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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
TMEM213 ENST00000442682 87.29 73.57 83.82 0.23 0.52 0.34 0.38 1.03 0.42
EMCN ENST00000296420 87.30 53.55 73.16 0.23 0.63 0.43 0.38 1.70 0.79
FAM131C ENST00000375662 87.30 46.41 68.91 0.23 0.73 0.46 0.38 2.04 1.04
TTC40 ENST00000368586 87.31 35.78 62.38 0.23 0.78 0.48 0.38 1.58 1.41
MS4A3 ENST00000278865 87.31 64.43 79.21 0.23 0.48 0.38 0.38 1.22 0.54
PKD1L1 ENST00000289672 87.32 38.51 64.20 0.23 0.73 0.51 0.38 1.68 1.36
NDUFC1 ENST00000544855 87.33 70.24 82.17 0.23 0.52 0.35 0.38 1.12 0.45
FAM184B ENST00000265018 87.33 46.18 68.78 0.23 0.73 0.46 0.38 2.04 1.06
DEFB116 ENST00000400549 87.34 96.76 94.75 0.23 0.23 0.09 0.38 0.19 0.11
ANXA8L2 ENST00000374277 87.34 87.34 90.38 0.23 0.22 0.15 0.38 0.41 0.21
HEPN1 ENST00000408930 87.35 99.51 96.20 0.23 0.16 0.07 0.38 0.13 0.10
DHRS2 ENST00000344777 87.35 77.65 85.81 0.23 0.42 0.33 0.38 0.79 0.33
CCDC129 ENST00000451887 87.36 74.64 84.31 0.23 0.54 0.34 0.38 0.98 0.41
AL359736.1 ENST00000422229 87.36 91.56 92.11 0.23 0.23 0.14 0.38 0.32 0.16
MX2 ENST00000330714 87.37 43.03 66.93 0.23 0.61 0.53 0.38 1.89 1.19
UGT2B7 ENST00000305231 87.37 78.55 86.21 0.23 0.40 0.33 0.38 0.73 0.33
OR5T2 ENST00000313264 87.38 90.01 91.55 0.23 0.25 0.15 0.38 0.37 0.18
FANCF ENST00000327470 87.38 80.80 87.26 0.23 0.35 0.28 0.38 0.57 0.31
MAFF ENST00000338483 87.39 82.72 88.22 0.23 0.33 0.23 0.38 0.50 0.30
ZNF280A ENST00000302097 87.39 85.22 89.43 0.23 0.25 0.18 0.38 0.45 0.24
FLYWCH1 ENST00000416288 87.40 73.10 83.63 0.23 0.53 0.33 0.38 1.02 0.40
SERPINB4 ENST00000341074 87.40 93.69 93.25 0.23 0.28 0.14 0.38 0.27 0.15
HIST1H1C ENST00000343677 87.41 92.04 92.42 0.23 0.24 0.14 0.38 0.33 0.15
ENTHD2 ENST00000300714 87.41 67.65 80.84 0.23 0.53 0.39 0.38 1.19 0.51
TPSAB1 ENST00000338844 87.42 96.75 94.81 0.23 0.23 0.09 0.38 0.19 0.11

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