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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
SLCO6A1 ENST00000506729 97.37 53.19 78.51 0.10 0.66 0.38 0.11 1.75 0.55
PDPN ENST00000294489 96.78 62.84 83.20 0.11 0.51 0.29 0.11 1.29 0.40
MUC4 ENST00000463781 96.19 48.95 75.50 0.11 0.65 0.38 0.11 2.04 0.66
APOBEC3C ENST00000361441 98.54 52.03 78.51 0.10 0.61 0.38 0.11 1.86 0.55
AC074389.6 ENST00000382528 97.95 99.54 99.80 0.11 0.16 0.12 0.11 0.13 0.04
RLN1 ENST00000223862 97.36 91.90 97.30 0.10 0.23 0.08 0.11 0.32 0.07
IFNA17 ENST00000413767 96.77 98.50 99.36 0.11 0.21 0.11 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
CALML5 ENST00000380332 98.53 98.56 99.76 0.10 0.20 0.12 0.11 0.15 0.04
OR5L1 ENST00000333973 97.94 99.27 99.77 0.11 0.15 0.12 0.11 0.13 0.04
CT62 ENST00000449977 97.36 95.71 98.65 0.10 0.23 0.10 0.11 0.20 0.05
USP26 ENST00000511190 96.77 97.70 99.10 0.11 0.21 0.11 0.11 0.18 0.04
ZNF799 ENST00000430385 96.18 81.79 91.80 0.11 0.34 0.14 0.11 0.51 0.18
CSF2RA ENST00000417535 96.17 61.24 82.08 0.11 0.53 0.35 0.11 1.40 0.46
OR13C5 ENST00000374779 96.76 98.86 99.45 0.11 0.16 0.11 0.11 0.14 0.05
ZNF841 ENST00000389534 97.35 75.68 89.64 0.10 0.44 0.18 0.11 0.89 0.23
SLFN12L ENST00000260908 97.94 83.42 93.41 0.11 0.27 0.11 0.11 0.47 0.15
CATSPERD ENST00000381624 98.53 51.35 78.20 0.10 0.63 0.39 0.11 1.90 0.55
ZNF44 ENST00000356109 96.17 69.37 86.01 0.11 0.56 0.33 0.11 1.14 0.33
ZNF556 ENST00000307635 96.76 84.93 93.61 0.11 0.27 0.13 0.11 0.44 0.15
JSRP1 ENST00000300961 97.35 93.52 97.93 0.10 0.28 0.09 0.11 0.28 0.04
TMEM154 ENST00000304385 97.93 80.12 91.82 0.11 0.37 0.14 0.11 0.60 0.18
PRB2 ENST00000389362 98.52 97.34 99.46 0.10 0.23 0.11 0.11 0.19 0.05
TEX13B ENST00000302917 96.16 85.92 93.82 0.11 0.28 0.10 0.11 0.43 0.13
CD1A ENST00000289429 96.75 96.26 98.64 0.11 0.22 0.10 0.11 0.19 0.05

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