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Aliases for MSH4 Gene

Aliases for MSH4 Gene

  • MutS Homolog 4 2 3 5
  • HMSH4 3 4
  • MutS (E. Coli) Homolog 4 2
  • MutS Homolog 4 (E. Coli) 2
  • MutS Protein Homolog 4 3

External Ids for MSH4 Gene

Previous GeneCards Identifiers for MSH4 Gene

  • GC01P076382
  • GC01P075197
  • GC01P075678
  • GC01P075685
  • GC01P075974
  • GC01P076035
  • GC01P076262
  • GC01P074392

Summaries for MSH4 Gene

Entrez Gene Summary for MSH4 Gene

  • This gene encodes a member of the DNA mismatch repair mutS family. This member is a meiosis-specific protein that is not involved in DNA mismatch correction, but is required for reciprocal recombination and proper segregation of homologous chromosomes at meiosis I. This protein and MSH5 form a heterodimer which binds uniquely to a Holliday Junction and its developmental progenitor, thus provoking ADP-ATP exchange, and stabilizing the interaction between parental chromosomes during meiosis double-stranded break repair. [provided by RefSeq, Aug 2011]

GeneCards Summary for MSH4 Gene

MSH4 (MutS Homolog 4) is a Protein Coding gene. Diseases associated with MSH4 include Neurilemmomatosis. Among its related pathways are Cell Cycle, Mitotic and Meiosis. Gene Ontology (GO) annotations related to this gene include damaged DNA binding and mismatched DNA binding.

UniProtKB/Swiss-Prot for MSH4 Gene

  • Involved in meiotic recombination. Required for reciprocal recombination and proper segregation of homologous chromosomes at meiosis.

Gene Wiki entry for MSH4 Gene

Additional gene information for MSH4 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for MSH4 Gene

Genomics for MSH4 Gene

GeneHancer (GH) Regulatory Elements for MSH4 Gene

Promoters and enhancers for MSH4 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J075797 Promoter/Enhancer 1.3 EPDnew ENCODE 650.7 0.0 -34 0.1 HDAC1 HDGF HNRNPUL1 FUS RB1 ARNT SIN3A STAT5A ZNF48 POLR2B MSH4 SNORD45B
GH01J075796 Enhancer 0.8 ENCODE 650.7 +0.2 190 0.3 HNRNPUL1 PTBP1 FUS RB1 ZNF48 POLR2B E2F8 EGR1 ZFP91 CREM MSH4 DLSTP1 GC01M075828
GH01J075784 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 22.5 -8.9 -8927 7.7 PKNOX1 FOXA2 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B RABGGTB SNORD45A SNORD45B SNORD45C GC01P075800 GC01P075799 GC01P075797 MSH4 DLSTP1 ACADM
GH01J075722 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE 11.6 -71.8 -71759 6 HDGF PKNOX1 FOXA2 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ACADM ENSG00000178193 SLC44A5 RABGGTB SNORD45A SNORD45C MSH4 DLSTP1 PIR54256
GH01J075614 Promoter/Enhancer 1.9 EPDnew FANTOM5 Ensembl ENCODE 8.9 -181.1 -181127 2.6 SIN3A ZNF2 YY1 TCF12 GLIS2 YY2 REST ZNF610 GLIS1 KDM1A SLC44A5 MSH4 GC01M075617 GC01M075599
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around MSH4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the MSH4 gene promoter:
  • AML1a
  • FOXO3b
  • FOXO3a
  • FOXO3
  • POU2F1a
  • POU2F1
  • Evi-1
  • AP-4
  • E4BP4
  • C/EBPalpha

Genomic Locations for MSH4 Gene

Genomic Locations for MSH4 Gene
116,368 bases
Plus strand
116,357 bases
Plus strand

Genomic View for MSH4 Gene

Genes around MSH4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
MSH4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for MSH4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for MSH4 Gene

Proteins for MSH4 Gene

  • Protein details for MSH4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    MutS protein homolog 4
    Protein Accession:
    Secondary Accessions:
    • Q5T4U6
    • Q8NEB3
    • Q9UNP8

    Protein attributes for MSH4 Gene

    936 amino acids
    Molecular mass:
    104756 Da
    Quaternary structure:
    • Heterooligomer of MSH4 and MSH5.

neXtProt entry for MSH4 Gene

Post-translational modifications for MSH4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for MSH4 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for MSH4 Gene

Domains & Families for MSH4 Gene

Gene Families for MSH4 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for MSH4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the DNA mismatch repair MutS family.
  • Belongs to the DNA mismatch repair MutS family.
genes like me logo Genes that share domains with MSH4: view

Function for MSH4 Gene

Molecular function for MSH4 Gene

UniProtKB/Swiss-Prot Function:
Involved in meiotic recombination. Required for reciprocal recombination and proper segregation of homologous chromosomes at meiosis.
GENATLAS Biochemistry:
yeast meiosis-specific protein (Mut S homolog 4) expressed in testis and ovary,interacting with MSH5,not involved in mismatch repair

Phenotypes From GWAS Catalog for MSH4 Gene

Gene Ontology (GO) - Molecular Function for MSH4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding TAS 9299235
GO:0003684 NOT damaged DNA binding IBA --
GO:0005515 protein binding IPI 16397227
GO:0005524 ATP binding IEA --
GO:0008094 DNA-dependent ATPase activity IBA --
genes like me logo Genes that share ontologies with MSH4: view
genes like me logo Genes that share phenotypes with MSH4: view

Animal Models for MSH4 Gene

MGI Knock Outs for MSH4:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for MSH4 Gene

Localization for MSH4 Gene

Subcellular locations from

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 MSH4 gene
Compartment Confidence
nucleus 5
cytosol 1

Gene Ontology (GO) - Cellular Components for MSH4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000228 nuclear chromosome IBA --
GO:0000793 condensed chromosome IEA --
GO:0000794 condensed nuclear chromosome IEA --
GO:0000795 synaptonemal complex IBA,IEA --
GO:0005634 nucleus IEA,TAS 9299235
genes like me logo Genes that share ontologies with MSH4: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for MSH4 Gene

Pathways & Interactions for MSH4 Gene

SuperPathway Contained pathways
1 Meiosis
2 Cell Cycle, Mitotic
genes like me logo Genes that share pathways with MSH4: view

Pathways by source for MSH4 Gene

3 Reactome pathways for MSH4 Gene

Gene Ontology (GO) - Biological Process for MSH4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001541 ovarian follicle development IEA --
GO:0006298 mismatch repair IBA --
GO:0007129 synapsis IEA --
GO:0007131 reciprocal meiotic recombination TAS 9299235
GO:0007283 spermatogenesis IEA --
genes like me logo Genes that share ontologies with MSH4: view

No data available for SIGNOR curated interactions for MSH4 Gene

Drugs & Compounds for MSH4 Gene

No Compound Related Data Available

Transcripts for MSH4 Gene

mRNA/cDNA for MSH4 Gene

(1) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(18) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for MSH4 Gene

MutS homolog 4 (E. coli):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for MSH4 Gene

No ASD Table

Relevant External Links for MSH4 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for MSH4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for MSH4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for MSH4 Gene

This gene is overexpressed in Testis (x6.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for MSH4 Gene

NURSA nuclear receptor signaling pathways regulating expression of MSH4 Gene:


SOURCE GeneReport for Unigene cluster for MSH4 Gene:


mRNA Expression by UniProt/SwissProt for MSH4 Gene:

Tissue specificity: Testis and ovary specific.

Evidence on tissue expression from TISSUES for MSH4 Gene

  • Skin(2)
genes like me logo Genes that share expression patterns with MSH4: view

No data available for Protein differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for MSH4 Gene

Orthologs for MSH4 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for MSH4 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia MSH4 34 33
  • 99.57 (n)
(Canis familiaris)
Mammalia MSH4 34 33
  • 94.04 (n)
(Bos Taurus)
Mammalia MSH4 34 33
  • 92.65 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 87 (a)
-- 34
  • 78 (a)
-- 34
  • 76 (a)
-- 34
  • 73 (a)
(Mus musculus)
Mammalia Msh4 16 34 33
  • 83.46 (n)
(Rattus norvegicus)
Mammalia Msh4 33
  • 83.06 (n)
(Monodelphis domestica)
Mammalia MSH4 34
  • 65 (a)
(Gallus gallus)
Aves MSH4 34 33
  • 74.4 (n)
(Anolis carolinensis)
Reptilia MSH4 34
  • 80 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia msh4 33
  • 74.12 (n)
(Danio rerio)
Actinopterygii msh4 34 33
  • 59.97 (n)
(Caenorhabditis elegans)
Secernentea him-14 34 35 33
  • 46.69 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes MSH4 34 33
  • 48.83 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F11022g 33
  • 47.05 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons MSH4 33
  • 47.51 (n)
(Oryza sativa)
Liliopsida Os07g0486000 33
  • 46.15 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 53 (a)
Species where no ortholog for MSH4 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)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • 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 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for MSH4 Gene

Gene Tree for MSH4 (if available)
Gene Tree for MSH4 (if available)
Evolutionary constrained regions (ECRs) for MSH4: view image

Paralogs for MSH4 Gene

(1) SIMAP similar genes for MSH4 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with MSH4: view

No data available for Paralogs for MSH4 Gene

Variants for MSH4 Gene

Sequence variations from dbSNP and Humsavar for MSH4 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000020497 -- 75,835,104(+) C/T intron_variant
rs1000031869 -- 75,910,351(+) G/T intron_variant
rs1000049858 -- 75,904,532(+) G/GG intron_variant
rs1000078829 -- 75,872,321(+) G/A intron_variant
rs1000143208 -- 75,823,624(+) C/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for MSH4 Gene

Variant ID Type Subtype PubMed ID
esv1103396 CNV deletion 17803354
esv1540402 CNV insertion 17803354
esv1749246 CNV insertion 17803354
esv1918463 CNV deletion 18987734
esv2475692 CNV insertion 19546169
esv2575184 CNV loss 19546169
esv2749996 CNV deletion 23290073
esv3586491 CNV loss 21293372
nsv1004669 CNV loss 25217958
nsv1466 CNV deletion 18451855
nsv472748 CNV novel sequence insertion 20440878
nsv519329 CNV gain 19592680
nsv954757 CNV deletion 24416366

Variation tolerance for MSH4 Gene

Residual Variation Intolerance Score: 11.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.68; 65.92% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for MSH4 Gene

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

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for MSH4 Gene

Disorders for MSH4 Gene

MalaCards: The human disease database

(1) MalaCards diseases for MSH4 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
  • schwannomatosis
- elite association - COSMIC cancer census association via MalaCards
Search MSH4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for MSH4

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with MSH4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for MSH4 Gene

Publications for MSH4 Gene

  1. Cloning and expression analysis of a meiosis-specific MutS homolog: the human MSH4 gene. (PMID: 9299235) Paquis-Flucklinger V … Desnuelle C (Genomics 1997) 2 3 4 22 58
  2. Evaluation of 172 candidate polymorphisms for association with oligozoospermia or azoospermia in a large cohort of men of European descent. (PMID: 20378615) Aston KI … Carrell DT (Human reproduction (Oxford, England) 2010) 3 44 58
  3. Polymorphism in the IL18 gene and epithelial ovarian cancer in non-Hispanic white women. (PMID: 19064572) Palmieri RT … Australian Ovarian Cancer Study Group (Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 2008) 3 44 58
  4. Genetic investigation of four meiotic genes in women with premature ovarian failure. (PMID: 18166824) Mandon-Pépin B … Fellous M (European journal of endocrinology 2008) 3 44 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for MSH4 Gene

Sources for MSH4 Gene

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