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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
SERTAD4 ENST00000367012 27.90 31.84 28.06 1.16 0.94 0.82 1.45 1.48 1.28
EVX1 ENST00000496902 27.90 81.26 54.08 1.16 0.34 0.59 1.45 0.54 1.75
ZFHX4 ENST00000521891 27.91 2.25 12.65 1.16 3.65 2.19 1.46 0.30 0.52
RPS13 ENST00000525634 27.91 20.48 22.38 1.16 1.43 1.16 1.46 0.77 0.96
ORAI1 ENST00000330079 27.92 89.57 58.85 1.16 0.27 0.51 1.46 0.37 1.65
BCL2L2 ENST00000250405 27.92 43.47 33.86 1.16 0.61 0.89 1.46 1.96 1.73
SZT2 ENST00000562955 27.93 20.16 22.21 1.16 1.43 1.15 1.46 0.75 0.96
MGLL ENST00000265052 27.93 43.98 34.16 1.16 0.61 0.89 1.46 1.97 1.75
CNTN3 ENST00000263665 27.94 25.73 24.86 1.16 1.24 1.02 1.46 1.05 1.10
PPP1R9A ENST00000433360 27.94 23.57 23.83 1.16 1.39 1.10 1.46 0.93 1.04
TRIB1 ENST00000311922 27.95 22.16 23.15 1.16 1.52 1.19 1.46 0.82 1.01
SLC46A1 ENST00000440501 27.95 41.11 32.73 1.16 0.59 0.86 1.46 1.82 1.65
PHKA2 ENST00000379942 27.96 16.25 20.18 1.16 1.78 1.48 1.47 0.69 0.87
FARSB ENST00000281828 27.96 28.62 26.39 1.16 1.18 1.01 1.47 1.29 1.25
SEPT5 ENST00000455784 27.97 16.07 20.08 1.16 1.82 1.49 1.47 0.69 0.86
TMEM185A ENST00000316916 27.97 57.47 40.93 1.16 0.56 0.78 1.47 1.48 2.06
TMEM39B ENST00000336294 27.98 31.63 27.98 1.16 0.95 0.82 1.48 1.44 1.27
COMMD2 ENST00000473414 27.98 91.58 60.22 1.16 0.23 0.47 1.48 0.33 1.60
GGCX ENST00000233838 27.99 53.26 38.95 1.16 0.66 0.80 1.48 1.73 2.06
INPP5F ENST00000361976 27.99 25.96 25.05 1.16 1.20 1.05 1.48 1.10 1.15
NUP93 ENST00000308159 28.00 28.85 26.54 1.16 1.15 0.99 1.48 1.29 1.25
PDSS1 ENST00000376215 28.00 49.31 36.87 1.16 0.65 0.81 1.48 2.02 1.94
UNC50 ENST00000357765 28.01 55.26 39.97 1.16 0.57 0.81 1.48 1.62 2.00
ICAM5 ENST00000221980 28.02 28.03 26.19 1.15 1.20 0.99 1.48 1.19 1.25
ZC3H18 ENST00000301011 28.02 2.08 12.63 1.16 3.70 2.20 1.48 0.29 0.52

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