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ERLEC1 endoplasmic reticulum lectin 1 [ Homo sapiens (human) ]

Gene ID: 27248, updated on 11-Apr-2024

Summary

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Official Symbol
ERLEC1provided by HGNC
Official Full Name
endoplasmic reticulum lectin 1provided by HGNC
Primary source
HGNC:HGNC:25222
See related
Ensembl:ENSG00000068912 MIM:611229; AllianceGenome:HGNC:25222
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
CIM; HEL117; XTP3-B; C2orf30; CL24936; CL25084; XTP3TPB
Summary
This gene encodes a resident endoplasmic reticulum (ER) protein that functions in N-glycan recognition. This protein is thought to be involved in ER-associated degradation via its interaction with the membrane-associated ubiquitin ligase complex. It also functions as a regulator of multiple cellular stress-response pathways in a manner that promotes metastatic cell survival. Alternative splicing results in multiple transcript variants. A related pseudogene has been identified on chromosome 21. [provided by RefSeq, Aug 2011]
Expression
Ubiquitous expression in thyroid (RPKM 36.0), prostate (RPKM 29.5) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
2p16.2
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (53787044..53818796)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (53783247..53814984)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (54014181..54045933)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374600 Neighboring gene GPR75-ASB3 readthrough Neighboring gene ankyrin repeat and SOCS box containing 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15753 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15754 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:54013580-54014238 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:54019308-54019522 Neighboring gene ChaC glutathione specific gamma-glutamylcyclotransferase 2 Neighboring gene uncharacterized LOC112268415 Neighboring gene Sharpr-MPRA regulatory region 2358 Neighboring gene uncharacterized LOC124906183 Neighboring gene microRNA 3682

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 pathogenic variants of ERLEC1 in individuals with Class III malocclusion by exome sequencing. Rao C, et al. Hum Mutat, 2020 Aug. PMID 32442352
  2. Mannose 6-phosphate receptor homology (MRH) domain-containing lectins in the secretory pathway. Castonguay AC, et al. Biochim Biophys Acta, 2011 Sep. PMID 21723917, Free PMC Article
  3. Mannose 6-phosphate receptor homology domain-containing lectins in mammalian endoplasmic reticulum-associated degradation. Hosokawa N, et al. Methods Enzymol, 2010. PMID 20816211
  4. Sweet bays of ERAD. Tamura T, et al. Trends Biochem Sci, 2008 Jul. PMID 18538572
  5. Redundant and Antagonistic Roles of XTP3B and OS9 in Decoding Glycan and Non-glycan Degrons in ER-Associated Degradation. van der Goot AT, et al. Mol Cell, 2018 May 3. PMID 29706535, Free PMC Article

See all (64) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Identification of pathogenic variants of ERLEC1 in individuals with Class III malocclusion by exome sequencing.
    Title: Identification of pathogenic variants of ERLEC1 in individuals with Class III malocclusion by exome sequencing.
  2. The relative expression of OS9 and XTP3B and the distribution of glycan and non-glycan degrons within the same protein contribute to the fidelity.
    Title: Redundant and Antagonistic Roles of XTP3B and OS9 in Decoding Glycan and Non-glycan Degrons in ER-Associated Degradation.
  3. Data indicate that the interaction of OS-9 and XTP3-B with CD147(CG) was inhibited by mutations to conserved residues in their lectin domains.
    Title: Unassembled CD147 is an endogenous endoplasmic reticulum-associated degradation substrate.
  4. Lectin activity of XTP3-B is required for its interaction with the misfolded glycoprotein alpha1-antitrypsin variant.
    Title: Endoplasmic reticulum lectin XTP3-B inhibits endoplasmic reticulum-associated degradation of a misfolded α1-antitrypsin variant.
  5. It regulates endoplasmic reticulum-associated degradation. (review)
    Title: [OS-9 and XTP3-B: lectins that regulate endoplasmic reticulum-associated degradation (ERAD)].
  6. mannose trimming enables delivery of a substrate glycoprotein from EDEM1 to late endoplsmic reticulum degredation steps through association with XTP3-B
    Title: Mannose trimming is required for delivery of a glycoprotein from EDEM1 to XTP3-B and to late endoplasmic reticulum-associated degradation steps.
  7. Findings shed light on how tolerance to multiple cellular stresses at a metastatic site can be evoked by an integrated mechanism involving CIM, ERLEC1, which can function to coordinate those responses in a manner that promotes metastatic cell survival.
    Title: Novel metastasis-related gene CIM functions in the regulation of multiple cellular stress-response pathways.
  8. XTP3-B specifically binds to AT(NHK), which is a well-known substrate of ERAD, via a C-terminal MRH domain in a glycan-dependent manner.
    Title: Human XTP3-B binds to alpha1-antitrypsin variant null(Hong Kong) via the C-terminal MRH domain in a glycan-dependent manner.
  9. XTP3-B forms an endoplasmic reticulum quality control scaffold with the HRD1-SEL1L ubiquitin ligase complex and BiP
    Title: Human XTP3-B forms an endoplasmic reticulum quality control scaffold with the HRD1-SEL1L ubiquitin ligase complex and BiP.
  10. Erlectin functions in N-glycan recognition in the endoplasmic reticulum and may regulate glycoprotein traffic
    Title: The MRH protein Erlectin is a member of the endoplasmic reticulum synexpression group and functions in N-glycan recognition.
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

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

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 is identified to have a physical interaction with endoplasmic reticulum lectin 1 (ERLEC1; XTP3B) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed
Envelope transmembrane glycoprotein gp41 env HIV-1 gp41 is identified to have a physical interaction with endoplasmic reticulum lectin 1 (ERLEC1; XTP3B) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables unfolded protein binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in ERAD pathway TAS
Traceable Author Statement
more info
 PubMed 
involved_in endoplasmic reticulum unfolded protein response IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of retrograde protein transport, ER to cytosol IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in retrograde protein transport, ER to cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in endoplasmic reticulum lumen IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum lumen IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum quality control compartment TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
endoplasmic reticulum lectin 1
Names
ER lectin
XTP3-transactivated gene B protein
XTP3-transactivated protein B
cancer invasion and metastasis-related
epididymis luminal protein 117
erlectin 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.

Genomic

  1. NG_029742.1 RefSeqGene

    Range
    5114..36866
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001127397.3 → NP_001120869.1  endoplasmic reticulum lectin 1 isoform 2 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1.
    Source sequence(s)
    BC013129, BQ017438, DB451941
    Consensus CDS
    CCDS46283.1
    UniProtKB/TrEMBL
    A0A8I5KWJ1
    Related
    ENSP00000385629.3, ENST00000405123.7
    Conserved Domains (2) summary
    pfam07915
    Location:111 → 199
    PRKCSH; Glucosidase II beta subunit-like protein
    cl06793
    Location:206 → 250
    PRKCSH; Glucosidase II beta subunit-like protein

  2. NM_001127398.3 → NP_001120870.1  endoplasmic reticulum lectin 1 isoform 3 precursor

    See identical proteins and their annotated locations for NP_001120870.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (3, also known as hXTP3-B-short) that is shorter than isoform 1.
    Source sequence(s)
    AY358717, DB451941
    Consensus CDS
    CCDS46284.1
    UniProtKB/TrEMBL
    A0A8I5KTC7
    Related
    ENSP00000367485.5, ENST00000378239.5
    Conserved Domains (2) summary
    pfam07915
    Location:294 → 367
    PRKCSH; Glucosidase II beta subunit-like protein
    cl06793
    Location:206 → 250
    PRKCSH; Glucosidase II beta subunit-like protein

  3. NM_015701.5 → NP_056516.2  endoplasmic reticulum lectin 1 isoform 1 precursor

    See identical proteins and their annotated locations for NP_056516.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1, also known as hXTP3-B-long).
    Source sequence(s)
    BC013129, DB451941
    Consensus CDS
    CCDS1848.1
    UniProtKB/Swiss-Prot
    B2RDB4, B5MC72, O95901, Q6UWN7, Q96DZ1, Q9NUY7, Q9UQL4
    UniProtKB/TrEMBL
    A0A8I5KWJ1, V9HWD3
    Related
    ENSP00000185150.4, ENST00000185150.9
    Conserved Domains (2) summary
    pfam07915
    Location:342 → 421
    PRKCSH; Glucosidase II beta subunit-like protein
    cl06793
    Location:206 → 250
    PRKCSH; Glucosidase II beta subunit-like protein

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    53787044..53818796
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    53783247..53814984
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96DZ1.1 GenPept UniProtKB/Swiss-Prot:Q96DZ1

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