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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
PBLD ENST00000358769 31.25 80.46 55.51 0.96 0.37 0.51 1.69 0.59 1.74
RIF1 ENST00000243326 31.26 1.52 14.10 0.96 3.88 2.05 1.69 0.26 0.60
PCDHGC3 ENST00000308177 31.26 24.51 26.08 0.96 1.30 0.99 1.69 1.02 1.25
NDRG2 ENST00000556147 31.27 38.02 32.82 0.96 0.77 0.85 1.68 1.71 1.65
BLOC1S1 ENST00000548925 31.27 54.51 41.11 0.96 0.59 0.76 1.68 1.65 2.05
MARCH1 ENST00000503008 31.28 41.38 34.55 0.96 0.62 0.90 1.68 1.80 1.77
ITGA9 ENST00000264741 31.28 20.01 23.75 0.96 1.43 1.14 1.68 0.73 1.02
PKN3 ENST00000291906 31.29 53.14 40.47 0.96 0.66 0.80 1.68 1.77 2.04
POLR2F ENST00000442738 31.29 46.54 37.20 0.96 0.75 0.81 1.68 2.02 1.97
GTF2H3 ENST00000543341 31.30 56.63 42.20 0.96 0.53 0.68 1.68 1.55 2.02
ARAP1 ENST00000393609 31.31 15.58 21.57 0.96 1.87 1.28 1.68 0.67 0.93
NDST4 ENST00000264363 31.31 32.25 29.96 0.96 0.86 0.85 1.68 1.46 1.46
BIN1 ENST00000316724 31.32 16.78 22.18 0.96 1.67 1.15 1.68 0.71 0.96
UBE2S ENST00000264552 31.32 33.25 30.53 0.96 0.82 0.80 1.68 1.50 1.47
IL6ST ENST00000381298 31.33 5.73 16.34 0.96 2.92 1.71 1.68 0.34 0.67
SCML2 ENST00000251900 31.33 2.42 14.62 0.96 3.60 1.97 1.68 0.29 0.59
SERPINE2 ENST00000447280 31.34 20.85 24.12 0.96 1.42 1.11 1.69 0.83 1.06
PLEKHM1 ENST00000430334 31.34 23.27 25.40 0.95 1.43 1.04 1.69 0.93 1.17
RSPO1 ENST00000356545 31.35 73.12 51.35 0.95 0.53 0.63 1.68 1.02 1.91
ILDR2 ENST00000271417 31.35 14.67 21.14 0.95 2.00 1.42 1.68 0.62 0.90
MAML2 ENST00000524717 31.36 7.09 17.09 0.95 2.57 1.66 1.68 0.37 0.72
ADD3 ENST00000356080 31.36 9.38 18.31 0.95 2.49 1.66 1.68 0.49 0.80
GATSL3 ENST00000407689 31.37 39.98 33.84 0.95 0.63 0.89 1.68 1.68 1.73
COLEC11 ENST00000418971 31.37 44.27 35.94 0.95 0.61 0.86 1.68 1.96 1.78
CITED2 ENST00000367651 31.38 34.67 31.23 0.95 0.80 0.86 1.68 1.54 1.56

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