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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
CT62 ENST00000449977 97.36 95.71 98.65 0.10 0.23 0.10 0.11 0.20 0.05
OR5L1 ENST00000333973 97.94 99.27 99.77 0.11 0.15 0.12 0.11 0.13 0.04
CALML5 ENST00000380332 98.53 98.56 99.76 0.10 0.20 0.12 0.11 0.15 0.04
BLID ENST00000560104 96.18 99.49 99.43 0.11 0.16 0.11 0.11 0.13 0.05
IFNA17 ENST00000413767 96.77 98.50 99.36 0.11 0.21 0.11 0.11 0.15 0.04
RLN1 ENST00000223862 97.36 91.90 97.30 0.10 0.23 0.08 0.11 0.32 0.07
AC074389.6 ENST00000382528 97.95 99.54 99.80 0.11 0.16 0.12 0.11 0.13 0.04
APOBEC3C ENST00000361441 98.54 52.03 78.51 0.10 0.61 0.38 0.11 1.86 0.55
MUC4 ENST00000463781 96.19 48.95 75.50 0.11 0.65 0.38 0.11 2.04 0.66
PDPN ENST00000294489 96.78 62.84 83.20 0.11 0.51 0.29 0.11 1.29 0.40
SLCO6A1 ENST00000506729 97.37 53.19 78.51 0.10 0.66 0.38 0.11 1.75 0.55
C8orf31 ENST00000395172 97.95 91.37 97.33 0.11 0.23 0.08 0.11 0.34 0.07
HBM ENST00000356815 96.19 85.52 93.62 0.11 0.27 0.13 0.11 0.45 0.15
IGFL2 ENST00000434646 98.54 83.25 93.66 0.10 0.28 0.11 0.11 0.47 0.15
C9orf37 ENST00000371417 96.78 98.29 99.30 0.11 0.21 0.11 0.11 0.15 0.04
PBOV1 ENST00000527246 97.37 99.14 99.62 0.10 0.15 0.12 0.11 0.14 0.05
NCR1 ENST00000291890 96.20 77.76 90.07 0.11 0.42 0.18 0.11 0.79 0.22
PRSS21 ENST00000005995 97.96 70.97 87.60 0.11 0.49 0.27 0.11 1.06 0.31
RFPL3 ENST00000249007 96.79 95.96 98.55 0.11 0.22 0.10 0.11 0.20 0.05
DEFB126 ENST00000382398 98.55 85.09 94.55 0.10 0.25 0.09 0.11 0.45 0.12
DAOA ENST00000375936 97.38 85.62 94.25 0.10 0.27 0.10 0.11 0.44 0.12
C17orf97 ENST00000360127 96.20 97.22 98.77 0.12 0.24 0.10 0.11 0.19 0.05
MAGEC3 ENST00000298296 97.96 88.51 95.97 0.11 0.23 0.07 0.11 0.36 0.10
SIGLEC11 ENST00000447370 96.79 80.54 91.53 0.11 0.37 0.15 0.11 0.59 0.18
PAGE2 ENST00000374968 98.55 83.85 93.99 0.10 0.28 0.09 0.11 0.47 0.11

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