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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
OR1S1 ENST00000309433 82.26 92.60 90.49 0.30 0.29 0.14 0.57 0.31 0.21
CDRT1 ENST00000312127 82.26 85.17 86.91 0.30 0.25 0.29 0.57 0.45 0.31
OR2T33 ENST00000318021 82.27 82.75 85.82 0.30 0.33 0.33 0.57 0.50 0.33
REG4 ENST00000354219 82.27 64.97 76.70 0.30 0.49 0.34 0.57 1.24 0.61
LRCH2 ENST00000317135 82.28 8.77 43.92 0.30 2.47 0.61 0.57 0.48 2.02
IL6 ENST00000404625 82.28 38.91 61.27 0.30 0.70 0.44 0.57 1.65 1.48
OPN1MW2 ENST00000369929 82.29 75.14 82.07 0.30 0.51 0.35 0.56 0.91 0.46
CCER1 ENST00000358859 82.29 59.85 73.85 0.30 0.52 0.42 0.56 1.36 0.71
GPR35 ENST00000438013 82.30 78.45 83.76 0.30 0.43 0.34 0.56 0.74 0.41
RGPD3 ENST00000409886 82.30 87.24 87.90 0.30 0.20 0.24 0.56 0.41 0.32
NAT2 ENST00000286479 82.31 88.33 88.45 0.30 0.23 0.22 0.56 0.37 0.29
CLNK ENST00000226951 82.31 88.66 88.63 0.30 0.24 0.22 0.56 0.35 0.28
ODF3B ENST00000329363 82.32 61.52 74.83 0.30 0.54 0.39 0.56 1.40 0.65
ALPP ENST00000392027 82.33 70.80 79.87 0.30 0.49 0.37 0.57 1.08 0.52
GLIPR1 ENST00000266659 82.33 88.82 88.71 0.30 0.25 0.20 0.57 0.35 0.28
C10orf55 ENST00000409178 82.34 95.87 91.88 0.30 0.22 0.14 0.57 0.20 0.17
CCDC120 ENST00000422185 82.34 28.63 55.06 0.30 1.19 0.51 0.57 1.29 1.74
SYTL3 ENST00000297239 82.35 69.65 79.30 0.30 0.53 0.38 0.57 1.12 0.53
ASPSCR1 ENST00000306729 82.35 50.52 68.44 0.30 0.63 0.47 0.57 1.95 1.06
MIF ENST00000215754 82.36 86.71 87.68 0.30 0.24 0.24 0.57 0.40 0.31
FAM72B ENST00000369390 82.36 93.34 90.90 0.30 0.28 0.15 0.57 0.29 0.20
FAM209A ENST00000371328 82.37 77.25 83.19 0.30 0.42 0.29 0.57 0.78 0.40
OR5K2 ENST00000427338 82.37 91.36 89.94 0.30 0.23 0.18 0.57 0.34 0.23
HLA-C ENST00000376228 82.38 56.51 72.06 0.30 0.52 0.43 0.57 1.53 0.81
TAF1D ENST00000448108 82.38 74.50 81.81 0.30 0.53 0.37 0.57 1.00 0.46

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