Why are these genes missing?

HLA-A https://www.ncbi.nlm.nih.gov/gene/3105

HLA-B https://www.ncbi.nlm.nih.gov/gene/3106

For example, I found that EnsDb.Hsapiens.v86 has them, but this package does not provide the same type of object. So, it's not compatible with the same functions.

library(TxDb.Hsapiens.UCSC.hg38.knownGene)

regions <- genes(TxDb.Hsapiens.UCSC.hg38.knownGene)

regions$gene_id[1:5]
#> [1] "1"         "10"        "100"       "1000"      "100009613"

ids <- c("HLA-A" = "3105", "HLA-B" = "3106", "VIM" = "7431")

ids %in% regions$gene_id
#> [1] FALSE FALSE  TRUE

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] reprex_0.3.0
 [2] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [3] EnsDb.Hsapiens.v86_2.99.0
 [4] ensembldb_2.8.1
 [5] AnnotationFilter_1.8.0
 [6] karyoploteR_1.10.5
 [7] regioneR_1.16.5
 [8] TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.6
 [9] GenomicFeatures_1.36.4
[10] AnnotationDbi_1.46.1
[11] Biobase_2.44.0
[12] GenomicRanges_1.36.1
[13] GenomeInfoDb_1.20.0
[14] IRanges_2.18.2
[15] S4Vectors_0.22.1
[16] BiocGenerics_0.30.0
[17] devtools_2.2.1
[18] usethis_1.5.1

^{Created on 2020-01-12 by the reprex package (v0.3.0)}

Try setting the single.strand.genes.only argument for genes() to FALSE, then you will be able to access these genes.

> library(TxDb.Hsapiens.UCSC.hg38.knownGene)
> regions <- genes(TxDb.Hsapiens.UCSC.hg38.knownGene, single.strand.genes.only = FALSE)
> names(regions)[1:5]
[1] "1"     "10"    "100"   "1000"  "10000"
> ids <- c("HLA-A" = "3105", "HLA-B" = "3106", "VIM" = "7431")
> ids %in% names(regions)
[1] TRUE TRUE TRUE
> which(names(regions) == "3105")
[1] 13534
> which(names(regions) == "3106")
[1] 13535
> regions[13534]
GRangesList object of length 1:
$`3105`
GRanges object with 8 ranges and 0 metadata columns:
                 seqnames            ranges strand
                    <Rle>         <IRanges>  <Rle>
  [1]                chr6 29941260-29945884      +
  [2] chr6_GL000250v2_alt   1147348-1267669      +
  [3] chr6_GL000251v2_alt   1369022-1489345      +
  [4] chr6_GL000252v2_alt   1144955-1265390      +
  [5] chr6_GL000253v2_alt   1195801-1200442      +
  [6] chr6_GL000254v2_alt   1286636-1289979      +
  [7] chr6_GL000255v2_alt   1196218-1264879      +
  [8] chr6_GL000256v2_alt   1239073-1307767      +
  -------
  seqinfo: 595 sequences (1 circular) from hg38 genome

> regions[13535]
GRangesList object of length 1:
$`3106`
GRanges object with 6 ranges and 0 metadata columns:
                 seqnames            ranges strand
                    <Rle>         <IRanges>  <Rle>
  [1]                chr6 31269491-31357188      -
  [2] chr6_GL000251v2_alt   2750417-2837604      -
  [3] chr6_GL000253v2_alt   2578541-2665857      -
  [4] chr6_GL000254v2_alt   2612219-2699230      -
  [5] chr6_GL000255v2_alt   2524921-2612898      -
  [6] chr6_GL000256v2_alt   2571447-2659467      -
  -------
  seqinfo: 595 sequences (1 circular) from hg38 genome

>

Hope this helps!