Free for academic non-profit institutions. Other users need a Commercial license

HMSD Gene(Protein Coding)

Histocompatibility Minor Serpin Domain Containing

GCID:
GC18P063949
GIFtS:
42
Genes Participants
UDN Logo

Aliases for HMSD Gene

Aliases for HMSD Gene

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

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 Plague. GO annotations related to this gene include serine-type endopeptidase inhibitor activity.

UniProtKB/Swiss-Prot 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.

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HMSD Gene

Genomics for HMSD Gene

Products:

  1. Regulatory Element

Regulatory Elements for HMSD Gene

Enhancers for HMSD Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH18G063948 0.8 ENCODE 0.7 0.0 -36 1.0 HDGF TBP CTCF RAD21 ZBTB40 RELA GLIS2 ARID3A POLR2A EED SERPINB10 HMSD
GH18G063935 1.4 Ensembl ENCODE dbSUPER 0.4 -12.7 -12677 1.7 ELF3 RAD21 GLIS2 GATA2 SCRT2 ZNF143 FOS ETV6 CREM ZNF263 SERPINB10 SERPINB8 HMSD
GH18G063908 1.1 FANTOM5 Ensembl dbSUPER 0.3 -40.4 -40350 0.6 PKNOX1 JUNB CREM RELA SERPINB10 SERPINB2 SERPINB8 VPS4B HMSD
GH18G063963 0.7 ENCODE 0.4 +14.6 14572 0.2 CTCF PKNOX1 TRIM22 RAD21 FOXA1 JUND GATA3 HNF4G SMC3 ZNF143 SERPINB10 SERPINB8 HMSD
GH18G063927 0.6 dbSUPER 0.4 -19.3 -19347 4.2 MAFF PRDM6 IRF2 ZNF239 IRF1 ZNF843 MAFK EZH2 SERPINB10 SERPINB8 HMSD
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HMSD on UCSC Golden Path with GeneCards custom track

Promoters for HMSD Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000104574 150 800 HDGF CTCF RAD21 RELA ARID3A POLR2A EED SCRT2 RELB ETV6

Transcription factor binding sites by QIAGEN in the HMSD gene promoter:

Genomic Location for HMSD Gene

Chromosome:
18
Start:
63,949,250 bp from pter
End:
63,981,774 bp from pter
Size:
32,525 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

Products:

  1. Antibody
  2. Protein
  3. Assay

  • 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:

  • 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.

    Alternative splice isoforms for HMSD Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for HMSD Gene

Post-translational modifications for HMSD Gene

  • Glycosylation at posLast=5050
  • 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:

Protein Domains for HMSD Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for HMSD Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

A8MTL9

UniProtKB/Swiss-Prot:

HMSDV_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

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

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.

Gene Ontology (GO) - Molecular Function for HMSD Gene

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

Phenotypes for HMSD Gene

GenomeRNAi human phenotypes for HMSD:
genes like me logo Genes that share phenotypes with HMSD: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

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 4
plasma membrane 1
mitochondrion 1
nucleus 1
cytosol 1

Gene Ontology (GO) - Cellular Components for HMSD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space IBA,IEA --
GO:0005737 cytoplasm IBA --
genes like me logo Genes that share ontologies with HMSD: view

Pathways & Interactions for HMSD Gene

SuperPathways for HMSD Gene

PathCards logo More details on SuperPathways for HMSD
No Data Available

Interacting Proteins for HMSD Gene

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)
http://string-db.org/version_10/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000386207%0d%0a9606.ENSP00000348639%0d%0a9606.ENSP00000306390%0d%0a9606.ENSP00000348170%0d%0a9606.ENSP00000372224%0d%0a9606.ENSP00000375683%0d%0a
Selected Interacting proteins: ENSP00000386207 for HMSD Gene via STRING

Gene Ontology (GO) - Biological Process for HMSD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0010466 negative regulation of peptidase activity IEA --
GO:0010951 negative regulation of endopeptidase activity IEA --
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

Products:

  1. Drug
No Compound Related Data Available

Transcripts for HMSD Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for HMSD Gene

(3) REFSEQ mRNAs :
(0) Additional mRNA sequences :
-
(66) Selected AceView cDNA sequences:
(4) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for HMSD Gene

Histocompatibility (minor) serpin domain containing:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

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

No ASD Table

Relevant External Links for HMSD Gene

GeneLoc Exon Structure for
HMSD
ECgene alternative splicing isoforms for
HMSD

Expression for HMSD Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HMSD Gene

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

NURSA nuclear receptor signaling pathways regulating expression of HMSD Gene:

HMSD

SOURCE GeneReport for Unigene cluster for HMSD Gene:

Hs.721604

mRNA Expression by UniProt/SwissProt for HMSD Gene:

A8MTL9-HMSD_HUMAN
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.
genes like me logo Genes that share expression patterns with HMSD: view

Primer Products

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 34 35
  • 98.8 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia HMSD 35
  • 17 (a)
 OneToOne
Species where no ortholog for HMSD was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 squirt (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)

Paralogs for HMSD Gene

(15) SIMAP similar genes for HMSD Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with HMSD: view

No data available for Paralogs for HMSD Gene

Variants for HMSD Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for HMSD Gene

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.
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.

Sequence variations from dbSNP and Humsavar for HMSD Gene

SNP ID Clin Chr 18 pos Sequence Context AA Info Type
rs1000161655 -- 63,961,354(+) ATATT(G/T)TTCCT intron-variant
rs1000220067 -- 63,960,027(+) ATTCC(A/T)CATCT intron-variant
rs1000236114 -- 63,966,413(+) TGGGA(A/G)AACTG intron-variant, nc-transcript-variant
rs1000274470 -- 63,948,466(+) CTAAT(-/ATC)ATACT upstream-variant-2KB
rs1000380111 -- 63,954,235(+) GGCAT(A/G)GGTAG intron-variant

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)

Relevant External Links for HMSD Gene

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

Disorders for HMSD Gene

MalaCards: The human disease database

(1) MalaCards diseases for HMSD Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
plague
  • yersiniosis
- elite association - COSMIC cancer census association via MalaCards
Search HMSD in MalaCards View complete list of genes associated with diseases

Relevant External Links for HMSD

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HMSD
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 64
  2. DNA sequence and analysis of human chromosome 18. (PMID: 16177791) Nusbaum C. … Lander E.S. (Nature 2005) 3 4 64
  3. Normalization and subtraction: two approaches to facilitate gene discovery. (PMID: 8889548) Bonaldo M.F. … Soares M.B. (Genome Res. 1996) 3 4 64

Products for HMSD Gene

Sources for HMSD Gene

Content
Loading form....