HMSD Gene (Protein Coding)

Histocompatibility Minor Serpin Domain Containing

GC18P063949
GIFtS:
27
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] See more...

Aliases for HMSD Gene

Aliases for HMSD Gene

  • Histocompatibility Minor Serpin Domain Containing 2 3 5
  • Minor Histocompatibility Protein HMSD 3 4
  • Serpin-Like Protein HMSD 3 4
  • C18orf53 3 4
  • HSMD-V 3 4
  • ACC-6 2 3
  • ACC6 2 3
  • Minor Histocompatibility Serpin Domain-Containing Protein 4
  • Histocompatibility (Minor) Serpin Domain Containing 2
  • Minor Histocompatibility Protein HMSD Variant Form 4
  • HMSD 5

External Ids for HMSD Gene

Previous HGNC Symbols for HMSD Gene

  • C18orf53

Previous GeneCards Identifiers for HMSD Gene

  • GC18P059768
  • GC18P061616
  • GC18P058317

Summaries for HMSD Gene

Entrez Gene Summary for HMSD Gene

  • 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]

GeneCards Summary for HMSD Gene

HMSD (Histocompatibility Minor Serpin Domain Containing) is a Protein Coding gene. Diseases associated with HMSD include Pneumonic Plague and Bubonic Plague. Gene Ontology (GO) annotations related to this gene include serine-type endopeptidase inhibitor activity. An important paralog of this gene is SERPINB6.

UniProtKB/Swiss-Prot Summary for HMSD Gene

  • 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.
  • Putative serine protease inhibitor.

Additional gene information for HMSD Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for HMSD Gene

Genomics for HMSD Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for HMSD Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH18J063948 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE CraniofacialAtlas 250.7 +0.4 395 1.9 BCL11A POLR2A CTCF VEZF1 EBF1 GABPB1 SMARCA5 SP2 CBFB ZNF189 HMSD SERPINB8 SERPINB10 HSALNG0122075
GH18J063950 Enhancer 0.2 Ensembl 250.7 +1.6 1642 0.2 HMSD HSALNG0122075 SERPINB8
GH18J063979 Promoter/Enhancer 1.1 Ensembl ENCODE dbSUPER 5.5 +30.6 30586 0.9 CTCF TRIM22 SMC3 RAD21 TEAD3 SPI1 ZFP37 ELF1 ZNF143 ELF3 HSALNG0122078 SERPINB8 SERPINB10 HMSD NONHSAG024062.2
GH18J063968 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 0.3 +21.4 21416 3.4 ZBTB10 CEBPA ETS1 POLR2A ZIC2 THAP11 CEBPB SIN3A ELK1 GABPA SERPINB8 ENSG00000283667 LOC105372165 SERPINB10 HMSD
GH18J063935 Promoter/Enhancer 1.3 ENCODE CraniofacialAtlas dbSUPER 0.4 -12.8 -12816 1.4 ZBTB10 CTCF ELF1 IRF4 TRIM22 EBF1 SMC3 GABPB1 RAD21 YY1 HSALNG0122074 SERPINB10 SERPINB8 piR-48759-147 HMSD
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HMSD on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for HMSD

Top Transcription factor binding sites by QIAGEN in the HMSD gene promoter:
  • aMEF-2
  • FOXL1
  • FOXO3
  • FOXO3a
  • FOXO3b
  • LCR-F1
  • MEF-2A
  • POU2F1
  • POU2F1a
  • POU3F1

Genomic Locations for HMSD Gene

Latest Assembly
chr18:63,949,259-63,981,774
(GRCh38/hg38)
Size:
32,516 bases
Orientation:
Plus strand

Previous Assembly
chr18:61,616,535-61,629,069
(GRCh37/hg19 by Entrez Gene)
Size:
12,535 bases
Orientation:
Plus strand

chr18:61,616,535-61,649,008
(GRCh37/hg19 by Ensembl)
Size:
32,474 bases
Orientation:
Plus strand

Genomic View for HMSD Gene

Genes around HMSD on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HMSD Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HMSD Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for HMSD Gene

Proteins for HMSD Gene

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  1. Antibodies for research
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  • Protein details for HMSD Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P0C7T4-HMSDV_HUMAN
    Recommended name:
    Minor histocompatibility protein HMSD variant form
    Protein Accession:
    P0C7T4

    Protein attributes for HMSD Gene

    Size:
    53 amino acids
    Molecular mass:
    6023 Da
    Quaternary structure:
    • ACC-6 forms a complex with MHC HLA-B*4403.
    Miscellaneous:
    • [Isoform 2]: This alternative splicing event arises as a consequence of an intronic polymorphism.

    Alternative splice isoforms for HMSD Gene

    UniProtKB/Swiss-Prot:

  • Protein details for HMSD Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    A8MTL9-HMSD_HUMAN
    Recommended name:
    Serpin-like protein HMSD
    Protein Accession:
    A8MTL9

    Protein attributes for HMSD Gene

    Size:
    139 amino acids
    Molecular mass:
    15355 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for HMSD Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for HMSD Gene

Post-translational modifications for HMSD Gene

  • Glycosylation at Asn50
  • Modification sites at PhosphoSitePlus

Other Protein References for HMSD Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HMSD Gene

Domains & Families for HMSD Gene

Gene Families for HMSD Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for HMSD Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for HMSD Gene

GenScript: Design optimal peptide antigens:
  • Minor histocompatibility protein HMSD variant form (HMSDV_HUMAN)
  • Minor histocompatibility serpin domain-containing protein (HMSD_HUMAN)

Graphical View of Domain Structure for InterPro Entry

A8MTL9

UniProtKB/Swiss-Prot:

HMSD_HUMAN :
  • Belongs to the serpin family.
Family:
  • Belongs to the serpin family.
genes like me logo Genes that share domains with HMSD: view

Function for HMSD Gene

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  3. miRNA products for research
  4. Inhibitory RNAs for research
  5. Clone products for research
  6. Cell Lines for research

Molecular function for HMSD Gene

UniProtKB/Swiss-Prot 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 Function:
Putative serine protease inhibitor.

Phenotypes From GWAS Catalog for HMSD Gene

Gene Ontology (GO) - Molecular Function for HMSD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0004867 serine-type endopeptidase inhibitor activity IEA --
GO:0030414 peptidase inhibitor activity IEA --
genes like me logo Genes that share ontologies with HMSD: view
genes like me logo Genes that share phenotypes with HMSD: view

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HMSD

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for HMSD Gene

Localization for HMSD Gene

Subcellular locations from UniProtKB/Swiss-Prot for HMSD Gene

Secreted.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HMSD gene
Compartment Confidence
extracellular 3
plasma membrane 1
nucleus 1
cytosol 1
golgi apparatus 1
mitochondrion 0

Gene Ontology (GO) - Cellular Components for HMSD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space IEA --
genes like me logo Genes that share ontologies with HMSD: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for HMSD Gene

Pathways & Interactions for HMSD Gene

PathCards logo

SuperPathways for HMSD Gene

No Data Available

Interacting Proteins for HMSD Gene

STRING Interaction Network Preview (showing top 5 STRING interactants - click image to see top 25)
STRING Interaction Network
Selected Interacting proteins: ENSP00000386207 for HMSD Gene via STRING

GPS-Prot Interaction Network for HMSD

Gene Ontology (GO) - Biological Process for HMSD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002253 activation of immune response IMP,IDA 17409267
GO:0010466 negative regulation of peptidase activity IEA --
GO:0010951 negative regulation of endopeptidase activity IEA --
GO:0019835 cytolysis IMP --
GO:0032729 positive regulation of interferon-gamma production IMP --
genes like me logo Genes that share ontologies with HMSD: view

No data available for Pathways by source and SIGNOR curated interactions for HMSD Gene

Drugs & Compounds for HMSD Gene

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  1. Drug products for research
No Compound Related Data Available

Transcripts for HMSD Gene

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  2. miRNA products for research
  3. Inhibitory RNAs for research
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mRNA/cDNA for HMSD Gene

1 REFSEQ mRNAs :
2 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HMSD

Alternative Splicing Database (ASD) splice patterns (SP) for HMSD Gene

No ASD Table

Relevant External Links for HMSD Gene

GeneLoc Exon Structure for
HMSD

Expression for HMSD Gene

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  1. Primer products for research
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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for HMSD Gene

mRNA expression in normal human tissues for HMSD Gene
mRNA expression by GTEx for HMSD GenemRNA expression by BioGPS for HMSD Gene

mRNA differential expression in normal tissues according to GTEx for HMSD Gene

This gene is overexpressed in Brain - Spinal cord (cervical c-1) (x13.1) and Brain - Substantia nigra (x5.1).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for HMSD

SOURCE GeneReport for Unigene cluster for HMSD Gene:

Hs.721604

mRNA Expression by UniProt/SwissProt for HMSD Gene:

P0C7T4-HMSDV_HUMAN
Tissue specificity: Highly expressed in dendritic cells and primary leukemia cells, especially those of myeloid lineage.
genes like me logo Genes that share expression patterns with HMSD: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for HMSD Gene

Orthologs for HMSD Gene

This gene was present in the common ancestor of mammals.

Orthologs for HMSD Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia HMSD 30 31
  • 98.8 (n)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia HMSD 31
  • 17 (a)
 OneToOne
Species where no ortholog for HMSD was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • Cow (Bos Taurus)
  • Dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Mouse (Mus musculus)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for HMSD Gene

ENSEMBL:
Gene Tree for HMSD (if available)
TreeFam:
Gene Tree for HMSD (if available)
Aminode:
Evolutionary constrained regions (ECRs) for HMSD: view image

Paralogs for HMSD Gene

Variants for HMSD Gene

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  1. SNP Genotyping and Copy Number Assays for research

Polymorphic Variants from UniProtKB/Swiss-Prot for HMSD Gene

HMSDV_HUMAN-P0C7T4
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.
HMSD_HUMAN-A8MTL9
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.

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for HMSD Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for HMSD Gene

Variant ID Type Subtype PubMed ID
esv21739 CNV gain 19812545
esv3642785 CNV gain 21293372
esv3642788 CNV gain 21293372
nsv1066552 CNV gain 25217958
nsv1067311 CNV loss 25217958
nsv833673 CNV gain 17160897

Variation tolerance for HMSD Gene

Residual Variation Intolerance Score: 63.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.00; 20.57% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HMSD Gene

Human Gene Mutation Database (HGMD)
HMSD
SNPedia medical, phenotypic, and genealogical associations of SNPs for
HMSD

SNP Genotyping and Copy Number Assays for research

No data available for Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for HMSD Gene

Disorders for HMSD Gene

MalaCards: The human disease database

(7) MalaCards diseases for HMSD Gene - From: COP

Disorder Aliases PubMed IDs
pneumonic plague
  • primary pneumonic plague
bubonic plague
  • black death
plague
  • yersiniosis
otopalatodigital syndrome, type ii
  • opd2
non-secretory myeloma
- elite association - COSMIC cancer census association via MalaCards
Search HMSD in MalaCards View complete list of genes associated with diseases

Additional Disease Information for HMSD

Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with HMSD: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HMSD Gene

Publications for HMSD Gene

  1. Alternative splicing due to an intronic SNP in HMSD generates a novel minor histocompatibility antigen. (PMID: 17409267) Kawase T … Takahashi T (Blood 2007) 2 3 4
  2. DNA sequence and analysis of human chromosome 18. (PMID: 16177791) Nusbaum C … Lander ES (Nature 2005) 3 4
  3. Normalization and subtraction: two approaches to facilitate gene discovery. (PMID: 8889548) Bonaldo MF … Soares MB (Genome research 1996) 3 4
  4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. (PMID: 21873635) Gaudet P … Thomas PD (Briefings in bioinformatics 2011) 3

ExternalLinks

View latest publications for HMSD gene in Mastermind

Products for HMSD Gene

Sources for HMSD Gene