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    LMAN2L lectin, mannose binding 2 like [ Homo sapiens (human) ]

    Gene ID: 81562, updated on 3-Nov-2024

    Summary

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    Official Symbol
    LMAN2Lprovided by HGNC
    Official Full Name
    lectin, mannose binding 2 likeprovided by HGNC
    Primary source
    HGNC:HGNC:19263
    See related
    Ensembl:ENSG00000114988 MIM:609552; AllianceGenome:HGNC:19263
    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
    VIPL; MRD69; MRT52
    Summary
    This gene encodes a protein belonging to the L-type lectin group of type 1 membrane proteins, which function in the mammalian early secretory pathway. These proteins contain luminal carbohydrate recognition domains, which display homology to leguminous lectins. Unlike other proteins of the group, which cycle in the early secretory pathway and are predominantly associated with post endoplasmic reticulum membranes, the protein encoded by this gene is a non-cycling resident protein of the ER, where it functions as a cargo receptor for glycoproteins. It is proposed to regulate exchange of folded proteins for transport to the Golgi and exchange of misfolded glycoproteins for transport to the ubiquitin-proteasome pathway. [provided by RefSeq, Apr 2016]
    Expression
    Ubiquitous expression in ovary (RPKM 11.7), thyroid (RPKM 11.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LMAN2L in Genome Data Viewer
    Location:
    2q11.2
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (96705929..96740064, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (97212567..97246702, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (97371666..97405801, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene KAT8 regulatory NSL complex subunit 3 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:97273727-97274926 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16223 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11773 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:97326800-97327300 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:97327301-97327801 Neighboring gene fer-1 like family member 5 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:97351655-97352380 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:97359457-97359958 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:97360677-97361221 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:97361222-97361765 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:97404177-97405116 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:97405117-97406054 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16224 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr2:97426686-97427275 and GRCh37_chr2:97427276-97427864 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11775 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16226 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16227 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:97435174-97436108 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16228 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16229 Neighboring gene cyclin and CBS domain divalent metal cation transport mediator 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16230 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16231 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16232 Neighboring gene microRNA 3127 Neighboring gene CNNM3 divergent transcript

    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 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. Homozygous missense mutation in the LMAN2L gene segregates with intellectual disability in a large consanguineous Pakistani family. Rafiullah R, et al. J Med Genet, 2016 Feb. PMID 26566883
    2. Dominant LMAN2L mutation causes intellectual disability with remitting epilepsy. Alkhater RA, et al. Ann Clin Transl Neurol, 2019 Apr. PMID 31020005, Free PMC Article
    3. Genetic association of LMAN2L gene in schizophrenia and bipolar disorder and its interaction with ANK3 gene polymorphism. Lim CH, et al. Prog Neuropsychopharmacol Biol Psychiatry, 2014 Oct 3. PMID 24914473
    4. Molecular basis of sugar recognition by the human L-type lectins ERGIC-53, VIPL, and VIP36. Kamiya Y, et al. J Biol Chem, 2008 Jan 25. PMID 18025080
    5. Profile-based data base scanning for animal L-type lectins and characterization of VIPL, a novel VIP36-like endoplasmic reticulum protein. Nufer O, et al. J Biol Chem, 2003 May 2. PMID 12609988

    See all (49) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. segregate a NM_001142292.1:c.1073delT mutation that eliminates LMAN2L's endoplasmic reticulum retention signal and mislocalizes the protein from that compartment to the plasma membrane
      Title: Dominant LMAN2L mutation causes intellectual disability with remitting epilepsy.
    2. Homozygous missense mutation p.R53Q in the LMAN2L gene causes autosomal recessive intellectual disability and seizures.
      Title: Homozygous missense mutation in the LMAN2L gene segregates with intellectual disability in a large consanguineous Pakistani family.
    3. Study showed a significant association between LMAN2L and risk of both bipolar disorder and schizophrenia
      Title: Genetic association of LMAN2L gene in schizophrenia and bipolar disorder and its interaction with ANK3 gene polymorphism.
    4. The results of this study suggested that significant novel association signals near the genes LMAN2L and provide supportive evidence for the previously reported association signals near ANK3 and within the 3p21.1 locus.
      Title: Genome-wide association study meta-analysis of European and Asian-ancestry samples identifies three novel loci associated with bipolar disorder.
    5. selective interaction of VIPL and VIP36 with the deglucosylated trimannose in the D1 branch of high-mannose-type oligosaccharides but with different pH dependence.
      Title: Molecular basis of sugar recognition by the human L-type lectins ERGIC-53, VIPL, and VIP36.
    6. VIPL terminates in the sequence KRFY, characteristic for proteins recycling between the ER and ERGIC/cis-Golgi; and knock-down of VIPL mRNA slowed secretion of two glycoproteins (35 and 250 kDa), suggesting that VIPL may function as an ER export receptor.
      Title: VIPL, a VIP36-like membrane protein with a putative function in the export of glycoproteins from the endoplasmic reticulum.
    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

    Associated conditions

    Description Tests
    Intellectual developmental disorder, autosomal dominant 69
    MedGen: C5676896 OMIM: 617863 GeneReviews: Not available
    		Compare labs
    Intellectual disability, autosomal recessive 52
    MedGen: C4225168 OMIM: 616887 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association study meta-analysis of European and Asian-ancestry samples identifies three novel loci associated with bipolar disorder.
    EBI GWAS Catalog
    Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4.
    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

    • MGC11139, DKFZp564L2423

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables D-mannose binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables D-mannose binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endoplasmic reticulum to Golgi vesicle-mediated transport TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in protein folding NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in protein transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in COPII-coated ER to Golgi transport vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in COPII-coated ER to Golgi transport vesicle NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in Golgi membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 
    is_active_in endoplasmic reticulum-Golgi intermediate compartment IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    VIP36-like protein
    Names
    LMAN2-like protein

    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_046866.1 RefSeqGene

      Range
      5019..39154
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001142292.2 → NP_001135764.1  VIP36-like protein isoform 1 precursor

      See identical proteins and their annotated locations for NP_001135764.1

      Status: REVIEWED

      Source sequence(s)
      AK310100, BX648002
      Consensus CDS
      CCDS46365.1
      UniProtKB/TrEMBL
      B2R5N4
      Related
      ENSP00000366280.4, ENST00000377079.8
      Conserved Domains (1) summary
      cl14058
      Location:50 → 309
      lectin_L-type; legume lectins

    2. NM_001322346.2 → NP_001309275.1  VIP36-like protein isoform 3

      Status: REVIEWED

      Source sequence(s)
      AK299740, AK310100, BC000347
      UniProtKB/TrEMBL
      B4E308
      Conserved Domains (1) summary
      cl14058
      Location:35 → 164
      lectin_L-type; legume lectins

    3. NM_001322347.2 → NP_001309276.1  VIP36-like protein isoform 4

      Status: REVIEWED

      Source sequence(s)
      AK295463, BC000347
      UniProtKB/TrEMBL
      B4DI83, B4E308
      Conserved Domains (1) summary
      cl14058
      Location:1 → 171
      lectin_L-type; legume lectins

    4. NM_001322350.2 → NP_001309279.1  VIP36-like protein isoform 5

      Status: REVIEWED

      Source sequence(s)
      AK304515, AK310100, BC000347
      UniProtKB/TrEMBL
      B4E308
      Conserved Domains (1) summary
      cl14058
      Location:1 → 160
      lectin_L-type; legume lectins

    5. NM_001322351.2 → NP_001309280.1  VIP36-like protein isoform 6

      Status: REVIEWED

      Source sequence(s)
      AK301077, BC000347
      UniProtKB/TrEMBL
      B4DVH1, B4E308
      Conserved Domains (1) summary
      cl14058
      Location:21 → 153
      lectin_L-type; legume lectins

    6. NM_001322352.2 → NP_001309281.1  VIP36-like protein isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC068539, BC004505
      UniProtKB/TrEMBL
      B4DI83, B4E308
      Conserved Domains (1) summary
      cl14058
      Location:1 → 171
      lectin_L-type; legume lectins

    7. NM_001322354.2 → NP_001309283.1  VIP36-like protein isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC068539, BC004505, DA521101, DC354352
      UniProtKB/TrEMBL
      B4E308
      Conserved Domains (1) summary
      cl14058
      Location:35 → 164
      lectin_L-type; legume lectins

    8. NM_001322355.2 → NP_001309284.1  VIP36-like protein isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC068539, BC004505
      UniProtKB/TrEMBL
      B4DVH1, B4E308
      Conserved Domains (1) summary
      cl14058
      Location:21 → 153
      lectin_L-type; legume lectins

    9. NM_001322356.2 → NP_001309285.1  VIP36-like protein isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC068539, AK316331, BC004505
      UniProtKB/TrEMBL
      B4DVH1, B4E308
      Conserved Domains (1) summary
      cl14058
      Location:21 → 153
      lectin_L-type; legume lectins

    10. NM_030805.4 → NP_110432.1  VIP36-like protein isoform 2 precursor

      See identical proteins and their annotated locations for NP_110432.1

      Status: REVIEWED

      Source sequence(s)
      AK310100, BC000347
      Consensus CDS
      CCDS2023.1
      UniProtKB/Swiss-Prot
      B4DSH3, D3DXH6, Q53GV3, Q53S67, Q63HN6, Q8NBQ6, Q9BQ14, Q9H0V9
      UniProtKB/TrEMBL
      B2R5N4
      Related
      ENSP00000264963.4, ENST00000264963.9
      Conserved Domains (1) summary
      cl14058
      Location:50 → 298
      lectin_L-type; legume lectins

    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

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      96705929..96740064 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047445946.1 → XP_047301902.1  VIP36-like protein isoform X1

      Conserved Domains (1) summary
      cl14058
      Location:1 → 160
      lectin_L-type; legume lectins

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      97212567..97246702 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054344098.1 → XP_054200073.1  VIP36-like protein isoform X1

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NR_024518.1: Suppressed sequence

      Description
      NR_024518.1: This RefSeq was removed because it is now thought that this transcript does encode a protein.

    2. NR_024519.1: Suppressed sequence

      Description
      NR_024519.1: This RefSeq was removed because it is now thought that this transcript does encode a protein.

    3. NR_024520.1: Suppressed sequence

      Description
      NR_024520.1: This RefSeq was removed because it is now thought that this transcript does encode a protein.

    4. NR_024521.1: Suppressed sequence

      Description
      NR_024521.1: This RefSeq was removed because it is now thought that this transcript does encode a protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H0V9.1 GenPept UniProtKB/Swiss-Prot:Q9H0V9

    Gene LinkOut

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

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