2 → XP_011521694.1 E3 ubiquitin-protein ligase ZNRF1 isoform X3
XM_017023794.2 → XP_016879283.1 E3 ubiquitin-protein ligase ZNRF1 isoform X2

Alternate T2T-CHM13v2.0

Genomic

NC_060940.1 Alternate T2T-CHM13v2.0

Range

81045795..81157694

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

D3DUJ9, Q8ND25, Q9H083
XM_054314211.1 → XP_054170186.1 E3 ubiquitin-protein ligase ZNRF1 isoform X3