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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
RP13-996F3.5 ENST00000559949 91.81 61.58 79.00 0.14 0.54 0.39 0.20 1.41 0.53
PTGER1 ENST00000292513 91.82 79.44 88.96 0.14 0.38 0.19 0.20 0.66 0.28
SMIM9 ENST00000369529 91.82 91.35 94.35 0.14 0.23 0.10 0.20 0.34 0.12
C17orf107 ENST00000381365 91.83 80.30 89.38 0.14 0.37 0.18 0.20 0.58 0.24
RP11-17M16.1 ENST00000532511 91.83 90.25 93.81 0.14 0.25 0.10 0.20 0.38 0.13
GRID2IP ENST00000457091 91.84 19.07 54.04 0.14 1.52 0.59 0.20 0.76 1.76
RP11-706O15.1 ENST00000425492 91.84 88.26 93.02 0.14 0.23 0.14 0.20 0.37 0.15
AC226150.4 ENST00000545350 91.85 98.63 97.51 0.14 0.20 0.08 0.20 0.15 0.07
C21orf49 ENST00000382375 91.85 88.39 93.09 0.14 0.23 0.14 0.20 0.37 0.15
TMEM253 ENST00000418511 91.86 85.01 91.17 0.14 0.25 0.15 0.20 0.45 0.18
USP17L18 ENST00000504209 91.87 98.64 97.96 0.14 0.20 0.09 0.20 0.15 0.04
TMEM75 ENST00000539634 91.87 98.65 97.66 0.14 0.20 0.09 0.20 0.15 0.06
GOLGA8H ENST00000566740 91.88 97.36 96.26 0.14 0.22 0.07 0.20 0.19 0.09
AC124890.1 ENST00000399333 91.88 98.66 98.03 0.14 0.20 0.09 0.20 0.15 0.05
RP11-351M8.1 ENST00000560560 91.89 96.97 97.26 0.14 0.24 0.08 0.20 0.19 0.07
DEFB106A ENST00000335186 91.89 96.97 97.32 0.15 0.24 0.08 0.20 0.19 0.07
PPP1R3G ENST00000405617 91.90 83.06 90.70 0.15 0.30 0.15 0.20 0.49 0.20
PROB1 ENST00000434752 91.90 39.23 67.63 0.15 0.70 0.51 0.20 1.63 1.13
XXbac-BPG32J3.20 ENST00000461287 91.91 96.22 97.05 0.15 0.22 0.08 0.20 0.19 0.07
C9orf169 ENST00000359069 91.91 89.76 93.00 0.15 0.27 0.14 0.20 0.37 0.15
RBMY1F ENST00000303766 91.92 93.29 95.59 0.15 0.28 0.08 0.20 0.30 0.11
RP11-433C9.2 ENST00000419960 91.92 70.37 84.69 0.15 0.52 0.34 0.20 1.09 0.40
C20orf201 ENST00000308906 91.93 93.55 96.54 0.15 0.28 0.07 0.20 0.28 0.07
ZMYM6NB ENST00000373337 91.93 78.64 88.09 0.15 0.40 0.23 0.20 0.74 0.30
FOXD4L5 ENST00000377420 91.94 98.71 98.07 0.15 0.18 0.09 0.20 0.15 0.05

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