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variant(), var()

The variant(<expression>) or var(<expression>) function can be used as an argument within a geneAbundance(), rnaAbundance(), microRNAAbundance(), or proteinAbundance() to indicate a sequence variant of the specified abundance. The var() function takes HGVS variant description expression, e.g., for a substitution, insertion, or deletion variant. Multiple var() arguments may be applied to an abundance term.

Protein examples

reference allele
p(HGNC:CFTR, var(=))

This is different than p(HGNC:CFTR), the root protein abundance, which includes all variants.

unspecified variant
p(HGNC:CFTR, var(?))
substitution
p(HGNC:CFTR, var(p.Gly576Ala))
p(REF:NP_000483.3, var(p.Gly576Ala))

CFTR substitution variant Glycine 576 Alanine (HGVS NP_000483.3:p.Gly576Ala). Because a specific position is referenced, a namespace value for a non-ambiguous sequence like the RefSeq ID in the lower example is preferred over the HGNC gene symbol. The p. within the var() expression indicates that the numbering is based on a protein sequence.

deletion
p(HGNC:CFTR, var(p.Phe508del))
p(REF:NP_000483.3, var(p.Phe508del))

CFTR ΔF508 variant (HGVS NP_000483.3:p.Phe508del). Because a specific position is referenced, a namespace value for a non-ambiguous sequence like the RefSeq ID in the lower example is preferred over the HGNC gene symbol. The p. within the var() expression indicates that the numbering is based on a protein reference sequence.

frameshift
p(HGNC:CFTR, var(p.Thr1220Lysfs))
p(REF:NP_000483.3, var(p.Thr1220Lysfs))

CFTR frameshift variant (HGVS NP_000483.3:p.Thr1220Lysfs*7). Because a specific position is referenced, a namespace value for a non-ambiguous sequence like the RefSeq ID in the lower example is preferred over the HGNC gene symbol. The p. within the var() expression indicates that the numbering is based on a protein reference sequence.

DNA (gene) examples

These are all representations of CFTR ΔF508.

SNP
g(SNP:rs113993960, var(delCTT))
chromosome
g(REF:NC_000007.13, var(g.117199646_117199648delCTT))
gene - coding DNA reference sequence
g(HGNC:CFTR, var(c.1521_1523delCTT))
g(REF:NM_000492.3, var(c.1521_1523delCTT))

Because a specific position is referenced, a namespace value for a non-ambiguous sequence like the RefSeq ID in the lower example is preferred over the HGNC gene symbol. The c. within the var() expression indicates that the numbering is based on a coding DNA reference sequence.The coding DNA reference sequence covers the part of the transcript that is translated into protein; numbering starts at the A of the initiating ATG codon, and ends at the last nucleotide of the translation stop codon.

RNA examples

These are all representations of CFTR ΔF508.

coding reference sequence
r(HGNC:CFTR, var(c.1521_1523delCTT)) 
r(REF:NM_000492.3, var(c.1521_1523delCTT))

Because a specific position is referenced, a namespace value for a non-ambiguous sequence like the RefSeq ID in the lower example is preferred over the HGNC gene symbol. The c. within the var() expression indicates that the numbering is based on a coding DNA reference sequence. The coding DNA reference sequence covers the part of the transcript that is translated into protein; numbering starts at the A of the initiating ATG codon, and ends at the last nucleotide of the translation stop codon.

RNA reference sequence
r(HGNC:CFTR, var(r.1653_1655delcuu))
r(REF:NM_000492.3, var(r.1653_1655delcuu))

Because a specific position is referenced, a namespace value for a non-ambiguous sequence like the RefSeq ID in the lower example is preferred over the HGNC gene symbol. The r. within the var() expression indicates that the numbering is based on an RNA reference sequence. The RNA reference sequence covers the entire transcript except for the poly A-tail; numbering starts at the trascrption initiation site and ends at the transcription termination site.

 

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