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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
SAMM50 ENST00000350028 62.89 46.77 54.37 0.59 0.72 0.58 1.28 1.97 1.75
COL4A2 ENST00000360467 62.89 28.64 44.26 0.58 1.18 0.61 1.28 1.29 2.05
TMEM179B ENST00000333449 62.90 64.34 65.06 0.58 0.49 0.51 1.28 1.21 1.31
SLC39A4 ENST00000301305 62.90 36.76 48.70 0.58 0.76 0.68 1.27 1.65 1.85
GC ENST00000504199 62.91 57.17 60.60 0.58 0.56 0.44 1.27 1.50 1.58
RABEP2 ENST00000358201 62.92 28.07 43.86 0.58 1.19 0.62 1.27 1.19 2.02
NOX3 ENST00000159060 62.92 58.20 61.23 0.58 0.54 0.43 1.27 1.44 1.49
COA3 ENST00000328434 62.93 78.97 73.76 0.58 0.40 0.42 1.27 0.69 0.71
OR2AG2 ENST00000338569 62.93 80.94 74.84 0.58 0.35 0.39 1.27 0.57 0.64
MFSD10 ENST00000329687 62.94 68.93 67.83 0.58 0.54 0.51 1.27 1.16 1.11
TDGF1 ENST00000296145 62.94 94.98 82.33 0.58 0.23 0.33 1.27 0.21 0.44
EFCAB4B ENST00000440314 62.95 47.83 54.98 0.58 0.59 0.52 1.27 1.99 1.74
IL18R1 ENST00000409599 62.95 44.72 53.27 0.58 0.66 0.61 1.27 1.98 1.87
SPATS1 ENST00000288390 62.96 69.06 67.90 0.58 0.56 0.51 1.27 1.14 1.11
ATP10A ENST00000356865 62.96 22.25 40.78 0.58 1.53 0.81 1.27 0.82 2.04
NME6 ENST00000421967 62.97 74.76 71.40 0.58 0.54 0.44 1.27 0.96 0.87
RP11-867G23.8 ENST00000531602 62.97 93.83 81.76 0.58 0.27 0.35 1.27 0.26 0.47
CDKN1A ENST00000405375 62.98 73.69 70.68 0.58 0.52 0.43 1.27 1.02 0.88
TRIM68 ENST00000300747 62.98 78.43 73.49 0.58 0.43 0.40 1.27 0.73 0.75
VWA2 ENST00000603594 62.99 75.03 71.54 0.58 0.52 0.44 1.27 0.92 0.83
HIST1H2BI ENST00000377733 62.99 92.56 81.13 0.58 0.29 0.39 1.27 0.31 0.49
CRYBB1 ENST00000215939 63.00 55.14 59.30 0.58 0.57 0.51 1.27 1.63 1.69
NHLH1 ENST00000302101 63.00 71.70 69.53 0.58 0.52 0.44 1.27 1.07 0.96
SLC5A2 ENST00000330498 63.01 64.60 65.26 0.58 0.48 0.53 1.27 1.22 1.31
DMRT1 ENST00000382276 63.01 22.97 41.20 0.58 1.46 0.76 1.27 0.90 2.02

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