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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
ARID4A ENST00000355431 10.98 2.83 4.19 1.87 3.51 3.77 0.58 0.28 0.23
ALDH1A1 ENST00000297785 10.99 14.45 10.27 1.87 2.04 2.20 0.58 0.61 0.42
TMEM189-UBE2V1 ENST00000341698 10.99 34.60 20.92 1.86 0.80 1.44 0.58 1.54 0.87
TMEM189 ENST00000557021 11.00 34.64 20.95 1.86 0.80 1.43 0.58 1.53 0.88
XPO6 ENST00000304658 11.00 0.11 2.98 1.86 4.11 3.98 0.58 0.28 0.23
NKRF ENST00000542113 11.01 4.59 5.06 1.85 3.23 3.64 0.58 0.32 0.25
STYX ENST00000354586 11.01 26.21 16.40 1.85 1.19 1.71 0.58 1.08 0.68
TNKS2 ENST00000371627 11.02 24.08 15.32 1.85 1.37 1.80 0.58 0.98 0.66
STIM1 ENST00000300737 11.02 14.23 10.18 1.85 2.06 2.23 0.58 0.61 0.42
MAP3K4 ENST00000392142 11.03 5.08 5.35 1.85 3.21 3.53 0.58 0.33 0.25
VPS25 ENST00000253794 11.03 39.09 23.15 1.85 0.70 1.19 0.58 1.63 1.01
MTCP1 ENST00000369476 11.04 43.25 25.22 1.85 0.62 1.05 0.58 1.92 1.16
NEURL ENST00000369780 11.04 40.15 23.70 1.85 0.62 1.15 0.59 1.72 1.02
OAZ2 ENST00000326005 11.05 39.93 23.59 1.86 0.63 1.19 0.59 1.69 1.02
USP34 ENST00000398571 11.05 0.89 3.41 1.85 4.08 3.87 0.59 0.29 0.23
EPHA7 ENST00000369303 11.06 2.07 3.90 1.85 3.71 3.75 0.59 0.29 0.23
RPL35A ENST00000464167 11.06 18.33 12.29 1.85 1.51 2.25 0.59 0.75 0.50
TRPS1 ENST00000395715 11.07 1.43 3.64 1.85 3.94 3.84 0.59 0.26 0.23
TRPM3 ENST00000377110 11.07 22.23 14.37 1.83 1.53 2.01 0.59 0.81 0.59
DRG1 ENST00000331457 11.08 29.23 18.10 1.83 1.13 1.67 0.59 1.36 0.78
RBMS1 ENST00000348849 11.08 23.63 15.13 1.83 1.39 1.86 0.59 0.93 0.64
CCDC132 ENST00000305866 11.09 15.13 10.72 1.83 1.91 2.20 0.59 0.66 0.43
EFNA5 ENST00000333274 11.09 11.83 8.82 1.83 2.09 2.49 0.59 0.58 0.38
TRIM71 ENST00000383763 11.10 4.49 5.05 1.83 3.27 3.66 0.59 0.32 0.25
HOOK3 ENST00000307602 11.10 3.22 4.43 1.82 3.47 3.72 0.59 0.28 0.25

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