variant [var] v.2.0.0

Long form: variant() Short form: var()

The variant(””) or var(””) 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 a http://www.hgvs.org/mutnomen/HGVS variant description expression, e.g., for a substitution, insertion, or deletion variant. Multiple var(“”) arguments may be applied to an abundance term.

Note: For specific sequence changes, one should use a namespace for non-ambiguous sequences like http://www.ncbi.nlm.nih.gov/refseq over an ambiguous namespace like HGNC or MGI.

Function Signatures

variant(StrArg)
  1. String argument of following type(s): /\S+/

Examples

reference allele - this is different than p(HGNC:CFTR), the root protein abundance, which includes all variants.

p(HGNC:CFTR, var("="))

unspecified variant

p(HGNC:CFTR, var("?"))

CFTR substitution variant Glycine at position 576 replaced with Alanine (HGVS NP_000483.3:p.Gly576Ala). The p. within the var(“”) expression indicates that the numbering is based on a protein sequence. This is not a good example as the HGNC:CGFR reference does not specify a specific sequence.

p(HGNC:CFTR, var("p.Gly576Ala"))

CFTR substitution variant Glycine 576 Alanine (HGVS NP_000483.3:p.Gly576Ala). Uses the RefSeq namespace.

p(REF:"NP_000483.3", var("p.Gly576Ala"))

CFTR ΔF508 variant (HGVS NP_000483.3:p.Phe508del). Deletion of Phe at position 508.

p(REF:"NP_000483.3", var("p.Phe508del"))

CFTR frameshift variant (HGVS__ NP_000483.3:p.Thr1220Lysfs*7).

p(HGNC:CFTR, var("p.Thr1220Lysfs"))

CFTR frameshift variant (HGVS__ NP_000483.3:p.Thr1220Lysfs*7).

p(REF:"NP_000483.3", var("p.Thr1220Lysfs"))

DNA SNP CFTR frameshift at ΔF508

g(SNP:rs113993960, var("delCTT"))

DNA Chromosome CFTR frameshift at ΔF508

g(REF:"NC_000007.13", var("g.117199646_117199648delCTT"))

Coding sequence deletion. 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.

g(REF:"NM_000492.3", var("c.1521_1523delCTT"))

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 transcription initiation site and ends at the transcription termination site.

r(REF:"NM_000492.3", var("r.1653_1655delcuu"))
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