My apologies for omitting a line last time.
I fed this to R --vanilla CMD BATCH and the behavior remains as it was.
One might suppose that 3' UTR variants are a subset of AllVariants()...?

## code and sessionInfo() below
library(Homo.sapiens)
library(VariantAnnotation)

EIF2C3 <- org.Hs.egSYMBOL2EG[['EIF2C3']]
## [1] "192669"

EIF2C3.site <- GRanges(c('chr1'), IRanges(start=36521401, width=1))
EIF2C3.site %over%
transcriptsBy(TxDb.Hsapiens.UCSC.hg19.knownGene)[[EIF2C3]]
## TRUE

allVars <- locateVariants(EIF2C3.site, TxDb.Hsapiens.UCSC.hg19.knownGene,
                          AllVariants())
length(allVars)
## 0

threePrimeVars <- locateVariants(EIF2C3.site,
TxDb.Hsapiens.UCSC.hg19.knownGene,
                                 ThreeUTRVariants())
length(threePrimeVars)
## 2

#R Under development (unstable) (2013-02-13 r61937)
#Platform: x86_64-unknown-linux-gnu (64-bit)

#locale:
 #[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 #[3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 #[5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 #[7] LC_PAPER=C                 LC_NAME=C
 #[9] LC_ADDRESS=C               LC_TELEPHONE=C
#[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

#attached base packages:
#[1] parallel  stats     graphics  grDevices utils     datasets  methods
#[8] base

#other attached packages:
 #[1] VariantAnnotation_1.5.36
 #[2] Rsamtools_1.11.16
 #[3] Biostrings_2.27.11
 #[4] Homo.sapiens_1.0.0
 #[5] TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0
 #[6] org.Hs.eg.db_2.8.0
 #[7] GO.db_2.8.0
 #[8] RSQLite_0.11.2
 #[9] DBI_0.2-5
#[10] OrganismDbi_1.1.13
#[11] GenomicFeatures_1.11.8
#[12] GenomicRanges_1.11.29
#[13] IRanges_1.17.32
#[14] AnnotationDbi_1.21.10
#[15] Biobase_2.19.2
#[16] BiocGenerics_0.5.6

#loaded via a namespace (and not attached):
 #[1] biomaRt_2.15.0     bitops_1.0-5       BSgenome_1.27.1    graph_1.37.5

 #[5] RBGL_1.35.0        RCurl_1.95-3       rtracklayer_1.19.9 stats4_3.0.0

 #[9] tools_3.0.0        XML_3.95-0.1       zlibbioc_1.5.0

proc.time()
##   user  system elapsed
##  26.397   0.472  27.247


Thanks for any insight.  I'll also look to see if I can determine the cause.

-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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