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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
WDR83OS ENST00000596731 30.40 84.86 57.58 1.01 0.27 0.51 1.60 0.43 1.67
AL133373.1 ENST00000596306 99.61 97.63 99.75 0.12 0.22 0.12 0.13 0.19 0.04
MCM3 ENST00000596288 33.61 40.94 35.47 0.96 0.61 0.87 1.71 1.79 1.77
NUP62 ENST00000596217 62.67 14.22 36.53 0.59 2.06 0.85 1.29 0.61 1.90
ZNF99 ENST00000596209 96.27 75.14 88.81 0.12 0.51 0.19 0.11 0.91 0.28
ZNF714 ENST00000596143 97.19 87.65 95.15 0.10 0.24 0.09 0.11 0.36 0.10
AC114494.1 ENST00000596131 67.12 94.29 83.99 0.61 0.24 0.35 1.04 0.25 0.42
AL353354.2 ENST00000596102 90.12 97.78 96.88 0.16 0.21 0.08 0.25 0.17 0.07
RPS5 ENST00000596046 0.73 13.60 4.46 4.35 2.05 3.71 0.19 0.59 0.25
ZNF480 ENST00000595962 98.07 67.70 86.13 0.11 0.53 0.33 0.11 1.19 0.33
AC018867.2 ENST00000595956 89.68 88.43 94.01 0.16 0.23 0.09 0.29 0.37 0.11
IL4I1 ENST00000595948 78.41 49.03 65.18 0.34 0.66 0.52 0.66 2.03 1.30
AP000695.1 ENST00000595927 87.83 99.74 96.60 0.23 0.17 0.08 0.36 0.11 0.08
MBD3L1 ENST00000595891 80.24 99.48 92.10 0.32 0.16 0.14 0.58 0.13 0.16
SPIB ENST00000595883 73.54 9.00 39.63 0.34 2.44 0.78 0.78 0.47 2.04
KLK13 ENST00000595793 64.09 62.47 64.62 0.57 0.53 0.51 1.20 1.31 1.32
FAM71E1 ENST00000595790 71.18 82.03 79.91 0.42 0.34 0.37 0.86 0.50 0.52
AC022400.2 ENST00000595757 90.16 93.32 94.50 0.16 0.28 0.10 0.25 0.29 0.12
SLC35E1 ENST00000595753 25.64 35.93 28.93 1.33 0.80 0.81 1.20 1.58 1.31
ZNF473 ENST00000595661 72.07 21.99 45.73 0.34 1.48 0.67 0.81 0.81 1.98
ZNF468 ENST00000595646 96.87 96.07 98.63 0.09 0.21 0.10 0.11 0.20 0.05
ZNF320 ENST00000595635 98.30 79.48 91.73 0.09 0.38 0.14 0.10 0.66 0.18
MYO9B ENST00000595618 23.29 3.12 10.82 1.39 3.45 2.19 1.09 0.28 0.43
ZNF114 ENST00000595607 98.59 92.25 97.90 0.10 0.25 0.09 0.11 0.31 0.04
C5AR2 ENST00000595464 83.38 76.86 83.47 0.29 0.43 0.33 0.52 0.81 0.40

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