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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
NUPR1 ENST00000395641 75.41 94.85 88.31 0.37 0.23 0.22 0.75 0.24 0.30
ZNF597 ENST00000301744 75.42 52.77 65.72 0.37 0.66 0.51 0.75 1.80 1.26
FBXO36 ENST00000283946 75.42 91.25 86.53 0.37 0.23 0.30 0.75 0.34 0.33
SDC1 ENST00000381150 75.43 52.05 65.22 0.37 0.61 0.53 0.75 1.85 1.30
NCAN ENST00000252575 75.44 19.04 45.93 0.37 1.52 0.70 0.75 0.76 1.97
EMD ENST00000369842 75.44 15.92 44.13 0.37 1.89 0.61 0.75 0.68 2.02
VSIG4 ENST00000374737 75.45 89.71 85.86 0.37 0.27 0.33 0.75 0.37 0.33
DTX3L ENST00000296161 75.45 41.23 58.38 0.37 0.61 0.49 0.75 1.84 1.65
CHCHD6 ENST00000290913 75.46 78.69 80.39 0.37 0.40 0.38 0.75 0.73 0.50
DBI ENST00000542275 75.46 80.99 81.60 0.37 0.35 0.37 0.75 0.56 0.47
AGT ENST00000366667 75.47 78.70 80.41 0.37 0.40 0.38 0.75 0.73 0.50
ZNF501 ENST00000396048 75.47 41.48 58.56 0.37 0.62 0.51 0.75 1.82 1.65
OR4C3 ENST00000319856 75.48 97.26 89.47 0.37 0.23 0.18 0.75 0.19 0.24
MRPS28 ENST00000276585 75.48 93.12 87.47 0.37 0.28 0.28 0.75 0.30 0.30
PCDHB14 ENST00000239449 75.49 84.12 83.18 0.35 0.27 0.29 0.75 0.45 0.40
OR6M1 ENST00000309154 75.49 89.97 85.97 0.35 0.25 0.33 0.75 0.37 0.33
CILP2 ENST00000291495 75.50 35.83 55.26 0.35 0.80 0.51 0.75 1.59 1.74
SRD5A1 ENST00000274192 75.50 72.54 77.18 0.35 0.47 0.35 0.75 1.04 0.59
TTC22 ENST00000371276 75.51 52.52 65.57 0.35 0.66 0.52 0.75 1.83 1.30
OR4M1 ENST00000315957 75.51 76.69 79.39 0.35 0.40 0.39 0.75 0.83 0.52
SERPINB9 ENST00000380698 75.52 47.49 62.33 0.35 0.62 0.48 0.75 2.01 1.41
OR4F6 ENST00000328882 75.52 91.14 86.51 0.35 0.24 0.30 0.74 0.35 0.33
NDNL2 ENST00000332303 75.53 58.37 69.01 0.35 0.54 0.46 0.74 1.41 1.03
OR5K4 ENST00000354924 75.53 95.13 88.47 0.35 0.23 0.22 0.75 0.21 0.29
ZBBX ENST00000455345 75.54 55.98 67.59 0.35 0.49 0.51 0.75 1.56 1.13

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