Linked Annotation External Source PAT ID Label Synonyms Similar Term Definition Equivalent Term Annotation Term Definition Source Thing GV.01 Association to Pathogenicity association with pathogenicity associations to pathogenicity associations with pathogenicity disease associated variant disease associated variants disease causing variant disease causing variants pathogenicity association pathogenicity associations GV.01 GV.02 Chromosomal Variation TFBS fusion aberrant chromosome aberration, chromosomal aberration, chromosome aberration, cytogenetic aberrations, chromosomal aberrations, chromosome aberrations, cytogenetic abnormalities, autosome abnormalities, chromosomal abnormalities, chromosome abnormalities, cytogenetic abnormality, autosome abnormality, chromosomal abnormality, chromosome abnormality, cytogenetic autosome abnormalities autosome abnormality bidirectional gene fusion chimeric gene chromosomal aberration chromosomal aberrations chromosomal abnormalities chromosomal abnormality chromosomal alterations chromosome aberration chromosome abnormalities chromosome abnormality chromosome alterations chromosome anomalies chromosome mutation chromosome variation cytogenetic aberration cytogenetic aberrations cytogenetic abnormalities cytogenetic abnormality fusion gene fusion, gene fusions, gene gene fusion gene fusion abnormality gene fusions hybrid gene regulatory region fusion transcript fusion Variation at chromosomal level. GV.02 Variation Ontology (VariO) GV.02.01 Chromosomal Structure Variation chromosomal rearrangement chromosomal rearrangements chromosome rearrangement chromosome rearrangements chromosome structure variation complex chromosomal rearrangement rearrangement region structural chromosome aberration structural chromosome anomalies translocations, genetic Variation affecting structure of chromosome. GV.02.01 Variation Ontology (VariO) GV.02.01.01 Chromosomal Amplification TFBS amplification chromosomal duplication chromosomal duplications chromosome amplification chromosome duplication chromosome duplications duplication, chromosomal duplication, chromosome duplications, chromosomal duplications, chromosome free ring duplication gene amplification gene amplification abnormality interchromosomal duplication intrachromosomal duplication Increase in the frequency of a chromosomal region. GV.02.01.01 Variation Ontology (VariO) GV.02.01.02 Chromosomal Deletion Chromosomal microdeletion Chromosome microdeletion Germ line deletion Microdeletion chromosome deletion chromosome large deletion interstitial deletion mobile element deletion terminal deletion Deletion of chromosomal region. GV.02.01.02 Variation Ontology (VariO) GV.02.01.03 Chromosome Breakpoint DNA breakpoint DSB-induced small RNA DSB-induced small RNAs NHEJ aberration breakpoint aberration junction breakpoint sequence, chromosome breakpoint sequences, chromosome breakpoint, chromosome breakpoints, chromosome chromosome breakage sequence chromosome breakpoint sequence chromosome breakpoint sequences deletion breakpoint deletion junction diRNA insertion breakpoint interchromosomal breakpoint intrachromosomal breakpoint inversion breakpoint micro-homology end joining non-homologous end joining nonhomologous dna end joining sequence, chromosome breakpoint sequences, chromosome breakpoint translocation breakpoint The locations in specific DNA sequences where CHROMOSOME BREAKS have occurred. GV.02.01.03 Medical Subject Headings (MeSH) GV.02.01.04 Complex Chromosome Dicentric chromosome chromosome, ring chromosomes, ring compound chromosome compound chromosome arm dicentric hetero compound chromosome hetero-compound chromosome homo compound chromosome homo-compound chromosome isochromosome minicircle minicircle chromosome ring chromosome supernumerary circular chromosome Chromosome structure variation with four or more breakpoints. GV.02.01.04 Variation Ontology (VariO) GV.02.01.05 Chromosomal Translocation DNA translocation Robertsonian translocation TFBS translocation chromosomal translocation process chromosomal translocations chromosomal transposition chromosome translocation cyclic translocation deficient interchromosomal transposition deficient intrachromosomal transposition deficient translocation genetic translocation genetic translocations interchromosomal translocation interchromosomal transposition intrachromosomal translocation intrachromosomal transposition inverted interchromosomal transposition inverted intrachromosomal transposition reciprocal chromosomal translocation transchr translocated sequence translocation element translocation genet translocation, chromosomal translocation, genetic translocations, chromosomal transposition uninverted interchromosomal transposition uninverted intrachromosomal transposition unoriented interchromosomal transposition unoriented intrachromosomal transposition Translocation of chromosomal region. http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25756 GV.02.01.05 Variation Ontology (VariO) GV.02.01.06 Chromosomal Inversion DNA inversion DNA invertase target sequence RNA inversion bipartite inversion chromosomal inversion process chromosomal inversions chromosome inversions deficient inversion ftr site inv site inversion cum translocation inversion derived bipartite deficiency inversion derived bipartite duplication inversion derived deficiency plus aneuploid inversion derived deficiency plus duplication inversion derived duplication plus aneuploid inversion mutation inversion mutation abnormality inversion site inversion, chromosomal inversions, chromosomal inversions, chromosome inverted chromosome paracentric inversion pericentric inversion recombinationally inverted gene structural chromosomal abnormality A type of chromosome rearrangement in which a segment has been turned through 180 degrees (inverted), and inserted back into its original location on the chromosome. GV.02.01.06 National Cancer Institute Thesaurus (NCIT) GV.02.02 Aneuploidy abnormal mitotic chromosome separation accessory chromosome allopolyploid allopolyploidy alteration of chromosome number aneuploid aneuploid cell aneuploid cells aneuploid chromosome aneuploidies aneuploids autopolyploid autopolyploidy cell, aneuploid cells, aneuploid chromosomal triplication chromosomal triplications chromosome number abnormality chromosome number variation chromosome set number variation complete but unequal mitotic chromosome segregation complete but unequal mitotic sister chromatid separation hyperploid hypoploid hypoploidy inversion derived aneuploid chromosome nulliploidy nullisomy numerical chromosomal alterations variation in chromosome number whole chromosome depletion A chromosomal abnormality in which there is an addition or loss of chromosomes within a set (e.g., 23 + 22 or 23 + 24). GV.02.02 National Cancer Institute Thesaurus (NCIT) GV.02.02.01 Monosomy monosomies partial monosomy A chromosomal abnormality consisting of the absence of one chromosome from the normal diploid number.(WordNet) GV.02.02.01 National Cancer Institute Thesaurus (NCIT) GV.02.02.02 Disomy Heterodisomy Isodisomy Two copies of a chromosome in a cell or organism . GV.02.02.02 Variation Ontology (VariO) GV.02.02.02.01 Uniparental Disomy disomies, uniparental disomy, uniparental heterodisomies, uniparental heterodisomy, uniparental isodisomies, uniparental maternal uniparental disomy paternal uniparental disomy uniparental disomies uniparental heterodisomies uniparental heterodisomy uniparental isodisomies uniparental isodisomy A condition characterized by the inheritance of a chromosome pair from one parent and no chromosomal copies from the other parent. It results in developmental abnormalities or rare recessive disorders. Examples of uniparental disomy include the Prader-Willi syndrome and Angelman syndrome. GV.02.02.02.01 National Cancer Institute Thesaurus (NCIT) GV.02.02.03 Trisomy down syndrome partial trisomies partial trisomy trisomies trisomies, partial trisomy, partial trisomy, syndrome A chromosomal abnormality consisting of the presence of one chromosome in addition to the normal diploid number. GV.02.02.03 National Cancer Institute Thesaurus (NCIT) GV.02.02.04 Tetrasomy partial tetrasomies partial tetrasomy tetrasomies tetrasomies, partial tetrasomy, partial Four copies of a chromosome in a cell or organism. GV.02.02.04 Variation Ontology (VariO) GV.02.02.05 Polysomy Polysomies The condition of having additional copies of a chromosome present in a cell. GV.02.02.05 National Cancer Institute Thesaurus (NCIT) GV.02.03 Euploidy euploid normal karyotype Variation affecting number of entire chromosome sets. GV.02.03 Variation Ontology (VariO) GV.02.03.01 Haploid haploidy A chromosomal abnormality in which a somatic cell has a single member of each pair of homologous chromosomes. GV.02.03.01 National Cancer Institute Thesaurus (NCIT) GV.02.03.02 Monoploid monoploidy Variation with a single set of chromosomes. GV.02.03.02 Variation Ontology (VariO) GV.02.03.03 Diploid cell, diploid cells, diploid diploid cell diploid cells diploidies diploids diploidy Having two sets of homologous chromosomes. GV.02.03.03 National Cancer Institute Thesaurus (NCIT) GV.02.03.04 Triploid triploidies triploids triploidy triploidy syndrome A numerical chromosomal abnormality characterized by the presence of three complete sets of chromosomes. GV.02.03.04 National Cancer Institute Thesaurus (NCIT) GV.02.03.05 Tetraploid tetraploidies tetraploids tetraploidy A numerical chromosomal abnormality characterized by the presence of four complete sets of chromosomes. GV.02.03.05 National Cancer Institute Thesaurus (NCIT) GV.02.03.06 Pentaploid pentaploids pentaploidy Variation with five sets of chromosomes. GV.02.03.06 Variation Ontology (VariO) GV.02.03.07 Hexaploid hexaploidy Variation with six sets of chromosomes. GV.02.03.07 Variation Ontology (VariO) GV.02.03.08 Heptaploid heptaploidy GV.02.03.08 GV.02.03.09 Septaploid septaploids GV.02.03.09 GV.02.03.10 Polyploid cell, polyploid cells, polyploid polyploid cell polyploid cells polyploidies polyploids polyploidy polyploidy syndrome Variation with several sets of chromosomes. GV.02.03.10 Variation Ontology (VariO) GV.03 DNA Variation 2KB downstream variant 2KB upstream variant 3 prime UTR exon variant 3 prime UTR intron variant 3 prime UTR variant 5 prime UTR exon variant 5 prime UTR intron variant 5 prime UTR premature start codon gain variant 5 prime UTR premature start codon loss variant 5 prime UTR premature start codon variant 5 prime UTR variant 500B downstream variant 5KB downstream variant 5KB upstream variant CAGE cluster DNA chain variation DNA variation of genetic origin NMD transcript variant TF binding site variant UTR variant aberrant processed transcript artificial DNA variation benign variant cage peak coding complex coding complex-near-splice coding sequence variant coding transcript intron variant coding transcript variant coding transcript with retained intron coding variant codon change codon redefined codon variant common variant compensatory transcript secondary structure variant complex change in transcript complex chromosomal variation complex transcript variant conservation of DNA variation site conservation of protein variation site conserved intergenic variant conserved intron variant conserved region cryptic splice site variant de novo variant defect in DNA repair defective DNA replication disabled reading frame dna alteration dna sequence alteration downstream gene variant downstream transcript variant exon deleted exon loss exon loss variant exon variant exonic splice region variant fixed variant frame restoring sequence variant frame restoring variant gene alteration gene fragment gene structure variation gene variant gene with stop codon redefined as pyrrolysine gene with stop codon redefined as selenocysteine genetic diversity genic 3 prime transcript variant genic 3' transcript variant genic 5 prime transcript variant genic 5' transcript variant genic downstream transcript variant genic upstream transcript variant genomic variation germline variant haplotype in-frame deletion incomplete terminal codon variant incomplete transcript 3UTR variant incomplete transcript 5UTR variant incomplete transcript coding splice variant incomplete transcript variant inframe change in cds length inframe variant initiation codon change intergenic 1kb variant intergenic conserved intergenic variant internal eliminated sequence intragenic variant intron conserved intron gain intron gain variant intron variant intron-near-splice invariant region maternal variant misreplicated DNA mononucleotide expansion mutated variant site natural variant natural variant site nc transcript variant nmd transcript non coding transcript exon variant non coding transcript intron variant non coding transcript variant non synonymous stop nonframeshift block substitution nonframeshift substitution not wildtype not wt partial codon partially characterised change in dna sequence paternal variant population specific variant premature stop rare variant regulatory region variant removed stop sequence alteration sequence conflict sequence length alteration sequence length variant sequence rearrangement sequence variant sequence variant affecting 3D structure of polypeptide sequence variant affecting copy number sequence variant affecting editing sequence variant affecting gene structure sequence variant affecting level of translational product sequence variant affecting polyadenylation sequence variant affecting polypeptide amino acid sequence sequence variant affecting polypeptide function sequence variant affecting rate of transcription sequence variant affecting regulatory region sequence variant affecting splice acceptor sequence variant affecting splice donor sequence variant affecting splicing sequence variant affecting transcript processing sequence variant affecting transcript secondary structure sequence variant affecting transcript stability sequence variant affecting transcription sequence variant affecting translational product sequence variant causes exon loss sequence variant causes intron gain sequence variant causing amino acid coding codon change in transcript sequence variant causing amino acid deletion sequence variant causing amino acid insertion sequence variant causing amino acid substitution sequence variant causing compensatory transcript secondary structure mutation sequence variant causing complex 3D structural change sequence variant causing complex change of translational product sequence variant causing conformational change sequence variant causing conservative amino acid substitution sequence variant causing conservative missense codon change in transcript sequence variant causing cryptic splice acceptor activation sequence variant causing cryptic splice activation sequence variant causing cryptic splice donor activation sequence variant causing gene fusion sequence variant causing inactive catalytic site sequence variant causing inactive ligand binding site sequence variant causing initiator codon change in transcript sequence variant causing loss of function of polypeptide sequence variant causing minus 1 frameshift sequence variant causing minus 2 frameshift sequence variant causing missense codon change in transcript sequence variant causing no 3D structural change sequence variant causing no change in transcript sequence variant causing no change of translational product sequence variant causing non synonymous codon change in transcript sequence variant causing nonconservative amino acid substitution sequence variant causing nonconservative missense codon change in transcript sequence variant causing nonsense codon change in transcript sequence variant causing partial loss of function of polypeptide sequence variant causing plus 1 frameshift mutation sequence variant causing plus 2 frameshift sequence variant causing polypeptide elongation sequence variant causing polypeptide fusion sequence variant causing polypeptide localization change sequence variant causing polypeptide post translational processing change sequence variant causing polypeptide truncation sequence variant causing synonymous codon change in transcript sequence variant causing terminator codon change in transcript sequence variant decreasing level of translation product sequence variant decreasing rate of transcription sequence variant decreasing transcript stability sequence variant increasing level of translation product sequence variant increasing rate of transcription sequence variant increasing transcript stability sequence variation sequence variation affecting coding sequence sequence variation affecting reading frame sequence variation affecting transcript sequence variation affecting transcript sequence shortening, telomere shortenings, telomere simple sequence length variation somatic variant splice acceptor variant splice donor variant splice region variant splice site variant splicing variant start gained start lost start retained variant stop codon gained stop codon lost stop codon read through stop codon readthrough stop codon redefined as selenocysteine stop codon redefinition as pyrrolysine stop gain stop gained stop loss stop lost stop retained stop retained variant stop-gained stop-gained-near-splice stop-lost stop-lost-near-splice str change str contraction str expansion str variation synonymous stop telomere extension telomere length change telomere shortening telomere shortenings terminal codon variant terminator codon variant tetranucleotide expansion transcript function variant transcript processing variant transcript secondary structure variant transcript sequence variant transcript variant transcript with readthrough stop codon transcription variant uncharacterised change in nucleotide sequence uncharacterized chromosomal variation upstream gene variant variant genome variation at canonical five prime splice site variation at canonical three prime splice site variation at five prime cis splice site variation at intergenic DNA variation at non canonical five prime splice site variation at non canonical three prime splice site variation at recursive splice site variation at three prime cis splice site variation in exon variation in intron variation of chromosome structure wild type rescue gene GV.03 GV.03.01 Copy Number Variation copy number alteration copy number change copy number decrease copy number gain copy number increase copy number loss copy number polymorphism copy number variant Variation in the number of copies of a particular sequence within the genetic material of an individual. Large-scale copy number polymorphisms are common and widely distributed in the human genome. GV.03.01 National Cancer Institute Thesaurus (NCIT) GV.03.02 DNA Mutation five prime UTR premature start codon location variant gene mutant gene mutation gene mutation type genetic alteration genetic change genetic mutation genome mutation genomic mutation initiator codon variant interchromosomal mutation intrachromosomal mutation mutant mutated mutation mutation abnormality mutation causing inframe polypeptide N terminal elongation mutation causing polypeptide C terminal elongation mutation causing polypeptide N terminal elongation mutations mutaton causing inframe polypeptide C terminal elongation partially characterized chromosomal mutation purine to pyrimidine transversion purine transition pyrimidine to purine transversion pyrimidine transition somatic mutations termination codon change uncharacterized chromosomal mutation GV.03.02 GV.03.02.01 Point Mutation A to C transversion A to G transition A to T transversion C to A transversion C to G transversion C to T transition C to T transition at pCpG site DNA substitution G to A transition G to C transversion G to T transversion T to A transversion T to C transition T to G transversion coding-synon delete U mutation, point mutation, silent mutation, transition mutation, transversion mutations, point mutations, silent nucleotide transition abnormality nucleotide transversion abnormality point mutations silent mutation silent mutations silent substitution silent substitutions silent variation silent variations substitution mutation transition mutation transition mutations transversion transversion mutation transversion mutations transversions An alteration in a DNA sequence caused by the substitution of a single nucleotide for another nucleotide. GV.03.02.01 National Cancer Institute Thesaurus (NCIT) GV.03.02.01.01 Synonymous Mutation codon substitution, synonymous codon substitutions, synonymous exon synonymous mutation exonic synonymous mutation mutation, synonymous mutations, synonymous substitution, synonymous codon substitutions, synonymous codon synonymous coding synonymous codon synonymous codon substitution synonymous codon substitutions synonymous mutations synonymous snv synonymous variant synonymous variation synonymous variations synonymous-near-splice A point mutation occurring within the protein-coding region of a gene, and which codes for the same amino acid as expected. GV.03.02.01.01 National Cancer Institute Thesaurus (NCIT) GV.03.02.01.02 Non-Synonymous Mutation Mitochondrial nonsynonymous substitution Mitochondrial nonsynonymous substitutions exon non-synonymous mutation exonic non-synonymous mutation non synonymous coding nonsynonymous mutation nonsynonymous variant nonsynonymous variation GV.03.02.01.02 GV.03.02.01.02.01 Missense Mutation conservative missense codon conservative missense variant missense mutation abnormality missense mutations missense variant missense variation missense variations mutation, missense neutral missense codon non conservative missense codon non conservative missense variant quiet missense codon A point mutation occurring within the protein-coding region of a gene, and which codes for a different amino acid than expected. GV.03.02.01.02.01 National Cancer Institute Thesaurus (NCIT) GV.03.02.01.02.02 Nonsense Mutation non sense mutation non sense variation nonsense nonsense codon nonsense mutations nonsense variation nonsense variations A point mutation occurring within the protein-coding region of a gene, and which codes for a stop that can truncate the protein. GV.03.02.01.02.02 National Cancer Institute Thesaurus (NCIT) GV.03.02.02 Frameshift Mutation +1 frameshift variant +2 frameshift variant -1 frameshift variant -2 frameshift variant deletion fs deletion, out-of-frame deletions, out-of-frame frame shift frame shift mutation frame shift mutations frameshift frameshift block substitution frameshift coding frameshift deletion frameshift elongation frameshift insertion frameshift mutation abnormality frameshift mutations frameshift sequence variation frameshift substitution frameshift truncation frameshift variant frameshift-near-splice frameshifted mrna gene with mRNA with frameshift gene with transcript with translational frameshift insertion fs insertion, out-of-frame insertions, out-of-frame mRNA with frameshift mRNA with minus 1 frameshift mRNA with minus 2 frameshift mRNA with plus 1 frameshift mRNA with plus 2 frameshift minus 1 frameshift minus 1 frameshift variant minus 1 translationally frameshifted minus 2 frameshift minus 2 frameshift variant mutation causing out of frame polypeptide C terminal elongation mutation causing out of frame polypeptide N terminal elongation mutation, frame shift mutation, frameshift mutation, out-of-frame mutations, frame shift mutations, frameshift mutations, out-of-frame out of frame deletion out of frame insertion out of frame mutation out-of-frame deletion out-of-frame deletions out-of-frame indel out-of-frame insertion out-of-frame insertions out-of-frame mutation out-of-frame mutations plus 1 frameshift plus 1 frameshift variant plus 1 ribosomal frameshift plus 1 translational frameshift plus 1 translationally frameshifted plus 2 frameshift variant plus 2 framshift plus 2 ribosomal frameshift plus 2 translational frameshift reading frame shift mutation ribosomal frameshift translational frameshift translationally frameshifted A mutation occurring within the protein-coding region of a gene which results in a shift in the reading frame of the encoded protein. Frameshift mutations often result in the premature truncation of a gene product. GV.03.02.02 National Cancer Institute Thesaurus (NCIT) GV.03.03 Gene Duplication bipartite duplication deficiency plus duplication free duplication gene duplication abnormality insertional duplication inverted insertional duplication mirror duplication paralog paralogous region paralogue target site duplication uninverted insertional duplication unoriented insertional duplication Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES. GV.03.03 Medical Subject Headings (MeSH) GV.03.04 Polymorphism Single feature polymorphism genetic polymorphism polymorphic polymorphic sequence variant polymorphic variant polymorphism genet polymorphisms simple sequence length polymorphism A common change in the genetic code in DNA. Polymorphisms can have a harmful effect, a good effect, or no effect. Some polymorphisms have been shown to increase the risk of certain types of cancer. GV.03.04 National Cancer Institute Thesaurus (NCIT) GV.03.04.01 Single Nucleotide Polymorphism nucleotide polymorphism, single nucleotide polymorphisms, single polymorphism, single base polymorphism, single nucleotide polymorphisms, single nucleotide single nucleotide polymorphisms single nucleotide variant single-nucleotide polymorphism single-nucleotide polymorphisms A variation of a single nucleotide at a specific location of the genome due to base substitution, present at an appreciable frequency between individuals of a single interbreeding population. GV.03.04.01 National Cancer Institute Thesaurus (NCIT) GV.03.04.02 Tandem Repeat Polymorphism direct tandem duplication direct tandem repeat direct tandem repeats inverted tandem duplication loci, vntr locus, vntr nested tandem repeat region, vntr regions, vntr repeat sequence, tandem repeat sequences, tandem repeat, direct tandem repeat, short tandem repeat, tandem repeat, variable tandem repeats, direct tandem repeats, short tandem repeats, tandem repeats, variable tandem sequence, tandem repeat sequence, terminal repeat sequence, vntr sequences, tandem repeat sequences, vntr short tandem repeat short tandem repeat change short tandem repeat contraction short tandem repeat expansion short tandem repeat variation short tandem repeats tandem duplication tandem repeat tandem repeat sequence tandem repeat, direct tandem repeat, short tandem repeat, variable tandem repeats tandem repeats, direct tandem repeats, short tandem repeats, variable variable number of tandem repeat polymorphism variable number of tandem repeats variable number tandem repeat variable number tandem repeats variable tandem repeat variable tandem repeats vntr loci vntr locus vntr region vntr regions vntr sequence vntr sequences Short Tandem Repeat Polymorphism consists of variation between individuals in the number of repeat units of Simple Tandem Repeats at a specific location in the genome. These are used extensively as markers in gene mapping and linkage analysis. GV.03.04.02 National Cancer Institute Thesaurus (NCIT) GV.03.05 Indel DNA Indel cds-indel complex indel in-frame indel indel mutation inframe indel integration excision site sequence retaining amino acid indel A mutation class that includes insertion mutations, deletion mutations and mutation events where both an insertion and a deletion has occurred. GV.03.05 National Cancer Institute Thesaurus (NCIT) GV.03.05.01 DNA Insertion Alu insertion SVA insertion cloning site insertion nfs transgenic insertion Addition of one or more nucleotides between two adjacent nucleotides in the DNA sequence. GV.03.05.01 Variation Ontology (VariO) GV.03.05.02 DNA Deletion Alu deletion HERV deletion SVA deletion TFBS ablation complete gene deletion deletion nfs deletion, gene deletions, gene gene deletion gene deletion abnormality gene deletions partial gene deletion transcription factor binding site ablation Removal of one or more continuous nucleotides from DNA sequence. GV.03.05.02 Variation Ontology (VariO) GV.03.06 Nucleotide Pair Substitution nucleotide pair substitutions nucleotide-pair substitution GV.03.06 GV.03.07 DNA Sequence Repeat 3' tir 5' tir GT dinucleotide repeat LINE element R LTR region R five prime LTR region R three prime LTR region U5 five prime LTR region centromeric repeat delta element delta elements dg repeat dh repeat dinucleotide repeat microsatellite dinucleotide repeat microsatellite feature dinucleotide repeat microsatellite locus dinucleotide repeat microsatellite marker direct repeat direct repeats direct terminal repeat dispersed repeat dispersed repetitive sequence dispersed repetitive sequences dna repetitious region dna repetitious regions dna, satellite dna, satellite i dna, selfish dnas, satellite dnas, satellite i dnas, selfish element, delta element, interspersed repetitive elements, delta elements, interspersed repetitive five prime terminal inverted repeat flanking repeat sequence flanking repeat sequences gene, selfish genes, selfish i dna, satellite i dnas, satellite interspersed repeat interspersed repetitive element interspersed repetitive elements interspersed repetitive sequence inverted repeat inverted repeat sequence inverted terminal repeat lmr repeat lmr1l lmr1r long interspersed element long interspersed nuclear element long terminal repeat long terminal repeats low complexity region marker, microsatellite markers, microsatellite microsatellite microsatellite locus microsatellite marker microsatellite markers microsatellite repeat microsatellite repeats microsatellites minisatellite minisatellite repeat minisatellite repeats minisatellites monomeric repeat nested repeat non LTR retrotransposon polymeric tract nucleic acid repetitive sequences pentanucleotide repeat pentanucleotide repeats polypyrimidine tract r 3' long terminal repeat region r 5' long term repeat region r long terminal repeat region r repetitive sequence r repetitive sequences rDNA intergenic spacer element regional centromere inner repeat region regional centromere outer repeat region regulatory region ablation repeat family repeat fragment repeat region repeat sequence, flanking repeat sequence, terminal repeat sequences, flanking repeat sequences, terminal repeat, direct repeat, long terminal repeat, microsatellite repeat, minisatellite repeat, pentanucleotide repeat, simple sequence repeat, terminal repeat, tetranucleotide repeats, direct repeats, long terminal repeats, microsatellite repeats, minisatellite repeats, pentanucleotide repeats, simple sequence repeats, terminal repeats, tetranucleotide repetitious region, dna repetitious regions, dna repetitive element repetitive element, interspersed repetitive elements, interspersed repetitive region repetitive regions repetitive sequence repetitive sequence, dispersed repetitive sequence, interspersed repetitive sequence, r repetitive sequence, simple repetitive sequences repetitive sequences, dispersed repetitive sequences, interspersed repetitive sequences, r repetitive sequences, simple satellite DNA satellite dnas satellite i dna satellite i dnas selfish dna selfish dnas selfish gene selfish genes sequence repeat, simple sequence repeats, simple sequence, dispersed repetitive sequence, flanking repeat sequence, interspersed repetitive sequence, r repetitive sequence, simple repetitive sequences, dispersed repetitive sequences, flanking repeat sequences, interspersed repetitive sequences, r repetitive sequences, simple repetitive sequences, terminal repeat simple repetitive sequence simple repetitive sequences simple sequence repeat simple sequence repeats solo LTR telomeric repeat terminal inverted repeat element terminal repeat terminal repeat sequence terminal repeat, long terminal repeats terminal repeats, long tetranucleotide repeat tetranucleotide repeat microsatellite tetranucleotide repeats three prime terminal inverted repeat tir element u5 5' long terminal repeat region GV.03.07 GV.03.07.01 Tri-Nucleotide Repeat GTT trinucleotide repeat expanded trinucleotide repeat expanded trinucleotide repeats expansion, trinucleotide repeat expansions, trinucleotide repeat repeat expansion, trinucleotide repeat expansions, trinucleotide repeat, expanded trinucleotide repeats, expanded trinucleotide trinucleotide expansion trinucleotide repeat expansion trinucleotide repeat expansions trinucleotide repeat microsatellite trinucleotide repeat, expanded trinucleotide repeats, expanded Sequences of 3 nucleotides repeated in tandem on the same contiguous section of chromosome. A certain amount of normal (polymorphic) variation in repeat number with no clinical significance commonly occurs between individuals; however, repeat numbers over a certain threshold can, in some cases, lead to adverse effects on the function of the gene, resulting in genetic disease. GV.03.07.01 National Cancer Institute Thesaurus (NCIT) GV.03.08 DNA Rearrangement DNA rearrangements DNA sequence rearrangement DNA transfer to foreign host artificial gene transfer gene rearranged at DNA level gene rearrangements immunoglobulin class switching immunoglobulin genetic recombination mechanism molecular rearrangement rearranged at DNA level rearranged gene rearrangement, DNA rearrangement, gene rearrangements, DNA rearrangements, gene recombinant transgene recombinant transgenes site specific DNA recombination transgene transgene, recombinant transgenes, recombinant Any DNA sequence rearrangement that results in the creation of a novel protein-coding capacity. Within certain genes, gene rearrangement is a normal part of development, facilitating the affinity maturation of B and T lymphocytes as well as class switching of immunoglobulins. GV.03.08 National Cancer Institute Thesaurus (NCIT) GV.03.09 DNA Recombination DNA recombination process DNA recombinations NAHRR Non-allelic homologous recombination NAHR genetic recombination genetic recombinations meiotic recombination region mitotic recombination region non allelic homologous recombination region non-allelic homologous recombination recombination enhancer recombination genet recombination hotspot recombination regulatory region recombination signal sequence recombinationally rearranged recombinationally rearranged gene recombinationally rearranged vertebrate immune system gene recombinations, genetic site specific recombination target region Any type of DNA sequence rearrangement involving possible exchange and frequent loss of segments of DNA by either homologous recombination or non-homologous end-joining of broken DNA strands. Recombination is involved in assorting genes during reproduction, in repairing broken DNA, and in maintaining cell viability at the expense of long-term genomic stability. GV.03.09 National Cancer Institute Thesaurus (NCIT) GV.03.10 Pseudogene IG C pseudogene IG J pseudogene IG V pseudogene T cell receptor pseudogene TR J pseudogene TR V pseudogene beta tubulin pseudogene beta-tubulin pseudogene beta-tubulin pseudogenes cassette pseudogene cassette type psedogene disabled gene duplicated pseudogene gene, processed genes, processed ig joining pseudogene ig variable pseudogene immunoglobulin joining pseudogene immunoglobulin pseudogene immunoglobulin variable pseudogene junk dna non processed pseudogene nuclear mitochondrial pseudogene nuclear mt pseudogene polymorphic pseudogene polymorphic pseudogene processed transcript polymorphic pseudogene with retained intron processed gene processed genes processed pseudogene pseudogene by reverse transcription pseudogene by unequal crossing over pseudogene processed transcript pseudogene, beta-tubulin pseudogenes, beta-tubulin pseudogenic gene segment pseudogenic tRNA pseudogenic transcript pseudogenic transcript with retained intron retropseudogene t cell receptor j pseudogene t cell receptor joining pseudogene t cell receptor v pseudogene t cell receptor variable pseudogene transcribed non processed pseudogene transcribed processed pseudogene transcribed unprocessed pseudogene translated nonprocessed pseudogene translated processed pseudogene translated unprocessed pseudogene transposable element pseudogene unitary pseudogene vertebrate immune system pseudogene Nonfunctional DNA sequences that are very similar to the sequences of known genes. Many seem to have arisen as functional gene duplications that subsequently underwent mutation and loss of function. Others are structurally similar to mRNA and seem to have arisen by a reverse transcription event followed by integration into the genome. Some pseudogenes are transcribed and may play a role in regulation of its homologous gene. GV.03.10 National Cancer Institute Thesaurus (NCIT) GV.04 Epigenetic DNA Modification gene silenced gene silenced by DNA methylation gene silenced by DNA modification gene silenced by histone deacetylation gene silenced by histone methylation gene silenced by histone modification methylation-silenced gene regional centromere outer repeat transcript silenced by DNA modification silenced by histone deacetylation silenced by histone methylation silenced by histone modification silenced gene Hereditary variation of DNA not affecting primary sequence. GV.04 Variation Ontology (VariO) GV.04.01 Chromatin Remodeling chromatin assembly chromatin disassemblies chromatin disassembly chromatin modeling chromatin modelling chromatin remodelling chromatin structure variation disassembly, chromatin remodeling, chromatin Chromatin Remodeling involves alterations of the content or activity of DNA-binding and chromatin-associated proteins that affect the function and higher order conformational state of chromatin, as well as the activity of specific genes or functional DNA regions. GV.04.01 National Cancer Institute Thesaurus (NCIT) GV.05 Mobile Genetic Element LTR retrotransposon class i transposon class ii transposon conjugative transposon defective conjugative transposon dna insertion element dna insertion elements dna transposable element dna transposon dna transposons element, dna insertion element, dna transposable element, insertion sequence element, is element, mobile genetic element, retrovirus-like element, tn element, transposable elements, dna insertion elements, dna transposable elements, insertion sequence elements, is elements, mobile genetic elements, retrovirus-like elements, tn elements, transposable endogenous retroviral gene extrachromosomal mobile genetic element foreign transposable element gene, jumping genes, jumping genetic element, mobile genetic elements, mobile insertion element insertion element, dna insertion elements, dna insertion sequence insertion sequence element insertion sequence elements integrase coding region integrated mobile genetic element is element is elements jumping gene jumping genes long terminal repeat retrotransposon mdg1 retrotransposon mdg1 retrotransposons mobile dispersed genetic elements mobile dna mobile element insertion mobile genetic element insertion mobile genetic elements mobile intron natural transposable element nested transposon non LTR retrotransposon nucleic acid mobility p element retroelement retroposon retroposons retrotransposon retrotransposon element retrotransposon, mdg1 retrotransposons retrotransposons, mdg1 retrovirus like elements retrovirus-like element retrovirus-like elements sequence element, insertion sequence elements, insertion tn element tn elements transgenic transposable element transposable element transposable element CDS transposable element gene transposable element insertion site transposable element, dna transposable elements transposable elements, dna transposase transposon transposon element transposon site hybridization transposon, dna transposon, ty1 transposons, dna transposons, ty1 ty1 transposon ty1 transposons A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome. GV.05 Sequence Types and Features Ontology (SO) GV.06 Mosaicism mosaic The presence of more than one genetically distinct cell line in germ and/or somatic cells. GV.06 National Cancer Institute Thesaurus (NCIT) GV.07 Nucleobase Modification allelic frequency codon change plus codon deletion codon change plus codon insertion codon deletion codon insertion conservative decrease in cds length conservative increase in cds length conservative inframe deletion conservative inframe insertion covariant position cryptic gene cryptogene deleted sequence deletion abnormality deletion mutation disruptive decrease in cds length disruptive increase in cds length disruptive inframe deletion disruptive inframe insertion edited RNA edited by C insertion and dinucleotide insertion edited by G addition edited transcript editing variant in-frame insertion inframe codon gain inframe codon loss inframe decrease in cds length inframe deletion inframe increase in cds length inframe insertion insert AA insert AU insert C insert CU insert G insert GC insert GU insert U insert dinucleotide insert site insertion mutation insertion mutation abnormality insertion site mRNA not polyadenylated mistranscribed RNA modified DNA modified DNA base modified RNA modified RNA base modified cytosine modified guanine modified uridine mutation, deletion mutation, insertion nonframeshift deletion nonframeshift insertion novel sequence insertion nucleotide deletion nucleotide insertion GV.07 GV.08 Phenotypic Variation allelic loss allelic losses antimorphic protein variation complex change of translational product variant functional variant missing RNA missing protein neomorphic protein variation not related to clinical phenotype phenotypic variant polypeptide loss of function variant polypeptide partial loss of function protein loss of function related to clinical phenotype variant phenotype Any mutation that encodes an altered gene product that acts to antagonize the wild-type allele. Dominant negative mutations are characterized by a dominant or semi-dominant phenotype, and usually result in loss of function. GV.08 National Cancer Institute Thesaurus (NCIT) GV.08.01 Dominant Negative Variant dominant negative dominant negative protein variation dominant negative variation A variant where the mutated gene product adversely affects the other (wild type) gene product. GV.08.01 Sequence Types and Features Ontology (SO) GV.08.02 Gain of Function Variant gain of function variation polypeptide gain of function variant protein gain of function sequence variant causing gain of function of polypeptide A sequence variant whereby new or enhanced function is conferred on the gene product. GV.08.02 Sequence Types and Features Ontology (SO) GV.08.03 Gene Expression Variation DPE motif RNA degradation by decay RNA degradation by no-go mediated decay RNA degradation by nonsense-mediated decay RNA degradation by nonstop-mediated decay UAA stop codon signal allelically excluded gene attachment site blocked reading frame cis regulatory frameshift element decayed RNA decreased transcript level variant decreased transcript stability variant decreased transcription rate variant decreased translational product level downstream core promoter element downstream-gene gene silenced by RNA interference gene silenced by rnai gene with non canonical start codon gene with start codon CUG gene with stop codon read through increased transcript level variant increased transcript stability variant increased transcription rate variant increased translational product level level of transcript variant ncrna ncrna exonic ncrna intronic ncrna utr3 ncrna utr5 near-gene-3 near-gene-5 rate of transcription variant regulatory region ribosensor ribosensors riboswitch riboswitch rna riboswitches rna interference silenced gene rnai silenced gene sense intronic ncRNA sequence variation affecting level of transcript sequence variation decreasing level of transcript sequence variation increasing level of transcript silenced by RNA interference silencer transcript stability variant transcriptionally repressed translational product level variant upstream-gene GV.08.03 GV.08.04 Genetic Interaction additive genetic interaction defined by inequality asynthetic genetic interaction defined by inequality conditional genetic interaction defined by inequality double nonmonotonic genetic interaction defined by inequality double nonmonotonic interaction epistatic genetic interaction epistatic genetic interaction defined by inequality epistatis genetic inequality genetic interaction defined by inequality negative gen int negative genetic interaction neutral genetic interaction neutral gent int noninteractive genetic interaction defined by inequality positive genetic interaction positive gent int single nonmonotonic genetic interaction defined by inequality suppressive genetic interaction defined by inequality synthetic genetic interaction defined by inequality Two genes A and B "genetically interact" when the phenotype generated as the result of variations in both genes (double variant ab) is unexpectedly not just a combination of the phenotypes of the two single variants a and b. GV.08.04 Variation Ontology (VariO) GV.08.05 Lethal Variant lethal variants GV.08.05 GV.08.06 Loss of Function Variation loss of function variant A sequence variant whereby the gene product has diminished or abolished function. GV.08.06 Sequence Types and Features Ontology (SO) GV.08.07 Loss of Heterozygosity Variant heterozygosity loss heterozygosity, loss of loss of heterozygosity A functional variant whereby the sequence alteration causes a loss of function of one allele of a gene. GV.08.07 Sequence Types and Features Ontology (SO) GV.08.08 Null Mutation null mutations A variant whereby the gene product is not functional or the gene product is not produced. GV.08.08 Sequence Types and Features Ontology (SO) GV.09 Protein Variation 3D polypeptide structure variant C-terminal protein elongation N-terminal protein elongation artificial protein variation changed domain orientation conformational change variant deletion of a post translational modification site elongated in frame polypeptide C terminal elongated in frame polypeptide N terminal elongation elongated out of frame polypeptide C terminal elongated out of frame polypeptide N terminal generation of a novel post translational modification site global protein conformation change inactive catalytic site inactive ligand binding site intein intein containing intein encoding region intervening protein sequence intervening protein sequences intron, protein introns, protein local protein conformation change mistranslated protein polypeptide function variant polypeptide fusion polypeptide localization variant polypeptide post translational processing variant polypeptide sequence variant polypeptide truncation polypeptide variation site post translational modification post translationally regulated by protein stability post-translational modification post-translational modification alteration post-translationally regulated by protein stability posttranslational modification prion acquisition prion formation protein altering variant protein conformational change protein fusion protein intron protein introns protein modification protein overpacking protein sequence, intervening protein sequences, intervening protein truncation protein truncation abnormality protein variation of genetic origin protein/amino acid biochemistry, post-translational modification pyrrolysine loss selenocysteine loss sequence retaining amino acid insertion sequence, intervening protein sequences, intervening protein structural interaction variant translational product function variant translational product structure variant truncation variation affecting protein variation affecting protein function variation affecting protein property variation affecting protein structure variation burying exposed region variation emerging at protein level variation exposing buried region variation generating a novel protein processing site variation preventing polypeptide processing wobble base pair wobble pair Effects of a variation on protein level. GV.09 Variation Ontology (VariO) GV.09.01 Amino Acid Variation amino acid deletion amino acid indel amino acid insertion amino acid substitution amino acid substitutions amphigoric amino acid indel amphigoric amino acid insertion modarg modified L arginine modified L phenylalanine modified L proline modified L tryptophan modified L valine modified l-arginine modified l-phenylalanine modified l-proline modified l-tryptophan modified l-valine modphe modpro modtrp modval non conservative amino acid substitution rare amino acid rare amino acid variant sequence retaining amino acid deletion substitution, amino acid substitutions, amino acid GV.09.01 GV.10 RNA Variation RNA Variations artificial RNA variation conservation of RNA variation site mature miRNA variant Effects of a variation on RNA level. GV.10 Variation Ontology (VariO) GV.10.01 Alternative Transcript 3' splice site 3' splice sites 5' splice site 5' splice sites Alternative pre-mRNA transcript acceptor site, splice acceptor sites, splice alternate sequence site alternately spliced gene alternately spliced gene encoding greater than one transcript alternately spliced gene encoding one transcript alternative splice site alternative splice sites alternatively spliced gene encoding greater than 1 polypeptide coding regions overlapping alternatively spliced transcript alternatively spliced transcript encoding greater than 1 polypeptide different start codon different stop codon coding regions non overlapping coding RNA sequence coding-near-splice coding-notmod3-near-splice coding-unknown-near-splice cryptic splice acceptor cryptic splice acceptor activation cryptic splice donor cryptic splice donor activation cryptic splice signal cryptic splice site cryptic splice site activation cryptic splice sites decreased polyadenylation variant donor site, splice donor sites, splice encodes alternate transcription start sites encodes alternately spliced transcripts encodes different polypeptides different stop encodes overlapping peptides different start end overlap essential splice site extended intronic splice region variant gene with trans spliced transcript incomplete transcript exonic variant incomplete transcript intronic variant incomplete transcript splice region variant increased polyadenylation variant non coding transcript splice region variant non-coding region of protein coding RNA sequence non-coding-exon non-coding-exon-near-splice polyadenylation variant splice acceptor site splice acceptor sites splice donor 5th base variant splice donor region variant splice donor site splice donor sites splice overlap splice polypyrimidine tract variant splice site acceptor splice site branch splice site branch u12 splice site donor splice site region splice site, 3' splice site, 5' splice site, alternative splice site, cryptic splice sites, 3' splice sites, 5' splice sites, alternative splice sites, cryptic splice-acceptor splice-donor spliceosomal intron three prime UTR intron trans spliced transcript trans-spliced transcript upstream transcript variant GV.10.01 GV.10.02 RNA Base Substitution RNA substitution edited by A to I substitution edited by C to U substitution edited transcript by A to I substitution substitute A to I substitute C to U Substitution of RNA nucleotide. GV.10.02 Variation Ontology (VariO) GV.10.03 RNA Indel transcript edited by U insertion/deletion A complex RNA variation consisting of both nucleotide insertion(s) and deletion(s). GV.10.03 Variation Ontology (VariO) GV.10.03.01 RNA Insertion RNA insertions Addition of one or more nucleotides between adjacent nucleotides in RNA sequence. GV.10.03.01 Variation Ontology (VariO) GV.10.03.02 RNA Deletion 5 prime UTR truncation utr 5 deleted One or more continuous nucleotides are missing from RNA sequence. GV.10.03.02 Variation Ontology (VariO) GV.10.04 RNA Modification RNA Modifications RNA modification by nonsense-associated altered splicing Post transcriptionally modified RNA. GV.10.04 Variation Ontology (VariO) Sub Class Of