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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
ITGB6 ENST00000283249 53.20 66.75 60.49 0.63 0.56 0.44 1.75 1.22 1.58
MOB3C ENST00000271139 53.21 64.65 59.10 0.63 0.48 0.49 1.75 1.23 1.68
KCNK13 ENST00000282146 53.22 35.20 42.48 0.63 0.76 0.68 1.75 1.58 2.00
DIS3L ENST00000319212 53.22 48.98 50.10 0.63 0.65 0.62 1.75 2.04 1.90
RIPK1 ENST00000259808 53.23 25.72 37.70 0.63 1.24 0.84 1.75 1.05 2.01
TMEM240 ENST00000378733 53.23 47.05 49.03 0.63 0.68 0.72 1.75 1.99 1.83
GIF ENST00000257248 53.24 42.60 46.60 0.63 0.59 0.66 1.75 1.89 1.89
C1QL1 ENST00000253407 53.24 94.64 77.08 0.63 0.23 0.37 1.75 0.24 0.61
TRIM72 ENST00000322122 53.25 55.01 53.56 0.63 0.57 0.63 1.75 1.63 1.80
SLC3A2 ENST00000377891 53.25 50.35 50.87 0.63 0.66 0.67 1.75 1.96 1.85
ACP5 ENST00000592828 53.26 39.56 45.05 0.63 0.68 0.70 1.75 1.65 2.02
TIMM50 ENST00000314349 53.26 32.67 41.16 0.63 0.85 0.76 1.75 1.45 2.02
CEP135 ENST00000257287 53.27 44.18 47.47 0.63 0.62 0.63 1.75 1.95 1.89
TANGO6 ENST00000261778 53.27 44.12 47.46 0.63 0.61 0.63 1.75 1.98 1.88
SYTL1 ENST00000543823 53.28 56.49 54.43 0.63 0.52 0.57 1.74 1.54 1.75
RPP25L ENST00000297613 53.28 58.73 55.73 0.63 0.54 0.53 1.74 1.43 1.74
PPP1R18 ENST00000274853 53.29 36.05 43.03 0.63 0.80 0.67 1.74 1.58 2.02
ACPP ENST00000351273 53.29 76.44 66.52 0.63 0.43 0.51 1.74 0.85 1.21
CCL5 ENST00000293272 53.30 90.62 74.86 0.63 0.25 0.39 1.74 0.37 0.64
ACTR5 ENST00000243903 53.30 55.03 53.62 0.62 0.57 0.63 1.74 1.63 1.82
ESPNL ENST00000343063 53.31 48.88 50.07 0.62 0.63 0.62 1.74 2.03 1.92
KRT76 ENST00000332411 53.31 76.51 66.60 0.62 0.42 0.52 1.74 0.83 1.20
PVRL2 ENST00000252483 53.32 14.84 32.27 0.62 1.92 0.90 1.75 0.62 1.61
C12orf49 ENST00000261318 53.32 55.52 53.89 0.62 0.56 0.61 1.75 1.61 1.77
FUCA2 ENST00000002165 53.33 50.09 50.77 0.62 0.67 0.66 1.75 1.98 1.84

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