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DERL3 derlin 3 [ Homo sapiens (human) ]

Gene ID: 91319, updated on 11-Apr-2024

Summary

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Official Symbol
DERL3provided by HGNC
Official Full Name
derlin 3provided by HGNC
Primary source
HGNC:HGNC:14236
See related
Ensembl:ENSG00000099958 MIM:610305; AllianceGenome:HGNC:14236
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
IZP6; LLN2; C22orf14; derlin-3
Summary
The protein encoded by this gene belongs to the derlin family, and resides in the endoplasmic reticulum (ER). Proteins that are unfolded or misfolded in the ER must be refolded or degraded to maintain the homeostasis of the ER. This protein appears to be involved in the degradation of misfolded glycoproteins in the ER. Several alternatively spliced transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Oct 2008]
Expression
Broad expression in stomach (RPKM 12.2), duodenum (RPKM 11.1) and 22 other tissues See more
Orthologs
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Genomic context

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Location:
22q11.23
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (23834503..23839006, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (24281689..24286190, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (24176690..24181193, complement)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985577 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24122834-24123832 Neighboring gene matrix metallopeptidase 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24134505-24135005 Neighboring gene SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24145605-24146105 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24158117-24158618 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24158619-24159120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24166870-24167403 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:24167404-24167938 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:24168707-24169427 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:24181116-24181418 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:24184397-24184954 Neighboring gene skeletal muscle cis-regulatory module in DERL3 and SLC2A11 intergenic region Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr22:24189965-24190722 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:24190723-24191478 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:24191479-24192234 Neighboring gene solute carrier family 2 member 11 Neighboring gene RNA, 7SL, cytoplasmic 268, pseudogene Neighboring gene Sharpr-MPRA regulatory region 10281 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:24236245-24237052 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:24237053-24237860 Neighboring gene MIF antisense RNA 1 Neighboring gene macrophage migration inhibitory factor

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. Up-regulated DERL3 in fibroblast-like synoviocytes exacerbates inflammation of rheumatoid arthritis. Geng M, et al. Clin Immunol, 2020 Nov. PMID 32866644
  2. DERL3 functions as a tumor suppressor in gastric cancer. Li Y, et al. Comput Biol Chem, 2020 Feb. PMID 31862624
  3. Overexpression of Derlin 3 is associated with malignant phenotype of breast cancer cells. Shibata M, et al. Oncol Rep, 2017 Sep. PMID 28713959
  4. Repression of DERL3 via DNA methylation by Epstein-Barr virus latent membrane protein 1 in nasopharyngeal carcinoma. Kondo S, et al. Biochim Biophys Acta Mol Basis Dis, 2023 Feb. PMID 36372158
  5. A DERL3-associated defect in the degradation of SLC2A1 mediates the Warburg effect. Lopez-Serra P, et al. Nat Commun, 2014 Apr 3. PMID 24699711, Free PMC Article

See all (29) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Repression of DERL3 via DNA methylation by Epstein-Barr virus latent membrane protein 1 in nasopharyngeal carcinoma.
    Title: Repression of DERL3 via DNA methylation by Epstein-Barr virus latent membrane protein 1 in nasopharyngeal carcinoma.
  2. Up-regulated DERL3 in fibroblast-like synoviocytes exacerbates inflammation of rheumatoid arthritis.
    Title: Up-regulated DERL3 in fibroblast-like synoviocytes exacerbates inflammation of rheumatoid arthritis.
  3. DERL3 is both a tumor suppressor of and a methylation biomarker for gastric cancer.
    Title: DERL3 functions as a tumor suppressor in gastric cancer.
  4. DERL3 promotes malignant phenotype in BC cells.
    Title: Overexpression of Derlin 3 is associated with malignant phenotype of breast cancer cells.
  5. SLC2A1 overexpression mediated by DERL3 epigenetic loss contributes to the Warburg effect.
    Title: A DERL3-associated defect in the degradation of SLC2A1 mediates the Warburg effect.
  6. Findings indicate that Derlin-3 provides the missing link between EDEM and p97 in the process of degrading misfolded glycoproteins.
    Title: Derlin-2 and Derlin-3 are regulated by the mammalian unfolded protein response and are required for ER-associated degradation.
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
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
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

  • MGC71803

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-containing complex binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables signal recognition particle binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables signal recognition particle binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in ERAD pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in ERAD pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in ERAD pathway NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in ERAD pathway TAS
Traceable Author Statement
more info
 PubMed 
involved_in endoplasmic reticulum unfolded protein response IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in endoplasmic reticulum unfolded protein response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of retrograde protein transport, ER to cytosol IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein N-linked glycosylation via asparagine IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in endoplasmic reticulum membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
derlin-3
Names
DERtrin 3
Der1-like domain family, member 3
degradation in endoplasmic reticulum protein 3
der1-like protein 3

NCBI Reference Sequences (RefSeq)

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NEW Try the new Transcript table

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_001002862.3 → NP_001002862.1  derlin-3 isoform 2

    See identical proteins and their annotated locations for NP_001002862.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) is alternatively spliced at the 3' end compared to transcript variant 1, resulting in a slightly shorter isoform (2) with a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AK092582, AL389876, AP000350, BC057830, CA313370
    Consensus CDS
    CCDS33615.1
    UniProtKB/Swiss-Prot
    F2Z3B6, Q6ICJ6, Q6PEX0, Q6ZUB5, Q96Q80
    Related
    ENSP00000315303.8, ENST00000318109.12
    Conserved Domains (1) summary
    pfam04511
    Location:13 → 202
    DER1; Der1-like family

  2. NM_001135751.2 → NP_001129223.1  derlin-3 isoform 1

    See identical proteins and their annotated locations for NP_001129223.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AL389876, AW135031, BC057830, CA313370
    Consensus CDS
    CCDS46672.1
    UniProtKB/Swiss-Prot
    Q96Q80
    Related
    ENSP00000384744.3, ENST00000406855.7
    Conserved Domains (1) summary
    pfam04511
    Location:13 → 202
    DER1; Der1-like family

  3. NM_001363072.2 → NP_001350001.1  derlin-3 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) is alternatively spliced at the 3' end compared to transcript variant 1, resulting in a shorter isoform (4) with a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AP000350, CA313370
    Conserved Domains (1) summary
    pfam04511
    Location:13 → 202
    DER1; Der1-like family

  4. NM_198440.4 → NP_940842.2  derlin-3 isoform 3

    See identical proteins and their annotated locations for NP_940842.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains a long 3' terminal exon that is split into 2 exons in transcript variant 1. This results in early translation termination and a shorter isoform (3) compared to isoform 1.
    Source sequence(s)
    AK092582, AL389876, AP000350, BC057830, CA313370
    Consensus CDS
    CCDS42986.1
    UniProtKB/Swiss-Prot
    Q96Q80
    Related
    ENSP00000419399.1, ENST00000476077.1
    Conserved Domains (1) summary
    pfam04511
    Location:13 → 202
    DER1; Der1-like family

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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    23834503..23839006 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047441596.1 → XP_047297552.1  derlin-3 isoform X4

  2. XM_047441597.1 → XP_047297553.1  derlin-3 isoform X6

  3. XM_011530505.4 → XP_011528807.1  derlin-3 isoform X5

    See identical proteins and their annotated locations for XP_011528807.1

    Conserved Domains (1) summary
    pfam04511
    Location:13 → 201
    DER1; Der1-like family

  4. XM_047441595.1 → XP_047297551.1  derlin-3 isoform X3

  5. XM_017029078.3 → XP_016884567.2  derlin-3 isoform X1

  6. XM_047441594.1 → XP_047297550.1  derlin-3 isoform X2

    Related
    ENST00000290730.11

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187633.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    70865..75368 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054329460.1 → XP_054185435.1  derlin-3 isoform X4

  2. XM_054329462.1 → XP_054185437.1  derlin-3 isoform X6

  3. XM_054329461.1 → XP_054185436.1  derlin-3 isoform X5

  4. XM_054329459.1 → XP_054185434.1  derlin-3 isoform X3

  5. XM_054329457.1 → XP_054185432.1  derlin-3 isoform X1

  6. XM_054329458.1 → XP_054185433.1  derlin-3 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    24281689..24286190 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054326128.1 → XP_054182103.1  derlin-3 isoform X4

  2. XM_054326130.1 → XP_054182105.1  derlin-3 isoform X6

  3. XM_054326129.1 → XP_054182104.1  derlin-3 isoform X5

  4. XM_054326127.1 → XP_054182102.1  derlin-3 isoform X3

  5. XM_054326125.1 → XP_054182100.1  derlin-3 isoform X1

  6. XM_054326126.1 → XP_054182101.1  derlin-3 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96Q80.2 GenPept UniProtKB/Swiss-Prot:Q96Q80

Gene LinkOut

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

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