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    LEMD3 LEM domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 23592, updated on 9-Jun-2024

    Summary

    Official Symbol
    LEMD3provided by HGNC
    Official Full Name
    LEM domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:28887
    See related
    Ensembl:ENSG00000174106 MIM:607844; AllianceGenome:HGNC:28887
    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
    MAN1
    Summary
    This locus encodes a LEM domain-containing protein. The encoded protein functions to antagonize transforming growth factor-beta signaling at the inner nuclear membrane. Two transcript variants encoding different isoforms have been found for this gene. Mutations in this gene have been associated with osteopoikilosis, Buschke-Ollendorff syndrome and melorheostosis.[provided by RefSeq, Nov 2009]
    Expression
    Ubiquitous expression in testis (RPKM 11.8), bone marrow (RPKM 7.8) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See LEMD3 in Genome Data Viewer
    Location:
    12q14.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (65169583..65248355)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (65148505..65227374)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (65563363..65642135)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6605 Neighboring gene apolipoprotein O pseudogene 3 Neighboring gene uncharacterized LOC124902953 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6606 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:65563126-65563698 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4630 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:65564244-65564447 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6608 Neighboring gene Sharpr-MPRA regulatory region 14888 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4631 Neighboring gene MPRA-validated peak1765 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:65655701-65656202 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:65656203-65656702 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4632 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4633 Neighboring gene methionine sulfoxide reductase B3 Neighboring gene uncharacterized LOC124902954 Neighboring gene keratin 18 pseudogene 60

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Dermatofibrosis lenticularis disseminata
    MedGen: C0265514 OMIM: 166700 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2020-10-19)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2020-10-19)

    ClinGen Genome Curation PagePubMed

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables U1 snRNP binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nuclear inner membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nuclear membrane IDA
    Inferred from Direct Assay
    more info
     

    General protein information

    Preferred Names
    inner nuclear membrane protein Man1
    Names
    LEM domain-containing protein 3
    LEMD3/MKX fusion
    MAN antigen 1
    integral inner nuclear membrane protein

    NCBI Reference Sequences (RefSeq)

    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.

    Genomic

    1. NG_016210.2 RefSeqGene

      Range
      5013..83785
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001167614.2NP_001161086.1  inner nuclear membrane protein Man1 isoform 2

      See identical proteins and their annotated locations for NP_001161086.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AF112299, AK312473, BX390128
      UniProtKB/Swiss-Prot
      Q9Y2U8
      Conserved Domains (3) summary
      cd12286
      Location:784875
      RRM_Man1; RNA recognition motif in inner nuclear membrane protein Man1 (Man1) and similar proteins
      pfam09402
      Location:535747
      MSC; Man1-Src1p-C-terminal domain
      cl02649
      Location:951
      LEM; LEM (Lap2/Emerin/Man1) domain found in emerin, lamina-associated polypeptide 2 (LAP2), inner nuclear membrane protein Man1 and similar proteins
    2. NM_014319.5NP_055134.2  inner nuclear membrane protein Man1 isoform 1

      See identical proteins and their annotated locations for NP_055134.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AF112299, AK312473, BX390128
      Consensus CDS
      CCDS8972.1
      UniProtKB/Swiss-Prot
      Q9NT47, Q9NYA5, Q9Y2U8
      Related
      ENSP00000308369.2, ENST00000308330.3
      Conserved Domains (3) summary
      cd12286
      Location:785876
      RRM_Man1; RNA recognition motif in inner nuclear membrane protein Man1 (Man1) and similar proteins
      pfam09402
      Location:538748
      MSC; Man1-Src1p-C-terminal domain
      cl02649
      Location:951
      LEM; LEM (Lap2/Emerin/Man1) domain found in emerin, lamina-associated polypeptide 2 (LAP2), inner nuclear membrane protein Man1 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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      65169583..65248355
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      65148505..65227374
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)