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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
CDH5 ENST00000341529 49.98 20.23 33.23 0.54 1.43 0.87 1.80 0.74 1.68
PDHX ENST00000227868 49.98 36.91 41.67 0.54 0.76 0.72 1.80 1.70 2.00
CDH13 ENST00000268613 49.99 30.45 38.50 0.54 1.09 0.84 1.80 1.38 2.05
DENND1B ENST00000367396 49.99 21.86 34.11 0.54 1.47 0.89 1.80 0.81 1.75
RGS3 ENST00000374140 50.00 32.51 39.60 0.54 0.86 0.80 1.80 1.49 2.04
CCDC28A ENST00000332797 50.00 83.22 68.61 0.54 0.28 0.47 1.80 0.47 1.05
FIBIN ENST00000318627 50.01 49.13 48.43 0.54 0.66 0.67 1.80 2.04 1.87
RTL1 ENST00000534062 50.01 28.84 37.67 0.54 1.15 0.82 1.80 1.29 2.01
CRLF1 ENST00000392386 50.02 50.31 49.07 0.54 0.66 0.72 1.80 1.96 1.83
WDR83 ENST00000418543 50.02 81.43 67.54 0.54 0.33 0.51 1.81 0.54 1.13
PDX1 ENST00000381033 50.03 56.79 52.74 0.54 0.53 0.61 1.81 1.55 1.88
ICT1 ENST00000301585 50.03 72.92 62.30 0.54 0.49 0.49 1.81 1.02 1.42
CRTAC1 ENST00000370597 50.04 41.03 43.94 0.54 0.59 0.61 1.80 1.81 2.02
CC2D1A ENST00000318003 50.04 20.64 33.50 0.54 1.46 0.89 1.80 0.78 1.72
NBL1 ENST00000289749 50.05 56.60 52.64 0.54 0.53 0.59 1.80 1.55 1.89
KIAA1143 ENST00000296121 50.05 73.50 62.71 0.54 0.53 0.49 1.80 1.03 1.39
ZFP30 ENST00000351218 50.06 54.82 51.59 0.54 0.57 0.62 1.80 1.63 1.94
OSGEPL1 ENST00000264151 50.06 54.52 51.42 0.54 0.61 0.63 1.81 1.65 1.91
BAIAP2L1 ENST00000005260 50.07 35.32 40.88 0.54 0.77 0.78 1.81 1.58 2.06
THY1 ENST00000284240 50.07 67.81 59.14 0.56 0.52 0.51 1.81 1.18 1.68
GYS2 ENST00000261195 50.08 61.20 55.23 0.56 0.53 0.51 1.81 1.41 1.74
GPR56 ENST00000388812 50.09 50.91 49.38 0.56 0.63 0.70 1.81 1.94 1.84
WDR41 ENST00000296679 50.09 61.46 55.43 0.56 0.54 0.51 1.81 1.40 1.72
CAPZA3 ENST00000317658 50.10 74.55 63.49 0.56 0.53 0.49 1.81 1.00 1.39
KHK ENST00000260599 50.10 78.66 66.02 0.57 0.40 0.51 1.81 0.74 1.22

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