The UMD-MSH2 mutations database
Abbreviations and Terms of the database

Abbreviations

HNPCC : Hereditary NonPolyposis Colorectal Cancer

MLH1 : MutL Homolog 1

MMR : DNA Mismatch Repair

MSH2 : MutS Homolog 2

MSH6 : MutS Homolog 6

MSI : MicroSatellite Instability

MSS : MicroSatellite Stability

MUTYH : MutY Homolog

LOD score : Linkage Odd Disequilibrium score

PMS2 : PostMeiotic Segregation increased 2

rs : Reference SNP

SNP : Single Nucleotide Polymorphism

UMD: The Universal Mutation Database

UV : Unknown Variant

Terms of the database

Already described in: description of the variant in another database.

Biological significance: classification of the variant in this database

CpG: CpG sites are regions of DNA where a cytosine nucleotide occurs next to a guanine nucleotide in the linear sequence of bases along its length. "CpG" stands for cytosine and guanine separated by a phosphate (—C—phosphate—G—), which links the two nucleosides together in DNA. The "CpG" notation is used to distinguish a cytosine followed by guanine from a cytosine base paired to a guanine.

Exon #: exon number

HCD: highly conserved amino acid or interacting directly with a known partner.

Large rearrangement: variation affecting sequences, such as one or more exons

Last modification: last modification for this variant in the database

Missing exons: by large rearrangement

mRNA: impact on the RNA level

Mutation ID/UMD_ID: order of the family record in the database

Mutation name/Variation name: cDNA nomenclature of the variant with HGVS nomenclature

Mutation type: transition mutation (Ts) in which the base change does not change the pyrimidine-purine orientation. Transversion mutation (Tv) in which the purine-pyrimidine orientation is changed to pyrimidine-purine or vice versa.

Mutational event: sequence variation

Old nomenclature: nomenclature starting at exon 1

Protein nomenclature: characteristics of WT and mutant amino acid

Py-Py doublet: Pyrimidine double

Reference #: Anonymous number of laboratories in agreement with INCa

Sample ID: Anonymous number of family

Structure: location of the variant on the known tridimensional structure

Variation class: MS (missense), FS (frameshift), IFD (in frame deletion), IFI (in frame insertion, RGT (large rearrangement), NS (non-sens), ins/del (insertion-deletion)

Variation type: impact of the variation (ex: PTC=premature termination codon)