Aliases for MYSM1 Gene

Aliases for MYSM1 Gene

  • Myb Like, SWIRM And MPN Domains 1 2 3 5
  • Myb-Like, SWIRM And MPN Domain-Containing Protein 1 3 4
  • Histone H2A Deubiquitinase MYSM1 3 4
  • 2A-DUB 3 4
  • Myb-Like, SWIRM And MPN Domains 1 2
  • HSALNG0003947 167
  • NONHSAG001617 92
  • Lnc-TACSTD2-2 168
  • EC 3.1.2.15 52
  • EC 3.4.19.- 4
  • Lnc-JUN-11 168
  • KIAA1915 4
  • 2ADUB 3
  • BMFS4 3

External Ids for MYSM1 Gene

Previous GeneCards Identifiers for MYSM1 Gene

  • GC01M058833
  • GC01M058892
  • GC01M059120
  • GC01M057235

Summaries for MYSM1 Gene

GeneCards Summary for MYSM1 Gene

MYSM1 (Myb Like, SWIRM And MPN Domains 1) is a Protein Coding gene. Diseases associated with MYSM1 include Bone Marrow Failure Syndrome 4 and Congenital Progressive Bone Marrow Failure-B-Cell Immunodeficiency-Skeletal Dysplasia Syndrome. Among its related pathways are Metabolism of proteins and Deubiquitination. Gene Ontology (GO) annotations related to this gene include chromatin binding. An important paralog of this gene is SMARCC1.

UniProtKB/Swiss-Prot Summary for MYSM1 Gene

  • Metalloprotease that specifically deubiquitinates monoubiquitinated histone H2A, a specific tag for epigenetic transcriptional repression, thereby acting as a coactivator. Preferentially deubiquitinates monoubiquitinated H2A in hyperacetylated nucleosomes. Deubiquitination of histone H2A leads to facilitate the phosphorylation and dissociation of histone H1 from the nucleosome. Acts as a coactivator by participating in the initiation and elongation steps of androgen receptor (AR)-induced gene activation. Required for correct regulation of hematopoiesis and lymphocyte differentiation (PubMed:28115216, PubMed:26220525).

Additional gene information for MYSM1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for MYSM1 Gene

Genomics for MYSM1 Gene

GeneHancer (GH) Regulatory Elements for MYSM1 Gene

Promoters and enhancers for MYSM1 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
GH01J058698 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 508 +0.4 391 2.6 FOXK2 ZNF217 EP300 CTCF USF1 POLR2G SP1 GTF2E2 PHF8 ZNF639 MYSM1 lnc-JUN-10 ENSG00000272226 DAB1 OMA1 AK2P1
GH01J058779 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 21.2 -83.1 -83069 8 EP300 ZBTB40 CTCF TCF12 ZSCAN5C SIN3A NRF1 POLR2G SP1 NCOR1 LINC01135 JUN MYSM1 ENSG00000272226 FGGY LOC105378751
GH01J059153 Enhancer 0.7 Ensembl 47.1 -453.6 -453609 0.6 RBAK ZNF510 ZNF341 ZNF266 ZBTB11 ZNF426 OVOL3 ZNF213 ZNF664 ZNF34 MYSM1 ENSG00000224609 JUN LINC01135 FGGY HSD52 piR-33432-012 LINC01358
GH01J059498 Enhancer 1 Ensembl ENCODE 16.4 -800.1 -800109 5.6 EP300 ZSCAN5C TRIM28 TEAD1 ATF2 ZNF341 FOXA2 OSR2 ZNF266 ZNF316 MYSM1 piR-36573-002 piR-57176-029 FGGY
GH01J058921 Enhancer 1.1 Ensembl ENCODE dbSUPER 14.3 -221.6 -221610 5.8 TRIM28 MCM3 RBM25 NFIC GATA3 TRIM24 SRF NR3C1 NBN SPI1 LINC01135 MYSM1 JUN FGGY LINC01358 piR-35650 lnc-JUN-12 LINC02777
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around MYSM1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for MYSM1

Top Transcription factor binding sites by QIAGEN in the MYSM1 gene promoter:
  • aMEF-2
  • FOXJ2
  • FOXJ2 (long isoform)
  • FOXL1
  • HNF-1
  • HNF-1A
  • MEF-2A
  • TBP
  • TFIID
  • TGIF

Genomic Locations for MYSM1 Gene

Genomic Locations for MYSM1 Gene
chr1:58,643,440-58,700,092
(GRCh38/hg38)
Size:
56,653 bases
Orientation:
Minus strand
chr1:59,120,411-59,165,764
(GRCh37/hg19)
Size:
45,354 bases
Orientation:
Minus strand

Genomic View for MYSM1 Gene

Genes around MYSM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
MYSM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for MYSM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for MYSM1 Gene

Proteins for MYSM1 Gene

  • Protein details for MYSM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5VVJ2-MYSM1_HUMAN
    Recommended name:
    Histone H2A deubiquitinase MYSM1
    Protein Accession:
    Q5VVJ2
    Secondary Accessions:
    • A8KA54
    • B3KX65
    • Q68DD3
    • Q6AI53
    • Q7Z3G8
    • Q96PX3

    Protein attributes for MYSM1 Gene

    Size:
    828 amino acids
    Molecular mass:
    95032 Da
    Quaternary structure:
    • Component of a large chromatin remodeling complex, at least composed of MYSM1, PCAF, RBM10 and KIF11/TRIP5. Binds histones.
    SequenceCaution:
    • Sequence=BAB67808.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAG54377.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for MYSM1 Gene

    Alternative splice isoforms for MYSM1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for MYSM1 Gene

Selected DME Specific Peptides for MYSM1 Gene

Q5VVJ2:
  • NCGDVNCIGRIH
  • RLQSMRTR
  • IGAINFGCE
  • DPFQLIPC
  • FIGMIVSPYN
  • KTRWIIEKYR
  • WGNWCDAKDLEGQT
  • RDIDTQAKYQ
  • QCEMDPVSQTQASE
  • LTCLQKLL
  • RTVLQVKSYA
  • KTPERYLKIRN

Post-translational modifications for MYSM1 Gene

  • Ubiquitination at Lys675, Lys84, Lys90, and Lys135
  • Modification sites at PhosphoSitePlus

Domains & Families for MYSM1 Gene

Gene Families for MYSM1 Gene

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

Protein Domains for MYSM1 Gene

Blocks:
  • Mov34 family
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for MYSM1 Gene

GenScript: Design optimal peptide antigens:
  • Myb-like, SWIRM and MPN domain-containing protein 1 (MYSM1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q5VVJ2

UniProtKB/Swiss-Prot:

MYSM1_HUMAN :
  • Binds double-stranded DNA via the SANT domain. The SWIRM domain does not bind double-stranded DNA.
  • Belongs to the peptidase M67A family. MYSM1 subfamily.
Domain:
  • Binds double-stranded DNA via the SANT domain. The SWIRM domain does not bind double-stranded DNA.
Family:
  • Belongs to the peptidase M67A family. MYSM1 subfamily.
genes like me logo Genes that share domains with MYSM1: view

Function for MYSM1 Gene

Molecular function for MYSM1 Gene

UniProtKB/Swiss-Prot Function:
Metalloprotease that specifically deubiquitinates monoubiquitinated histone H2A, a specific tag for epigenetic transcriptional repression, thereby acting as a coactivator. Preferentially deubiquitinates monoubiquitinated H2A in hyperacetylated nucleosomes. Deubiquitination of histone H2A leads to facilitate the phosphorylation and dissociation of histone H1 from the nucleosome. Acts as a coactivator by participating in the initiation and elongation steps of androgen receptor (AR)-induced gene activation. Required for correct regulation of hematopoiesis and lymphocyte differentiation (PubMed:28115216, PubMed:26220525).

Enzyme Numbers (IUBMB) for MYSM1 Gene

Phenotypes From GWAS Catalog for MYSM1 Gene

Gene Ontology (GO) - Molecular Function for MYSM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISM 19274049
GO:0003677 DNA binding IEA --
GO:0003713 transcription coactivator activity IDA,IBA 17707232
GO:0004843 thiol-dependent ubiquitin-specific protease activity IDA,IBA 17707232
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with MYSM1: view
genes like me logo Genes that share phenotypes with MYSM1: view

Human Phenotype Ontology for MYSM1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for MYSM1 Gene

MGI Knock Outs for MYSM1:
  • Mysm1 Mysm1<tm1a(KOMP)Wtsi>
  • Mysm1 Mysm1<tm1b(KOMP)Wtsi>

Animal Model Products

CRISPR Products

miRNA for MYSM1 Gene

Clone Products

No data available for Transcription Factor Targets and HOMER Transcription for MYSM1 Gene

Localization for MYSM1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for MYSM1 Gene

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 MYSM1 gene
Compartment Confidence
nucleus 5
plasma membrane 4
cytoskeleton 2
cytosol 2
extracellular 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Plasma membrane (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for MYSM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 17707232
GO:0005654 nucleoplasm TAS --
GO:0005886 plasma membrane IDA --
GO:0016514 SWI/SNF complex IBA 21873635
GO:0032991 protein-containing complex IPI 17707232
genes like me logo Genes that share ontologies with MYSM1: view

Pathways & Interactions for MYSM1 Gene

genes like me logo Genes that share pathways with MYSM1: view

Pathways by source for MYSM1 Gene

Gene Ontology (GO) - Biological Process for MYSM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization IEA --
GO:0006338 chromatin remodeling IMP 17707232
GO:0006508 proteolysis IEA --
GO:0016579 protein deubiquitination TAS --
GO:0030334 regulation of cell migration IEA --
genes like me logo Genes that share ontologies with MYSM1: view

No data available for SIGNOR curated interactions for MYSM1 Gene

Drugs & Compounds for MYSM1 Gene

No Compound Related Data Available

Transcripts for MYSM1 Gene

mRNA/cDNA for MYSM1 Gene

1 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :
7 RNACentral transcripts :
4 NONCODE transcripts :
3 LncBook transcripts :
5 LNCipedia transcripts :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for MYSM1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17a · 17b
SP1: -
SP2: - -
SP3:

Relevant External Links for MYSM1 Gene

GeneLoc Exon Structure for
MYSM1

Expression for MYSM1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for MYSM1 Gene

Protein differential expression in normal tissues from HIPED for MYSM1 Gene

This gene is overexpressed in Liver (31.0), Pancreatic juice (26.3), and Blymphocyte (9.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for MYSM1 Gene



Protein tissue co-expression partners for MYSM1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for MYSM1

SOURCE GeneReport for Unigene cluster for MYSM1 Gene:

Hs.744921

Evidence on tissue expression from TISSUES for MYSM1 Gene

  • Nervous system(4.4)
  • Skin(4.3)
  • Liver(4.2)
  • Heart(2.1)
genes like me logo Genes that share expression patterns with MYSM1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for MYSM1 Gene

Orthologs for MYSM1 Gene

This gene was present in the common ancestor of animals.

Orthologs for MYSM1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia MYSM1 31 30
  • 99.56 (n)
OneToOne
dog
(Canis familiaris)
Mammalia MYSM1 31 30
  • 90.66 (n)
OneToOne
cow
(Bos Taurus)
Mammalia MYSM1 31 30
  • 90.45 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Mysm1 17 31 30
  • 85.48 (n)
rat
(Rattus norvegicus)
Mammalia Mysm1 30
  • 85.04 (n)
oppossum
(Monodelphis domestica)
Mammalia MYSM1 31
  • 72 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 22 (a)
ManyToMany
chicken
(Gallus gallus)
Aves MYSM1 31 30
  • 73.89 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia MYSM1 31
  • 69 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia mysm1 30
  • 57.41 (n)
Str.13159 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.3062 30
zebrafish
(Danio rerio)
Actinopterygii mysm1 31 30
  • 60.02 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG4751 31
  • 2 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 23 (a)
ManyToMany
-- 31
  • 17 (a)
ManyToMany
Species where no ortholog for MYSM1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for MYSM1 Gene

ENSEMBL:
Gene Tree for MYSM1 (if available)
TreeFam:
Gene Tree for MYSM1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for MYSM1: view image

Paralogs for MYSM1 Gene

Paralogs for MYSM1 Gene

genes like me logo Genes that share paralogs with MYSM1: view

Variants for MYSM1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for MYSM1 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs1557507208 Pathogenic: BONE MARROW FAILURE SYNDROME 4 58,667,102(-) T/C MISSENSE_VARIANT
rs1557518298 Pathogenic: BONE MARROW FAILURE SYNDROME 4 58,681,876(-) C/A NONSENSE
VAR_081185 Bone marrow failure syndrome 4 (BMFS4) [MIM:618116] p.His656Arg
rs12139511 - p.Thr264Ala
rs17118103 - p.Cys200Ser

Additional dbSNP identifiers (rs#s) for MYSM1 Gene

Structural Variations from Database of Genomic Variants (DGV) for MYSM1 Gene

Variant ID Type Subtype PubMed ID
dgv41n67 CNV gain 20364138
dgv42n67 CNV gain 20364138
dgv43n67 CNV gain 20364138
nsv1003930 CNV gain 25217958
nsv819698 CNV gain 19587683
nsv820181 CNV loss 19587683

Variation tolerance for MYSM1 Gene

Residual Variation Intolerance Score: 35% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.68; 91.46% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for MYSM1 Gene

Human Gene Mutation Database (HGMD)
MYSM1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
MYSM1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for MYSM1 Gene

Disorders for MYSM1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for MYSM1 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, Orphanet, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search MYSM1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

MYSM1_HUMAN
  • Bone marrow failure syndrome 4 (BMFS4) [MIM:618116]: A form of bone marrow failure syndrome, a heterogeneous group of life-threatening disorders characterized by hematopoietic defects in association with a range of variable extra hematopoietic features. BMFS4 is characterized by early-onset anemia, leukopenia, decreased B cells, and developmental aberrations including facial dysmorphism, mild skeletal anomalies, and neurodevelopmental delay. BMFS4 inheritance is autosomal recessive. {ECO:0000269 PubMed:24288411, ECO:0000269 PubMed:26220525, ECO:0000269 PubMed:28115216}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for MYSM1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with MYSM1: view

No data available for Genatlas for MYSM1 Gene

Publications for MYSM1 Gene

  1. Structural and functional differences of SWIRM domain subtypes. (PMID: 17428495) Yoneyama M … Yokoyama S (Journal of molecular biology 2007) 2 3 4 23 54
  2. A histone H2A deubiquitinase complex coordinating histone acetylation and H1 dissociation in transcriptional regulation. (PMID: 17707232) Zhu P … Rosenfeld MG (Molecular cell 2007) 2 3 4 54
  3. Prediction of the coding sequences of unidentified human genes. XXI. The complete sequences of 60 new cDNA clones from brain which code for large proteins. (PMID: 11572484) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2001) 2 3 4 54
  4. Myb-like, SWIRM, and MPN domains 1 (MYSM1) deficiency: Genotoxic stress-associated bone marrow failure and developmental aberrations. (PMID: 28115216) Bahrami E … Klein C (The Journal of allergy and clinical immunology 2017) 3 4 54
  5. An in vivo genetic reversion highlights the crucial role of Myb-Like, SWIRM, and MPN domains 1 (MYSM1) in human hematopoiesis and lymphocyte differentiation. (PMID: 26220525) Le Guen T … Revy P (The Journal of allergy and clinical immunology 2015) 3 4 54

Products for MYSM1 Gene

Sources for MYSM1 Gene