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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
C1QTNF6 ENST00000337843 65.60 80.67 76.20 0.58 0.37 0.37 1.08 0.56 0.62
VTN ENST00000226218 65.61 58.26 62.95 0.58 0.54 0.51 1.08 1.43 1.39
ST8SIA6 ENST00000377602 65.61 83.92 77.95 0.58 0.28 0.38 1.08 0.47 0.54
DNAL4 ENST00000216068 65.62 85.37 78.74 0.58 0.25 0.38 1.08 0.45 0.54
SPEF2 ENST00000356031 65.62 37.67 50.71 0.58 0.78 0.66 1.08 1.70 1.84
IL10RB ENST00000290200 65.63 61.01 64.69 0.58 0.54 0.51 1.08 1.40 1.32
VWCE ENST00000335613 65.63 42.93 53.70 0.58 0.63 0.62 1.08 1.90 1.81
MTFP1 ENST00000266263 65.64 66.65 68.12 0.58 0.56 0.49 1.08 1.22 1.09
CCDC108 ENST00000341552 65.64 41.14 52.71 0.58 0.59 0.61 1.08 1.82 1.88
PRR19 ENST00000499536 65.65 22.99 42.60 0.58 1.46 0.67 1.08 0.90 2.02
ZPBP2 ENST00000348931 65.65 53.97 60.26 0.58 0.65 0.47 1.08 1.70 1.60
PCDHGB4 ENST00000519479 65.66 51.67 58.77 0.58 0.61 0.52 1.08 1.87 1.64
ATF7IP2 ENST00000396560 65.66 23.41 42.84 0.58 1.42 0.68 1.07 0.93 2.01
RAD9B ENST00000392672 65.67 70.53 70.40 0.58 0.52 0.43 1.07 1.08 0.91
MARC1 ENST00000366910 65.67 70.95 70.62 0.58 0.49 0.43 1.07 1.05 0.90
XPC ENST00000285021 65.68 42.61 53.56 0.58 0.59 0.63 1.07 1.90 1.80
FOXL1 ENST00000320241 65.68 66.73 68.19 0.58 0.56 0.49 1.07 1.21 1.08
C22orf23 ENST00000249079 65.69 90.67 81.54 0.58 0.25 0.35 1.07 0.36 0.48
LMOD3 ENST00000420581 65.69 61.16 64.83 0.58 0.53 0.51 1.07 1.40 1.33
WDR34 ENST00000372715 65.70 55.33 61.12 0.58 0.57 0.43 1.07 1.61 1.51
ZNF214 ENST00000278314 65.70 78.32 74.94 0.58 0.43 0.39 1.07 0.74 0.64
LRP11 ENST00000239367 65.71 39.62 51.84 0.58 0.68 0.62 1.07 1.65 1.92
TNN ENST00000239462 65.71 59.26 63.73 0.58 0.49 0.49 1.07 1.43 1.38
GADD45GIP1 ENST00000316939 65.72 81.03 76.49 0.58 0.35 0.38 1.07 0.55 0.61
IGFALS ENST00000415638 65.72 88.65 80.51 0.58 0.24 0.39 1.07 0.35 0.51

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