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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
KLHDC9 ENST00000368011 53.85 80.31 69.16 0.65 0.37 0.44 1.75 0.58 0.99
RRBP1 ENST00000377807 53.86 34.83 42.64 0.65 0.76 0.68 1.75 1.55 2.02
NDUFAB1 ENST00000570319 53.86 39.92 45.63 0.65 0.63 0.68 1.75 1.69 1.98
MYOM1 ENST00000356443 53.87 51.18 51.68 0.65 0.66 0.62 1.75 1.91 1.94
LRRC42 ENST00000371370 53.87 60.62 57.15 0.65 0.53 0.52 1.75 1.41 1.69
WWC3 ENST00000380861 53.88 4.76 27.45 0.65 3.27 0.96 1.75 0.32 1.27
ATP6V0D2 ENST00000285393 53.88 74.73 65.92 0.65 0.54 0.51 1.75 0.96 1.23
VSX1 ENST00000376709 53.89 47.66 49.71 0.65 0.61 0.66 1.75 1.97 1.85
LSG1 ENST00000265245 53.89 48.72 50.36 0.65 0.63 0.66 1.75 1.99 1.91
COL8A2 ENST00000397799 53.90 35.15 42.83 0.65 0.76 0.68 1.76 1.58 2.01
MAZ ENST00000219782 53.90 7.41 28.78 0.65 2.54 0.80 1.75 0.39 1.32
POLR2E ENST00000215587 53.91 78.85 68.34 0.65 0.42 0.49 1.75 0.71 1.07
CENPO ENST00000380834 53.91 70.08 63.07 0.65 0.53 0.51 1.75 1.13 1.39
GATC ENST00000551765 53.92 87.78 73.63 0.63 0.24 0.40 1.75 0.37 0.74
COL17A1 ENST00000353479 53.92 39.35 45.33 0.63 0.70 0.70 1.75 1.65 2.00
MTMR10 ENST00000435680 53.93 35.44 43.08 0.63 0.77 0.65 1.75 1.56 2.01
C17orf98 ENST00000398575 53.93 66.01 60.48 0.63 0.56 0.44 1.75 1.22 1.58
CRYBA4 ENST00000354760 53.94 75.06 66.18 0.63 0.51 0.52 1.74 0.91 1.20
SCRG1 ENST00000296506 53.94 87.25 73.37 0.63 0.22 0.42 1.74 0.41 0.78
CREB3L4 ENST00000368607 53.95 56.74 54.90 0.63 0.53 0.51 1.74 1.55 1.74
MMP3 ENST00000299855 53.95 76.79 67.13 0.63 0.42 0.51 1.74 0.81 1.17
DIAPH2 ENST00000324765 53.96 9.72 30.00 0.63 2.44 0.85 1.74 0.50 1.46
NEK10 ENST00000341435 53.96 37.89 44.46 0.63 0.80 0.61 1.74 1.70 2.04
NHEJ1 ENST00000356853 53.97 38.82 45.02 0.63 0.70 0.70 1.73 1.66 2.05
ENDOU ENST00000422538 53.97 72.36 64.47 0.63 0.51 0.51 1.73 1.03 1.33

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