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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
SOS1 ENST00000426016 6.59 2.54 2.24 2.99 3.56 4.08 0.37 0.29 0.23
IVNS1ABP ENST00000367498 6.60 11.70 6.49 2.97 2.09 3.05 0.37 0.57 0.32
ZMYM2 ENST00000382869 6.60 10.98 6.08 2.97 2.09 3.26 0.37 0.52 0.30
PRPF31 ENST00000321030 6.61 8.15 4.73 2.97 2.56 3.68 0.37 0.44 0.25
IPO5 ENST00000261574 6.61 1.87 2.00 2.97 3.76 4.11 0.37 0.26 0.23
CHD1 ENST00000284049 6.62 2.38 2.18 2.97 3.62 4.06 0.37 0.29 0.23
HPCA ENST00000373467 6.62 32.06 17.19 2.97 0.91 1.64 0.37 1.47 0.73
GNB2 ENST00000303210 6.63 9.80 5.54 2.97 2.40 3.42 0.37 0.49 0.26
ARHGAP35 ENST00000404338 6.63 0.22 1.44 2.97 4.13 4.33 0.37 0.28 0.23
RSPRY1 ENST00000537866 6.64 4.95 3.24 2.97 3.26 3.88 0.37 0.32 0.24
TAOK2 ENST00000308893 6.64 6.00 3.70 2.97 2.82 3.81 0.37 0.35 0.23
RNFT2 ENST00000257575 6.65 41.94 22.47 2.97 0.61 1.16 0.37 1.83 0.97
JAK1 ENST00000342505 6.65 7.13 4.20 2.97 2.58 3.77 0.37 0.37 0.24
ING2 ENST00000302327 6.66 24.11 12.94 2.99 1.35 2.09 0.37 0.98 0.53
ACVR1 ENST00000263640 6.66 21.63 11.76 2.99 1.44 2.21 0.37 0.81 0.46
GABRG2 ENST00000414552 6.67 19.24 10.54 2.99 1.47 2.19 0.37 0.75 0.43
DDX1 ENST00000381341 6.67 9.16 5.19 2.99 2.48 3.59 0.37 0.47 0.26
RASA1 ENST00000274376 6.68 2.18 2.16 2.99 3.66 4.07 0.37 0.29 0.23
UBE2F ENST00000272930 6.68 16.53 8.98 2.99 1.78 2.45 0.37 0.69 0.38
BHLHE22 ENST00000321870 6.69 28.92 15.64 2.99 1.15 1.75 0.37 1.30 0.67
XPO4 ENST00000255305 6.69 2.72 2.38 2.99 3.53 4.05 0.37 0.29 0.23
ATP5G3 ENST00000284727 6.70 45.77 24.24 2.99 0.75 1.11 0.37 2.02 1.05
KDM1A ENST00000400181 6.70 9.35 5.28 2.99 2.48 3.54 0.37 0.49 0.25
IP6K2 ENST00000328631 6.71 14.25 7.85 2.99 2.06 2.63 0.37 0.61 0.35
KCNN3 ENST00000271915 6.71 13.55 7.50 2.99 2.06 2.77 0.37 0.60 0.33

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