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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

HMSD Gene

protein-coding   GIFtS: 36
GCID: GC18P061616

histocompatibility (minor) serpin domain containing


(Previous symbol: C18orf53)
 Explore 2 diseases affiliated with
HMSD via our new
 Human Malady Compendium 
Biological research products
for HMSD
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Histocompatibility (Minor) Serpin Domain Containing1 2     HSMD-V1
C18orf531 2 3     Serpin-Like Protein HMSD2
ACC-61 2     Minor Histocompatibility Serpin Domain-Containing Protein3
Minor Histocompatibility Protein HMSD2 3     

External Ids:    HGNC: 230371   Entrez Gene: 2842932   Ensembl: ENSG000002218877   OMIM: 6120865   UniProtKB: P0C7T43   
UniProtKB: A8MTL93   

Export aliases for HMSD gene to outside databases

Previous GC identifers: GC18P059768 GC18P058317


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for HMSD:
This gene encodes a serpin-domain containing protein that may function as a serine protease inhibitor. This gene is
primarily expressed in cells of myeloid lineage. A polymorphism in this gene may result in the expression a splice
variant that encodes a minor histocompatibility antigen. (provided by RefSeq, Oct 2010)

UniProtKB/Swiss-Prot: HMSD_HUMAN, A8MTL9
Function: Putative serine protease inhibitor (By similarity)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000018.9  NC_018929.1  NT_025028.14  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the HMSD gene promoter:
         POU3F1   FOXO3   LCR-F1   FOXO3b   FOXL1   MEF-2A   POU2F1   POU2F1a   FOXO3a   aMEF-2   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for HMSD

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat HMSD


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 18q22.1   Ensembl cytogenetic band:  18q22.1   HGNC cytogenetic band: 18q21.33

HMSD Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HMSD gene location

GeneLoc information about chromosome 18         GeneLoc Exon Structure

GeneLoc location for GC18P061616:  view genomic region     (about GC identifiers)

Start:
61,616,535 bp from pter      End:
61,649,008 bp from pter
Size:
32,474 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: HMSDV_HUMAN, P0C7T4 (See protein sequence)
Recommended Name: Minor histocompatibility protein HMSD variant form  
Size: 53 amino acids; 6023 Da
Subunit: ACC-6 forms a complex with MHC HLA-B*4403
Caution: Translation of HMSD-v form generating mHA ACC-6 is in a frame different from that resulting in HMSD non
variant form expression. Thus, the HMSD non variant form sequence does not contain the mHA ACC-6 peptide
Alternative splicing: 2 isoforms:  P0C7T4-1   A8MTL9-1   (This alternative splicing is due 1 intronic SNP)

UniProtKB/Swiss-Prot: HMSD_HUMAN, A8MTL9 (See protein sequence)

Recommended Name: Serpin-like protein HMSD precursor  
Size: 139 amino acids; 15355 Da
Subcellular location: Secreted (Potential)
Caution: Translation of HMSD-v form generating mHA ACC-6 is in a frame different from that resulting in HMSD non
variant form expression. Thus, HMSD sequence described in this entry does not contain the mHA ACC-6 peptide
Alternative splicing: 2 isoforms:  A8MTL9-1   P0C7T4-1   (This alternative splicing is due 1 intronic SNP)

Explore the universe of human proteins at neXtProt for HMSD: NX_A8MTL9

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_A8MTL9

  • HMSD Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_001116838.1  
    ENSEMBL proteins: 
     ENSP00000386207   ENSP00000431632  

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    Uscn Proteins for HMSD

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region IEA--


    HMSD for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    HMSD for domains           About GeneDecksing

    2 InterPro domains/families:
     IPR000215 Serpin_fam
     IPR023796 Serpin_dom

    Graphical View of Domain Structure for InterPro Entry P0C7T4
    Graphical View of Domain Structure for InterPro Entry A8MTL9

    ProtoNet protein and cluster: P0C7T4

    UniProtKB/Swiss-Prot: HMSD_HUMAN, A8MTL9
    Similarity: Belongs to the serpin family


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: HMSDV_HUMAN, P0C7T4
    Function: This allelic splice variant of HMSD is the precursor of the histocompatibility antigen ACC-6. More generally,
    minor histocompatibility antigens (mHags) refer to immunogenic peptide which, when complexed with MHC, can generate an
    immune response after recognition by specific T-cells. The peptides are derived from polymorphic intracellular
    proteins, which are cleaved by normal pathways of antigen processing. The binding of these peptides to MHC class I or
    class II molecules and its expression on the cell surface can stimulate T-cell responses and thereby trigger graft
    rejection or graft-versus-host disease (GVHD) after hematopoietic stem cell transplantation from HLA-identical sibling
    donor. GVHD is a frequent complication after bone marrow transplantation (BMT), due to mismatch of minor
    histocompatibility antigen in HLA-matched sibling marrow transplants. However, associated with GVHD, a favorable
    graft-versus-leukemia (GVL) can be induced by donor-recipient disparities in mHags. ACC-6 is presented to the cell
    surface by MHC HLA-B*4403. This complex specifically elicits donor-cytotoxic T-lymphocyte (CTL) reactivity against
    hematologic malignancies after treatment by HLA-identical allogenic BMT. It induces cell recognition and lysis by CTL.
    Immunogenicity of most autosomal mHags results from single-nucleotide polymorphisms that cause amino-acid
    substitutions within epitopes, leading to the differential recognition of peptides between donor and recipient

         UniProtKB/Swiss-Prot: HMSD_HUMAN, A8MTL9
    Function: Putative serine protease inhibitor (By similarity)

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    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004867serine-type endopeptidase inhibitor activity IEA--


    HMSD for ontologies           About GeneDecksing



    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for HMSD

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for HMSD
    Search CenterWatch for drugs/clinical trials and news about HMSD 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for HMSD gene: 
    NM_001123366.1  

    Unigene Cluster for HMSD:

    Histocompatibility (minor) serpin domain containing
    Hs.721604  [show with all ESTs]
    Unigene Representative Sequence: BM910193
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000408945(uc010dqj.3) ENST00000481726 ENST00000526932 ENST00000498680


    miRNA
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    Inhib. RNA
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat HMSD
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat HMSD

    1 DOTS entry:

    DT.75174437 

    24/66 AceView cDNA sequences (see all 66):

    AL711105 AA972628 NM_198833 BM696260 CK904587 AA360401 CK904586 NM_002640 
    CB122815 BC034528 CF130399 BP364026 AF118928 CA445967 L40377 BM987817 
    AL597104 BX571754 BQ435307 AL708543 CB151896 BM991416 AI767324 CD369662 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    HMSD expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GGGGCAAAGG

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image

    HMSD expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    Pancreatic endoderm/endocrine precursor-like cells (A scalable, suspensi...)
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See HMSD Protein Expression from SPIRE MOPED and PaxDB
    SOURCE GeneReport for Unigene cluster: Hs.721604

    UniProtKB/Swiss-Prot: HMSDV_HUMAN, P0C7T4
    Tissue specificity: Highly expressed in dendritic cells and primary leukemia cells, especially those of myeloid
    lineage. ACC-6 expression is limited to cells of the hematopoietic lineage

    UniProtKB/Swiss-Prot: HMSD_HUMAN, A8MTL9
    Tissue specificity: Highly expressed in dendritic cells and primary leukemia cells, especially those of myeloid lineage

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    In Situ
    Assay Products:
     

     
    Search Advanced Cell Diagnostics for RNAscope RNA in situ hybridization assays for HMSD

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section
      --

    ENSEMBL Gene Tree for HMSD (if available)
    TreeFam Gene Tree for HMSD (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
      --

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    UniProtKB/Swiss-Prot: HMSD_HUMAN, A8MTL9
    Polymorphism: Minor histocompatibility antigen ACC-6 (mHA ACC-6) is encoded by HMSD-v which is an allelic variant of
    HMSD. HMSD-v results from an intronic single-nucleotide polymorphism located at position 5 of HMSD intron 2 leading to
    a G to A substitution. This variation in intron 2 induces skipping of exon 2 and frameshift, resulting in expression
    of ACC-6
    Polymorphism: Minor histocompatibility antigen ACC-6 (mHA ACC-6) is encoded by HMSD-v which is an allelic variant of
    HMSD. HMSD-v results from an intronic single-nucleotide polymorphism located at position 5 of HMSD intron 2 leading to
    a G to A substitution. This variation in intron 2 induces skipping of exon 2 and frameshift, resulting in expression
    of ACC-6


    10/245 NCBI SNPs in HMSD are shown (see all 245    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 18 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs794371921,2
    F,--58316025(+) CAAATT/CTGATA 1 -- us2k11Minor allele frequency- C:0.04WA 118
    rs797256091,2
    --58316093(+) AGGAAA/GTAGAA 1 -- us2k12Minor allele frequency- G:0.19CSA WA 120
    rs751428861,2
    F,--58316141(+) AATAAT/ATAATA 1 -- us2k11Minor allele frequency- A:0.03WA 118
    rs745690671,2
    F,--58316362(+) CATTAG/ATATAG 1 -- us2k11Minor allele frequency- A:0.12WA 118
    rs793199291,2
    F,--58316446(+) CTAAGT/CAAGAT 1 -- us2k11Minor allele frequency- C:0.03WA 118
    rs734821291,2
    C,--58316607(+) ATTCAC/TCCGGG 1 -- us2k11Minor allele frequency- T:0.50WA 2
    rs1127269591,2
    C,--58316628(+) TGATTC/-AATAT 1 -- us2k11Minor allele frequency- -:0.50CSA 2
    rs756888191,2
    F,--58316815(+) AAAACC/TCACTG 1 -- us2k11Minor allele frequency- T:0.03WA 118
    rs789060761,2
    C,--58316879(+) ACAAGA/GCAAGG 1 -- us2k12Minor allele frequency- G:0.15WA 120
    rs774673741,2
    F,--58317463(+) GAACCA/GCGAAA 1 -- us2k11Minor allele frequency- G:0.07WA 118

    HapMap Linkage Disequilibrium report for HMSD (61616535 - 61649008 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 2 variations for HMSD
         2 CNVs: 88880 67377
    Human Gene Mutation Database (HGMD): HMSD

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing HMSD
    DNA2.0 Custom Variant and Variant Library Synthesis for HMSD

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    HMSD for disorders           About GeneDecksing

    OMIM gene information: 612086    OMIM disorders: --

    2 diseases for HMSD:    About MalaCards
    graft versus host disease    leukemia


    Export disorders for HMSD gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for HMSD gene integrated from 9 sources:
    (articles sorted by number of sources associating them with HMSD)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Alternative splicing due to an intronic SNP in HMSD generates a novel minor histocompatibility antigen. (PubMed id 17409267)1, 2, 3 Kawase T.... Takahashi T. (2007)
    2. DNA sequence and analysis of human chromosome 18. (PubMed id 16177791)1, 2 Nusbaum C.... Lander E.S. (2005)
    3. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1, 2 Bonaldo M.F.... Soares M.B. (1996)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 284293 HGNC: 23037 AceView: SERPINB8 Ensembl:ENSG00000221887 euGenes: HUgn284293
    ECgene: HMSD H-InvDB: HMSD

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for HMSD Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for HMSD gene:
    Search GeneIP for patents involving HMSD

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences),
    In Situ Hybridization Assays from
    Advanced Cell Diagnostics
    About This Section

     
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    GeneCards Homepage - Last full update: 19 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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    VWF
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    von Willebrand factor
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