HGVS Mutation Nomenclature Queries

Transcription

1 Molecular Genetics Participants Meeting 2014 HGVS Mutation Nomenclature Queries UK NATIONAL EXTERNAL QUALITY ASSESSMENT SERVICES

2 General Remark HGVS nomenclature aim: To provide unambiguous descriptions for professionals. Do no omit them! Suggestion: Explain their meaning to non-professionals p.? unknown effect on protein p.(tyr25*) Amino acid codon 25 predicted to change from Tyrosine to STOP

3 Q1 Please advise on most appropriate RNA &/or protein nomenclature for a nucleotide change at the last base of an exon which is predicted to abolish normal splicing (but no RNA evidence) Also is it acceptable to omit RNA & protein nomenclature in this instance (bearing in mind that p.? etc. may be confusing to those reading the clinical report). for example c.298g>c, which would lead to p.(ala100pro) if normally spliced but splice-site software indicates that normal splicing is very unlikely; can we just omit the protein nomenclature or should we use p.?; should we include r.spl? or r.(spl?) as well, or is this optional?

4 A1 UK NEQAS for Molecular Genetics RNA & protein descriptions should be provided, even if predicted Example: c.298g>c, r.(298g>c), p.(ala100pro) if normally spliced. Splice-site software: normal splicing is very unlikely: c.298g>c, r.(spl?), p.?

5 Q2 We have started to use genomic coordinates that reference the whole human chromosome when identifying variants, ie Chr6.hg19:g _ dupAGA. Can you provide guidance on appropriate nomenclature?

6 A2 chr6.hg19:g _ dup is correct. AGA is optional Alternatives: chr6:g _ dup (hg19) NC_ :g _ dup

7 Q3 I would like to discuss in general the nomenclature of whole gene deletions detected by MLPA testing

8 A3a Proposed MLPA deletion format: Similar to array-based deletions (last-position present_first-position-deleted)_ (last-position-deleted_first-position-present) c.(233+1_234-1)_(1234+1_1235-1)del

9 A3b Proposed MLPA duplication format: Similar to array-based tandem duplications (last-position normal_first-position-duplicated)_ (last-position-duplicated_first-position-normal) c.(233+1_234-1)_(1234+1_1235-1)dup

10 A3c MLPA insertion at unknown location Format? HGVS Insertion: c.?ins(233+1_234-1)_(1234+1_1235-1) ISCN: c.(233+1_234-1)_(1234+1_1235-1)x3

11 Q4 UK NEQAS for Molecular Genetics Are these the correct nomenclature for the following? Whole Gene Deletion: both breakpoints are unknown and outside the RB1 gene c.(?_-166)_(*1815_?)del NB start of known sequence of RB1 gene; Ref Seq NM_ *1815 RB1 gene poly A site

12 A4 Similar to MLPA Whole Gene Deletion: UK NEQAS for Molecular Genetics both breakpoints are unknown and outside the RB1 gene c.(?_-166)_(*1815_?)del Correct Preferred reference sequence: RefSeq Gene (NG_) or LRG

13 Q5 UK NEQAS for Molecular Genetics Are these the correct nomenclature for the following? Partial Deletion: a) 5 breakpoint is outside the RB1 gene, 3 breakpoint in intron 2 (ex2 is deleted but ex3 is not) c.(?_-166)_264+?del NB start of known sequence of RB1 gene; Ref Seq NM_ last base of RB1 exon 2 b) 5 breakpoint in intron 17 (ex17 is not deleted but ex18 is deleted) 3 breakpoint is outside the RB1 gene c.1696-?_(*1815+?) NB start of RB1 exon 18; *1815 RB1 gene poly A site

14 A5a Similar to MLPA Partial Deletion: a) 5 breakpoint is outside the RB1 gene, 3 breakpoint in intron 2 (ex2 is deleted but ex3 is not) c.(?_-166)_264+?del should be: c.(?_-166)_(264+1_265-1)del NB -166 start of known sequence of RB1 gene; Ref Seq NM_ last base of RB1 exon 2

15 A5b Similar to MLPA Partial Deletion: b) 5 breakpoint in intron 17 (ex17 is not deleted but ex18 is deleted) 3 breakpoint is outside the RB1 gene c.1696-?_(*1815+?) should be: c.(1695+1_1696-1)_(*1815+?) NB 1696 start of RB1 exon 18; *1815 RB1 gene poly A site

16 Q6 Numbering of variants in non-coding exons or 5' of the ATG site. How is this decided such as the GJB2 variant which is 3' of the non-coding exon 1. Deenoyelle et al calls this mutation -3170G>A or alternatively it is called: c.-23+1g>a

17 A6 Numbering of variants in 5 UTR intron: GJB2 variant c.-23+1g>a correct -3170G>A is wrong: c. missing c would refer to position in 5 UTR OR upstream intergenic position

18 Q&A7 Is there nomenclature to indicate acquired/somatic variants? / for mosaicism; // for chimerism c.[=/83g>c] or c.[=//83g>c]

19 Q&A8 We feel that the use of * as a stop codon does not immediately alert a clinician to the possible severity of a mutation, unless they are familiar with nomenclature Explain in text

20 Q9 * for termination codons - we still use X and don't want to use * as this is a wild-card term that would make these mutations unsearchable in databases. We also do not like "Ter" as we don't think this stands out enough compared to missense changes and could be misinterpreted as a missense change by a user not well versed in genetic terminology.

21 A9 Why * for termination codons: X: IUPAC code for unknown amino acid * wild-card: No problem when description between " " p.tyr25* 6 Pubmed hits p.tyr25* 0 Pubmed hits

22 Q10 Amino acid level brackets Which is correct: a) for a homozygous change - p.[(cys282tyr) (;) (Cys282Tyr)] or - p.[(cys282tyr);(cys282tyr)] b) for a heterozygous change - p.[(arg38trp) (;) (Ala44Ser)]

23 A10a Amino acid level allele descriptions Which is correct: a) for a homozygous change - p.[(cys282tyr)(;)(cys282tyr)] or - p.[(cys282tyr);(cys282tyr)] Neither! p.[(cys282tyr)];[(cys282tyr)]

24 A10a Amino acid level allele descriptions b) Heterozygous change, same allele - p.[(arg38trp);(ala44ser)];[=] Heterozygous change, phasing unknown - p.[(arg38trp)(;)(ala44ser)] Compound heterozygous change - p.[(arg38trp)];[(ala44ser)]

25 Q11 In the body of the text in a report we have been advised to use p.(cys282tyr) instead of (p.cys282tyr). We were using the second way in the grammatical sense rather than as HGVS nomenclature.

26 A11 p.(cys282tyr) correct when no RNA analyzed p.cys282tyr correct when RNA analyzed r.845g>a (p.cys282tyr) Only used in combination

27 Q12 In commonly described variants where the protein level change is known from the cdna change is it still necessary to use the () brackets e.g. p.(phe508del) rather than p.phe508del?

28 A12 In general: RNA analyzed, protein change known: p.phe508del Note: Unknown genetic background effects may affect your conclusion!

29 Q13 UK NEQAS for Molecular Genetics p.(glu123ala) we don't use the brackets as these seem unnecessary. HGVS states the brackets can only be omitted if protein/rna analysis have been done but protein and RNA analysis are not widely used for missense and synonymous changes unless there is a reasonable suspicion of a splicing defect. We don't feel that omitting the brackets is misleading to users.

30 A13 p.(glu123ala) indicates a prediction Your evidence only supports DNA level descriptions Missense, synonymous and nonsense changes affect splicing more often than you think. Misclassification can harm patients

31 Finally We would like reassurance that usage of X/Ter or alternative placing of brackets will not cause marks to be lost in NEQAS schemes as both are routinely understood and we will be making any deviations from HGVS clear in our supporting information with reports. For UK NEQAS to decide