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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
PCDHGA4 ENST00000571252 49.66 65.36 57.44 0.54 0.53 0.51 1.85 1.25 1.66
EGF ENST00000265171 49.67 38.88 42.54 0.54 0.70 0.68 1.85 1.65 2.02
FABP3 ENST00000373713 49.70 51.59 49.58 0.54 0.62 0.67 1.85 1.87 1.84
DDX49 ENST00000247003 49.70 66.87 58.34 0.54 0.53 0.49 1.85 1.24 1.65
TMEM206 ENST00000535273 50.71 68.41 59.98 0.59 0.52 0.49 1.85 1.21 1.62
IL17RC ENST00000295981 50.71 43.96 46.05 0.59 0.61 0.68 1.85 1.97 1.97
PCED1A ENST00000360652 50.97 33.34 40.42 0.62 0.85 0.80 1.85 1.51 2.02
GCA ENST00000437150 50.97 60.35 55.27 0.62 0.53 0.51 1.85 1.41 1.74
YARS2 ENST00000324868 50.98 68.05 59.93 0.62 0.52 0.49 1.85 1.19 1.63
AAMDC ENST00000526415 50.98 88.07 72.18 0.62 0.24 0.43 1.85 0.38 0.82
TRPA1 ENST00000262209 50.99 61.75 56.11 0.62 0.57 0.49 1.85 1.37 1.77
ASPRV1 ENST00000320256 50.99 73.36 63.30 0.62 0.54 0.48 1.85 1.02 1.36
DVL2 ENST00000005340 51.00 34.61 41.01 0.62 0.80 0.76 1.85 1.54 2.04
DUSP8 ENST00000397374 51.03 25.08 36.21 0.61 1.33 0.87 1.85 1.03 1.83
FDX1L ENST00000393708 51.04 78.78 66.58 0.61 0.42 0.52 1.85 0.71 1.21
IGJ ENST00000254801 51.04 66.54 58.92 0.61 0.57 0.49 1.85 1.22 1.65
MSH3 ENST00000265081 51.05 63.97 57.43 0.61 0.48 0.51 1.85 1.20 1.66
DEF8 ENST00000268676 51.05 29.10 38.37 0.61 1.14 0.85 1.85 1.32 2.04
RELL1 ENST00000454158 51.06 12.06 29.72 0.61 2.06 0.86 1.85 0.57 1.42
CNTRL ENST00000373855 51.06 48.10 48.44 0.61 0.63 0.67 1.85 1.99 1.87
SPIC ENST00000551346 51.10 32.08 39.94 0.61 0.91 0.81 1.85 1.46 2.01
SDK2 ENST00000392650 51.10 15.11 31.34 0.61 1.91 0.87 1.85 0.66 1.55
BTG4 ENST00000356018 51.11 42.02 45.27 0.61 0.59 0.70 1.85 1.84 2.01
FIS1 ENST00000223136 51.16 80.88 67.93 0.59 0.35 0.51 1.85 0.57 1.10
NDUFA6 ENST00000498737 51.17 85.50 70.66 0.59 0.27 0.43 1.85 0.45 0.88

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