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Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2017.

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Appendix: Quick Reference

Initial Posting: ; Last Update: September 1, 2016.

Naming conventions for human genes and sequence variants/pathogenic variants

Definitions

Variant

  • Change in a nucleotide sequence
  • Change may be neutral or pathogenic.

Pathogenic variant

  • Sequence variant that is disease causing or associated with increased risk for disease
  • The term likely pathogenic may be used to denote a variant for which there is strong, but not conclusive, evidence for pathogenicity.

Benign variant

  • Sequence variant that is neutral and does not cause disease
  • Sometimes defined as a polymorphism, neutral variant, or SNP (see below), benign variants often have population frequency greater than 1%; however, data may be available to classify much more rare variants as benign.
  • The term likely benign may be used to denote a variant for which there is strong, but not conclusive, evidence for non-pathogenicity.
  • SNP (single-nucleotide polymorphism) is a confusing term, as SNPs in commonly used databases may have a pathogenic, neutral, or unknown clinical consequence.

Summary of Standard Human Sequence Variation Nomenclature

PrefixType of Sequence from which the Number(s) are DerivedExampleInterpretationCommonly Describes
c.coding DNA sequence, where nucleotide #1 is the first nucleotide of the first codonc.535T>CThe T at nucleotide number 535 of the coding region changed to a C.Nucleotide changes in genes (exons, splice sites, untranslated regions)
p.protein amino acid sequence, where #1 is the first amino acid residue of the proteinp.Cys179ArgThe cysteine amino acid at residue 179 changed to an arginine.Amino acid changes in a protein
g.genomic DNA sequence, where #1 is the first nucleotide in a given reference sequenceg.66781T>CThe T at nucleotide 66781 in the genomic reference sequence changed to a C.Nucleotide changes in introns, regulatory, and intergenic regions
m.mitochondrial DNA sequence, where #1 is the first nucleotide in the sequence of the entire mitochondrion genomem.8994T>CThe T at nucleotide 8994 of the mitochondrial genome changed to a C.Coding and non-coding variants of mitochondrial genome

Abbreviations for Amino Acids

NameSymbol
3-Letter1-Letter
AlanineAlaA
ArginineArgR
AsparagineAsnN
Aspartic acidAspD
CysteineCysC
Glutamic acidGluE
GlutamineGlnQ
GlycineGlyG
HistidineHisH
IsoleucineIleI
LeucineLeuL
LysineLysK
MethionineMetM
PhenylalaninePheF
ProlineProP
SerineSerS
ThreonineThrT
TryptophanTrpW
TyrosineTyrY
ValineValV
stop codonTer 1
*

2

1.

Previously designated as X or *
2. Previously designated as X

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Bookshelf ID: NBK1528

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