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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
C5orf55 ENST00000408966 95.69 98.31 99.05 0.11 0.21 0.11 0.12 0.14 0.04
OR2T12 ENST00000317996 95.69 98.98 99.19 0.11 0.17 0.11 0.12 0.15 0.04
C6orf120 ENST00000332290 95.70 97.64 98.74 0.11 0.21 0.10 0.12 0.19 0.05
CRIPAK ENST00000324803 95.70 98.22 99.00 0.11 0.21 0.11 0.12 0.15 0.04
PRAMEF17 ENST00000376098 95.71 96.74 98.46 0.11 0.23 0.10 0.12 0.19 0.05
OAS1 ENST00000445409 95.71 48.30 74.93 0.11 0.63 0.39 0.12 1.99 0.64
SLC22A25 ENST00000306494 95.72 81.05 91.29 0.11 0.35 0.15 0.12 0.55 0.18
IL36A ENST00000259211 95.72 73.42 87.72 0.11 0.54 0.24 0.12 1.03 0.32
LRG1 ENST00000306390 95.73 93.03 97.12 0.11 0.28 0.08 0.12 0.30 0.07
GAGE10 ENST00000407599 95.73 92.94 97.09 0.11 0.29 0.08 0.12 0.30 0.07
IL9 ENST00000274520 95.74 94.60 97.74 0.11 0.23 0.09 0.12 0.24 0.05
CRYGN ENST00000337323 95.74 92.36 96.86 0.11 0.25 0.08 0.12 0.30 0.07
ANTXRL ENST00000447511 95.75 53.01 77.59 0.11 0.66 0.37 0.12 1.77 0.56
SELV ENST00000335426 95.75 94.83 97.86 0.11 0.23 0.09 0.12 0.24 0.04
ZNF43 ENST00000354959 95.76 88.54 94.92 0.11 0.24 0.09 0.11 0.36 0.11
CRLF2 ENST00000381567 95.76 76.01 89.01 0.11 0.44 0.19 0.11 0.86 0.27
C10orf120 ENST00000329446 95.77 94.62 97.77 0.11 0.23 0.09 0.11 0.24 0.04
PSG1 ENST00000244296 95.78 97.49 98.70 0.11 0.22 0.10 0.11 0.19 0.05
RFPL2 ENST00000400237 95.78 89.60 95.45 0.11 0.27 0.08 0.11 0.37 0.11
IFNA1 ENST00000276927 95.79 98.62 99.14 0.11 0.20 0.11 0.11 0.15 0.04
C14orf180 ENST00000557649 95.79 79.26 90.60 0.11 0.38 0.15 0.11 0.67 0.20
USP17L2 ENST00000333796 95.80 98.83 99.18 0.11 0.16 0.11 0.11 0.14 0.04
MRGPRX3 ENST00000396275 95.80 99.89 99.42 0.11 0.17 0.11 0.11 0.11 0.05
RP11-625H11.1 ENST00000558940 95.81 91.10 96.18 0.11 0.25 0.07 0.11 0.35 0.10
RP11-934B9.3 ENST00000555591 95.81 82.06 91.75 0.11 0.34 0.15 0.11 0.51 0.18

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