PMS1 Gene (Protein Coding)

PMS1 Homolog 1, Mismatch Repair System Component

GC02P189784
GIFtS:
42
This gene encodes a protein belonging to the DNA mismatch repair mutL/hexB family. This protein is thought to be involved in the repair of DNA mismatches, and it can form heterodimers with MLH1, a known DNA mismatch repair protein. Mutations in this gene cause hereditary nonpolyposis colorectal cancer type 3 (HNPCC3) either alone or in combination with mutations in other genes ... See more...

Aliases for PMS1 Gene

Aliases for PMS1 Gene

  • PMS1 Homolog 1, Mismatch Repair System Component 2 3 5
  • DNA Mismatch Repair Protein PMS1 3 4
  • PMS1 Protein Homolog 1 3 4
  • PMSL1 3 4
  • MLH2 2 3
  • PMS1 Postmeiotic Segregation Increased 1 (S. Cerevisiae) 2
  • Postmeiotic Segregation Increased (S. Cerevisiae) 1 2
  • PMS1 Postmeiotic Segregation Increased 1 3
  • Rhabdomyosarcoma Antigen MU-RMS-40.10B 3
  • Rhabdomyosarcoma Antigen MU-RMS-40.10E 3
  • Human Homolog Of Yeast MutL 3
  • Mismatch Repair Gene PMSL1 3
  • HNPCC3 3
  • HPMS1 3
  • PMS1 5

External Ids for PMS1 Gene

Previous HGNC Symbols for PMS1 Gene

  • PMSL1

Previous GeneCards Identifiers for PMS1 Gene

  • GC02P188823
  • GC02P189331
  • GC02P190612
  • GC02P190851
  • GC02P190474
  • GC02P190357
  • GC02P190648
  • GC02P182508

Summaries for PMS1 Gene

Entrez Gene Summary for PMS1 Gene

  • This gene encodes a protein belonging to the DNA mismatch repair mutL/hexB family. This protein is thought to be involved in the repair of DNA mismatches, and it can form heterodimers with MLH1, a known DNA mismatch repair protein. Mutations in this gene cause hereditary nonpolyposis colorectal cancer type 3 (HNPCC3) either alone or in combination with mutations in other genes involved in the HNPCC phenotype, which is also known as Lynch syndrome. [provided by RefSeq, Jul 2008]

GeneCards Summary for PMS1 Gene

PMS1 (PMS1 Homolog 1, Mismatch Repair System Component) is a Protein Coding gene. Diseases associated with PMS1 include Colorectal Cancer and Lynch Syndrome I. Among its related pathways are Mismatch repair. Gene Ontology (GO) annotations related to this gene include ATPase activity and mismatched DNA binding. An important paralog of this gene is PMS2.

UniProtKB/Swiss-Prot Summary for PMS1 Gene

Gene Wiki entry for PMS1 Gene

Additional gene information for PMS1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PMS1 Gene

Genomics for PMS1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for PMS1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PMS1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PMS1

Top Transcription factor binding sites by QIAGEN in the PMS1 gene promoter:
  • GATA-1
  • GATA-2
  • GATA-3
  • Ik-1
  • STAT1
  • STAT1alpha
  • STAT1beta
  • STAT2
  • STAT5B
  • STAT6

Genomic Locations for PMS1 Gene

Latest Assembly
chr2:189,784,085-189,877,629
(GRCh38/hg38)
Size:
93,545 bases
Orientation:
Plus strand

Previous Assembly
chr2:190,649,176-190,742,355
(GRCh37/hg19 by Entrez Gene)
Size:
93,180 bases
Orientation:
Plus strand

chr2:190,649,107-190,742,355
(GRCh37/hg19 by Ensembl)
Size:
93,249 bases
Orientation:
Plus strand

Genomic View for PMS1 Gene

Genes around PMS1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PMS1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PMS1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for PMS1 Gene

Proteins for PMS1 Gene

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  • Protein details for PMS1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P54277-PMS1_HUMAN
    Recommended name:
    PMS1 protein homolog 1
    Protein Accession:
    P54277
    Secondary Accessions:
    • D3DPI1
    • Q4VAL4
    • Q5FBZ3
    • Q5FBZ6
    • Q5FBZ8

    Protein attributes for PMS1 Gene

    Size:
    932 amino acids
    Molecular mass:
    105830 Da
    Quaternary structure:
    • Component of the DNA mismatch repair (MMR) complex composed at least of MSH2, MSH3, MSH6, PMS1 and MLH1 (PubMed:26300262). The MutL-beta complex is a heterodimer of PMS1 and MLH1 (PubMed:10748105). Interacts with MCM9 (PubMed:26300262).

    Three dimensional structures from OCA and Proteopedia for PMS1 Gene

    Alternative splice isoforms for PMS1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PMS1 Gene

Protein Expression for PMS1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for PMS1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PMS1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PMS1 Gene

Domains & Families for PMS1 Gene

Gene Families for PMS1 Gene

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

Protein Domains for PMS1 Gene

InterPro:
Blocks:
  • DNA mismatch repair protein

Suggested Antigen Peptide Sequences for PMS1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ59348, highly similar to PMS1 protein homolog 1 (B4DMF4_HUMAN)
  • cDNA, FLJ79114, highly similar to PMS1 protein homolog 1 (B7ZAA0_HUMAN)
  • DNA mismatch repair protein PMS1 (PMS1_HUMAN)
  • Rhabdomyosarcoma antigen MU-RMS-40.10B (Q3BDU4_HUMAN)
  • PMS1 protein (Q4VAL4_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P54277

UniProtKB/Swiss-Prot:

PMS1_HUMAN :
  • Belongs to the DNA mismatch repair MutL/HexB family.
Family:
  • Belongs to the DNA mismatch repair MutL/HexB family.
genes like me logo Genes that share domains with PMS1: view

Function for PMS1 Gene

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  6. Cell Lines for research

Molecular function for PMS1 Gene

UniProtKB/Swiss-Prot Function:
Probably involved in the repair of mismatches in DNA.
GENATLAS Biochemistry:
postmeiotic segregation increased (S cerevisiae) 1, yeast mutator gene homolog (bacterial mutL) heterodimerizing with MLH1,involved in mismatch repair

Phenotypes From GWAS Catalog for PMS1 Gene

Gene Ontology (GO) - Molecular Function for PMS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA,TAS 8072530
GO:0005515 protein binding IPI 11292842
GO:0005524 ATP binding IEA --
GO:0016887 ATPase activity IEA,IBA 21873635
GO:0019899 enzyme binding IPI 26300262
genes like me logo Genes that share ontologies with PMS1: view
genes like me logo Genes that share phenotypes with PMS1: view

Human Phenotype Ontology for PMS1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PMS1 Gene

MGI Knock Outs for PMS1:
  • Pms1 Pms1<tm1.1(KOMP)Vlcg>
  • Pms1 Pms1<tm1Lisk>

Animal Models for research

miRNA for PMS1 Gene

miRTarBase miRNAs that target PMS1

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PMS1

Clone products for research

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for PMS1 Gene

Localization for PMS1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PMS1 Gene

Nucleus.

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 PMS1 gene
Compartment Confidence
nucleus 5
cytoskeleton 2
plasma membrane 1
extracellular 1
mitochondrion 1
endoplasmic reticulum 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (3)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PMS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 26300262
GO:0032300 mismatch repair complex IEA,IBA 21873635
genes like me logo Genes that share ontologies with PMS1: view

Pathways & Interactions for PMS1 Gene

PathCards logo

SuperPathways for PMS1 Gene

SuperPathway Contained pathways
1 Mismatch repair
Mismatch Repair in Eukaryotes
.54
genes like me logo Genes that share pathways with PMS1: view

Pathways by source for PMS1 Gene

1 Qiagen pathway for PMS1 Gene
  • Mismatch Repair in Eukaryotes

Gene Ontology (GO) - Biological Process for PMS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006281 DNA repair IEA --
GO:0006298 mismatch repair IEA,IBA 21873635
GO:0006974 cellular response to DNA damage stimulus IEA --
GO:0042493 response to drug IEA --
genes like me logo Genes that share ontologies with PMS1: view

No data available for SIGNOR curated interactions for PMS1 Gene

Drugs & Compounds for PMS1 Gene

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(2) Additional Compounds for PMS1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with PMS1: view

Transcripts for PMS1 Gene

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mRNA/cDNA for PMS1 Gene

12 REFSEQ mRNAs :
38 NCBI additional mRNA sequence :
22 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 PMS1

Clone products for research

Alternative Splicing Database (ASD) splice patterns (SP) for PMS1 Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2 ^ 3a · 3b ^ 4a · 4b · 4c ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16a ·
SP1: - - - - - - - - -
SP2: - - - - - - -
SP3: - - - - - - -
SP4: - - - - - - -
SP5: - - - - - - -
SP6: - -
SP7: - - - - -
SP8: - -
SP9:
SP10: -
SP11: -
SP12: -
SP13:
SP14:
SP15: - - -
SP16: -
SP17:
SP18:
SP19: - -

ExUns: 16b ^ 17a · 17b · 17c ^ 18a · 18b ^ 19a · 19b · 19c · 19d ^ 20a · 20b · 20c · 20d
SP1: - - - -
SP2: - -
SP3: - - - - -
SP4: - -
SP5: - - - - -
SP6: - - -
SP7: - - - - -
SP8:
SP9:
SP10:
SP11:
SP12:
SP13: -
SP14: - -
SP15:
SP16: -
SP17: - -
SP18:
SP19: - - - - - -

Relevant External Links for PMS1 Gene

GeneLoc Exon Structure for
PMS1

Expression for PMS1 Gene

Products:

  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PMS1 Gene

mRNA expression in normal human tissues for PMS1 Gene
mRNA expression by BioGPS for PMS1 GenemRNA expression by GTEx for PMS1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PMS1 Gene

This gene is overexpressed in Testis (57.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PMS1 Gene



Protein tissue co-expression partners for PMS1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PMS1

SOURCE GeneReport for Unigene cluster for PMS1 Gene:

Hs.111749

Evidence on tissue expression from TISSUES for PMS1 Gene

  • Gall bladder(4.3)
  • Nervous system(4)
  • Intestine(2.6)
  • Skin(2.2)
  • Stomach(2.1)
  • Lymph node(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PMS1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • nervous
  • reproductive
  • urinary
Regions:
Abdomen:
  • biliary tract
  • gallbladder
  • intestine
  • kidney
  • large intestine
  • liver
  • pancreas
  • small intestine
  • stomach
Pelvis:
  • anus
  • ovary
  • rectum
  • uterus
General:
  • blood
  • red blood cell
genes like me logo Genes that share expression patterns with PMS1: view

Primer products for research

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for PMS1 Gene

Orthologs for PMS1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PMS1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia PMS1 29 30
  • 99.79 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia PMS1 29 30
  • 88.89 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia PMS1 29 30
  • 88.26 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Pms1 29 16 30
  • 82.22 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Pms1 29
  • 81.5 (n)
Oppossum
(Monodelphis domestica)
 Mammalia PMS1 30
  • 71 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia PMS1 30
  • 44 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves PMS1 29 30
  • 69.02 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia PMS1 30
  • 52 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia pms1 29
  • 59.17 (n)
Str.3995 29
African clawed frog
(Xenopus laevis)
 Amphibia MGC52779 29
Zebrafish
(Danio rerio)
 Actinopterygii pms1 29 30
  • 54.72 (n)
 OneToOne
Worm
(Caenorhabditis elegans)
 Secernentea pms-2 30
  • 22 (a)
 OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes PMS1 30
  • 20 (a)
 OneToMany
Species where no ortholog for PMS1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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 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)
  • Wheat (Triticum aestivum)

Evolution for PMS1 Gene

ENSEMBL:
Gene Tree for PMS1 (if available)
TreeFam:
Gene Tree for PMS1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PMS1: view image
Alliance of Genome Resources:
Additional Orthologs for PMS1

Paralogs for PMS1 Gene

Paralogs for PMS1 Gene

(12) SIMAP similar genes for PMS1 Gene using alignment to 19 proteins:

  • PMS1_HUMAN
  • B7ZAA0_HUMAN
  • C9J4L1_HUMAN
  • C9JF76_HUMAN
  • C9JKP0_HUMAN
  • E9PC40_HUMAN
  • E9PC65_HUMAN
  • E9PH88_HUMAN
  • F8W8L1_HUMAN
  • I6L9H5_HUMAN
  • Q3BDU3_HUMAN
  • Q3BDU4_HUMAN
  • Q5FBZ1_HUMAN
  • Q5FBZ2_HUMAN
  • Q5FBZ4_HUMAN
  • Q5FBZ5_HUMAN
  • Q5FBZ7_HUMAN
  • Q5FBZ9_HUMAN
  • Q5XG96_HUMAN
genes like me logo Genes that share paralogs with PMS1: view

Variants for PMS1 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PMS1 Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
930948 Uncertain Significance: Lynch syndrome I 189,818,038(+) G/A
NM_000534.5(PMS1):c.440G>A (p.Arg147Lys) 		MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,FIVE_PRIME_UTR
998151 Pathogenic: Colorectal cancer 189,877,397(+) AT/A
NM_000534.5(PMS1):c.2766del (p.His923fs) 		FRAMESHIFT_VARIANT,NON_CODING_TRANSCRIPT
rs1145231 Benign: not specified; not provided 189,854,453(+) T/Cp.Met394Thr
NM_000534.5(PMS1):c.1181T>C (p.Met394Thr) 		MISSENSE_VARIANT,NON_CODING_TRANSCRIPT
rs1145232 Benign: not specified; not provided 189,854,773(+) G/Ap.Gly501Arg
NM_000534.5(PMS1):c.1501G>A (p.Gly501Arg) 		MISSENSE_VARIANT,NON_CODING_TRANSCRIPT
rs1145234 Benign: not specified; not provided. Not Provided: not specified 189,867,833(+) T/CT/Gp.Tyr793His
NM_000534.5(PMS1):c.2377T>C (p.Tyr793His) 		MISSENSE_VARIANT,NON_CODING_TRANSCRIPT

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for PMS1 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 PMS1 Gene

Variant ID Type Subtype PubMed ID
esv3584245 CNV loss 25503493
nsv213327 CNV deletion 16902084
nsv3080 CNV deletion 18451855
nsv472452 CNV novel sequence insertion 20440878
nsv584063 CNV loss 21841781

Variation tolerance for PMS1 Gene

Residual Variation Intolerance Score: 81.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.09; 60.98% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PMS1 Gene

Human Gene Mutation Database (HGMD)
PMS1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PMS1
Leiden Open Variation Database (LOVD)
PMS1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PMS1 Gene

Disorders for PMS1 Gene

MalaCards: The human disease database

(18) MalaCards diseases for PMS1 Gene - From: CVR, GTR, ORP, COP, and GCD

Disorder Aliases PubMed IDs
colorectal cancer
  • crc
lynch syndrome i
  • colorectal cancer, hereditary nonpolyposis, type 1; hnpcc1
lynch syndrome
  • coca 1
hereditary nonpolyposis colon cancer
  • familial nonpolyposis colon cancer
rectum signet ring adenocarcinoma
  • signet ring cell adenocarcinoma of rectum
- elite association - COSMIC cancer census association via MalaCards
Search PMS1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PMS1

Human Genome Epidemiology Navigator
(HuGE)
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 PMS1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PMS1 Gene

Publications for PMS1 Gene

  1. Common germline variation in mismatch repair genes and survival after a diagnosis of colorectal cancer. (PMID: 19115210) Koessler T … Pharoah PD (International journal of cancer 2009) 3 22 40
  2. Mismatch repair gene polymorphisms and survival in invasive ovarian cancer patients. (PMID: 18723338) Mann A … Song H (European journal of cancer (Oxford, England : 1990) 2008) 3 22 40
  3. Common variants in mismatch repair genes and risk of colorectal cancer. (PMID: 18364438) Koessler T … Pharoah PD (Gut 2008) 3 22 40
  4. Common variants in mismatch repair genes and risk of invasive ovarian cancer. (PMID: 16774946) Song H … Gayther SA (Carcinogenesis 2006) 3 22 40
  5. Prevalence of germline mutations of hMLH1, hMSH2, hPMS1, hPMS2, and hMSH6 genes in 75 French kindreds with nonpolyposis colorectal cancer. (PMID: 10480359) Wang Q … Puisieux A (Human genetics 1999) 3 4 22

ExternalLinks

View latest publications for PMS1 gene in Mastermind

Products for PMS1 Gene

Sources for PMS1 Gene