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Genes Fold Enrichment Color Codes
  • Gene Name, Canonical Transcript - gene identifiers from gnomAD database (Build 37)
  • GeVIR % - gene rank measured in percentiles based on Gene Variation Intolerance Ranking (GeVIR) (low values indicate more variation intolerant genes, which is also true for "LOEUF %" and "VIRLoF %"). GeVIR is a method which we developed and applied on a list of 19,361 genes to sort them based on number, length and evolutionary conservation of regions without functional variants (i.e. between two missense, loss-of-function, insertion or delition variants) in gnomAD database (version 2.0.1). Only canonical transcripts were analysed.
  • LOEUF % - gene rank measured in percentiles based gnomAD loss-of-function observed/expected upper bound fraction (LOEUF) (see Figure 1). For more information about this metric, please read "Constraint" section of MacArthur Lab blog post. If you use this metric please cite gnomAD flagship paper and use most up-to-date values from gnomAD website.

    LoF observed/expected (o/e) upper Confidence Interval (CI)

    Figure 1. Screenshot of ELN gene constraint metrics from gnomAD browser

  • VIRLoF % - gene rank measured in percentiles based on both GeVIR and gnomAD LOEUF (shows the best overall performance, see Figure 2). If you use this metric please cite both GeVIR and gnomAD flagship paper.
  • GeVIR AD, LOEUF AD, VIRLoF AD, GeVIR AR, LOEUF AR, VIRLoF AR - to help users interpret gene ranks, we calculated fold enrichment of Autosomal Dominant (AD) and Autosomal Recessive (AR) genes with known molecular basis of disorder in OMIM in a range of +-5% of gene X (see Figure 2). Statistical significant fold enrichements (Fisher Exact Test p-value < 1e-5) are shown in bold in the table. For example CDK19 gene's GeVIR % is 2.37, so examined range is from 0 (2.37-5, rounded to minimal percentile) to 7.37% (2.37+5). Genes in this range are ~4 times more often (4.05 fold enrichement) associated with AD diseases and ~4 times less often (0.25 fold enrichement) associated with AR diseases. Both enrichment of AD genes and deficiency of AR genes is statistical significant. Thus GeVIR metric adds supportive evidence that CDK19 is more likely to be associated with AD than AR disease.

    Gene Percentiles AD AR Fold Enrichment

    Figure 2. Fold Enrichment of known Autosomal Dominant (AD) and Autosomal Recessive (AR) genes of each gene in the ranked lists (GeVIR, LOEUF, VIRLoF. AD genes are enriched among top ranked genes (lowest percentiles), whereas AR genes are enriched among middle ranked genes (approximetly 35-65 percentiles). Combined metric (VIRLoF, purple) shows the best perfornance, i.e. high ranked genes are more often associated with AD than AR diseases, low ranked genes are less often associated with both AD and AR diseases.
Gene Name Canonical Transcript GeVIR % LOEUF % VIRLoF % GeVIR AD LOEUF AD VIRLoF AD GeVIR AR LOEUF AR VIRLoF AR
NRTN ENST00000303212 68.57 72.91 73.54 0.56 0.49 0.40 0.95 1.02 0.74
ZNF70 ENST00000341976 68.58 43.06 55.48 0.56 0.61 0.51 0.95 1.90 1.73
FAM83C ENST00000374408 68.58 59.10 65.34 0.56 0.49 0.53 0.95 1.43 1.32
PCDHGA2 ENST00000394576 68.59 70.45 72.16 0.56 0.52 0.43 0.95 1.08 0.82
ZNF404 ENST00000587539 68.59 63.04 67.67 0.56 0.48 0.52 0.95 1.31 1.13
COL28A1 ENST00000399429 68.60 56.88 64.02 0.56 0.56 0.52 0.95 1.54 1.39
HEXIM2 ENST00000307275 68.60 42.70 55.25 0.56 0.61 0.51 0.95 1.92 1.74
SOX17 ENST00000297316 68.61 19.14 42.11 0.56 1.49 0.71 0.94 0.76 1.99
CYTL1 ENST00000307746 68.61 91.69 83.51 0.56 0.24 0.33 0.94 0.32 0.40
KCNK4 ENST00000539216 68.62 44.61 56.44 0.56 0.66 0.52 0.95 1.97 1.70
RIPPLY2 ENST00000369689 68.62 62.76 67.50 0.56 0.51 0.51 0.95 1.31 1.14
IQCF6 ENST00000398780 68.63 81.53 78.33 0.56 0.33 0.38 0.95 0.53 0.54
KCNN1 ENST00000222249 68.63 18.90 42.01 0.56 1.52 0.70 0.95 0.76 1.99
PLGRKT ENST00000223864 68.64 94.19 84.77 0.56 0.25 0.34 0.95 0.25 0.40
TGS1 ENST00000260129 68.64 48.75 58.79 0.56 0.63 0.51 0.94 2.00 1.65
BCAR1 ENST00000418647 68.65 8.78 36.93 0.56 2.47 0.80 0.94 0.48 1.94
SH2B2 ENST00000536178 68.65 49.22 59.11 0.56 0.66 0.49 0.94 2.02 1.68
METRNL ENST00000320095 68.66 27.21 46.63 0.56 1.25 0.66 0.95 1.15 1.87
CSH2 ENST00000392886 68.66 58.98 65.35 0.56 0.52 0.53 0.95 1.42 1.32
EXD1 ENST00000314992 68.67 72.33 73.26 0.56 0.51 0.43 0.95 1.03 0.79
CYYR1 ENST00000299340 68.67 89.44 82.45 0.56 0.27 0.33 0.95 0.37 0.44
FBXW10 ENST00000395665 68.68 62.04 67.11 0.56 0.56 0.51 0.95 1.37 1.16
MAGEH1 ENST00000342972 68.68 75.52 75.03 0.56 0.44 0.39 0.95 0.90 0.66
ZNF16 ENST00000276816 68.69 69.92 71.93 0.56 0.53 0.43 0.95 1.15 0.81
PRR14L ENST00000327423 68.69 9.91 37.55 0.56 2.33 0.84 0.95 0.50 2.01

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