Retina International's Scientific Newsletter
	Mutation Nomenclature

Recent update from: 07.12.2003

• Coding sequences are given in upper case letters, non-coding sequences are given in lower case letters.
• A number at the start followed by letters refers to the nucleotide (e.g. 54G>C), a letter at the start refers to the single letter code of amino acids (e.g. G54C).
• Deletions or insertions are referred by giving the first affected nucleotide on the coding strand followed by "del" or "ins" and the number of affected nucleotides or - if only few - the affected ncleotides. A prediction of the number of the remaining codons before the first downstream translation termination codon is added. Note - the codon numbered 1 is the codon of the first deleted nucleotide, the last codon is the predicted termination codon. Frameshifting is predicted before the number of remaining amino acids. (e.g. 567delGGfs4).
• In-frame deletions or insertions are referred like frameshifting changes. Since in-frame mutations do tot affect the following codons a prediction of the first downstream translation termination codon is omitted. (e.g. 567delGGT)
• Deletions of complete exons or genes are given by indication of the affected exons and/or flanking affected marker loci (e.g. del ex 5 - DXS165). Nucleotide / codon positions given indicate the last nucleotide / codon of the unaffected exon downstream.
• Missens mutations are given by the nucleotide exchange (e.g. G-C or g-c in introns).
• Introns are referred as IVS given the number of the previous exon. The mutations therein are given by the nucleotide position counting from the end of the previous exon indicating downstream nucleotides (e.g. IVS3+5deltt) or back from the beginning of the following exon indicating upstream nucleotides (e.g. IVS3-5g-c).
• Splice site mutations do not have a special indication. Mutations inside the exon affecting splice sites are given as usual exonic mutations. Mutations inside the introns are given as usual intronic mutations since the splice site effect depends on a set of nucleotides along the splice sites.
• Amino acid positions are given starting with the initiation codon being number 1.
• Amino acids are given by the standard triple letter code using ter for termination or stop codons.
• Polymorphisms, that do not change the amino acid, are given by the nucleotide position followed by the change in nucleotide divided by a slash (e.g. 2457G/C).
• Polymorphisms, that do change the amino acid, are given by the amino acid change divide by a slash and the codon number (e.g. Thr/Met 545)
• Additionally, herein the phrase UTR is used for the 5' and 3' untranslated region indicating the upstream UTR by positive numbers and the downstream UTR by negative numbers (e.g. UTR-3c-g, UTR+5insc).
• Also, all sequences that have been adjusted to a sequence as indicated will be presented as based on the cDNA.

Den Dunnen,J.T. and Paalman,M.H. Standardizing mutation nomenclature: why bother? 2003; Hum Mutat. 22: 181-182.
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