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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
PET117 ENST00000432901 92.59 90.74 93.57 0.15 0.25 0.13 0.18 0.35 0.15
ZNF843 ENST00000315678 92.59 99.10 97.53 0.15 0.15 0.08 0.18 0.14 0.07
PLGLB1 ENST00000355705 92.60 91.21 94.79 0.15 0.23 0.09 0.18 0.34 0.11
ZBED3 ENST00000255198 92.60 94.96 95.96 0.15 0.23 0.07 0.18 0.21 0.10
RP11-293M10.1 ENST00000553510 92.61 92.29 94.62 0.15 0.25 0.09 0.18 0.30 0.11
AC104057.1 ENST00000593865 92.61 92.77 94.40 0.15 0.29 0.10 0.18 0.30 0.12
MORN2 ENST00000410014 92.62 87.92 93.19 0.15 0.25 0.14 0.18 0.37 0.15
AC026310.1 ENST00000599478 92.62 99.10 98.38 0.15 0.15 0.10 0.18 0.14 0.05
CTAGE9 ENST00000314099 92.63 99.11 98.39 0.15 0.15 0.10 0.18 0.14 0.05
BHLHA9 ENST00000391429 92.63 93.29 95.85 0.15 0.28 0.07 0.18 0.30 0.11
C7orf73 ENST00000507606 92.64 66.48 82.43 0.15 0.57 0.33 0.18 1.21 0.44
RP11-1085N6.3 ENST00000556696 92.65 88.59 93.55 0.15 0.24 0.13 0.18 0.35 0.15
CBWD3 ENST00000360171 92.65 96.46 97.36 0.15 0.22 0.08 0.18 0.19 0.07
C14orf132 ENST00000555004 92.66 99.13 98.40 0.15 0.15 0.10 0.18 0.14 0.05
AC112693.2 ENST00000599897 92.66 99.13 97.72 0.15 0.15 0.09 0.17 0.14 0.05
LRRC63 ENST00000595396 92.67 54.12 75.95 0.15 0.65 0.38 0.17 1.68 0.62
LEUTX ENST00000396841 92.67 97.02 97.61 0.15 0.24 0.09 0.17 0.19 0.06
RP11-182J1.16 ENST00000558195 92.68 90.97 94.72 0.15 0.25 0.09 0.17 0.35 0.11
ZYG11A ENST00000371528 92.68 55.88 77.66 0.15 0.51 0.39 0.17 1.56 0.55
MARVELD1 ENST00000285605 92.69 54.73 77.05 0.15 0.58 0.37 0.17 1.64 0.61
RBMY1J ENST00000250831 92.69 93.73 96.13 0.15 0.28 0.07 0.17 0.26 0.10
AC006946.15 ENST00000441544 92.70 67.42 83.01 0.15 0.56 0.32 0.17 1.20 0.40
FAM132B ENST00000546354 92.70 71.95 85.37 0.15 0.51 0.34 0.17 1.07 0.35
CTC-360G5.1 ENST00000571838 92.71 48.22 72.76 0.15 0.63 0.43 0.17 2.00 0.81
AC006132.1 ENST00000593161 92.71 96.85 96.97 0.15 0.23 0.08 0.17 0.19 0.07

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