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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
B3GNT7 ENST00000287590 35.12 24.44 27.94 0.92 1.32 0.84 1.86 1.00 1.28
GDAP2 ENST00000369443 35.13 47.82 39.82 0.92 0.59 0.80 1.86 1.98 2.02
LTV1 ENST00000367576 35.13 46.74 39.33 0.92 0.72 0.80 1.86 1.97 2.04
MTTP ENST00000457717 35.14 29.51 30.57 0.92 1.10 0.80 1.86 1.39 1.47
ICA1L ENST00000392237 35.14 33.14 32.33 0.92 0.82 0.90 1.86 1.51 1.61
PYGL ENST00000216392 35.15 51.39 41.51 0.92 0.63 0.73 1.86 1.89 2.02
PARD3 ENST00000374789 35.15 13.21 22.33 0.91 2.06 1.16 1.86 0.60 0.97
SH3D19 ENST00000304527 35.20 31.70 31.65 0.92 0.95 0.89 1.86 1.46 1.58
TRIP4 ENST00000261884 35.21 35.16 33.34 0.92 0.76 0.87 1.86 1.58 1.72
DOPEY2 ENST00000399151 35.22 31.80 31.71 0.92 0.94 0.89 1.86 1.48 1.58
PPHLN1 ENST00000395568 35.23 42.62 37.21 0.92 0.59 0.81 1.86 1.90 1.97
VCAM1 ENST00000294728 35.24 18.48 24.90 0.92 1.48 1.02 1.86 0.76 1.11
TPX2 ENST00000300403 35.30 7.07 19.18 0.92 2.57 1.53 1.86 0.37 0.85
MYL1 ENST00000352451 35.31 67.25 50.32 0.92 0.56 0.66 1.86 1.22 1.92
SCN9A ENST00000409672 35.31 36.58 34.14 0.92 0.78 0.89 1.86 1.63 1.75
RIOK2 ENST00000283109 36.02 39.45 35.82 0.94 0.70 0.86 1.86 1.64 1.79
FAM63B ENST00000559228 36.03 33.92 33.12 0.94 0.84 0.87 1.86 1.56 1.69
CPNE3 ENST00000521271 51.39 80.37 67.74 0.59 0.37 0.52 1.86 0.59 1.12
FAM83B ENST00000306858 51.43 35.11 41.51 0.59 0.76 0.75 1.86 1.58 2.02
CAT ENST00000241052 51.43 57.61 54.01 0.59 0.56 0.59 1.86 1.48 1.77
PMAIP1 ENST00000316660 51.44 91.17 74.15 0.59 0.24 0.39 1.86 0.35 0.69
CSDC2 ENST00000306149 51.44 79.46 67.22 0.59 0.38 0.52 1.86 0.66 1.16
ACOT9 ENST00000379303 51.45 67.97 60.12 0.59 0.52 0.47 1.86 1.17 1.61
PIBF1 ENST00000326291 51.45 39.72 43.99 0.59 0.66 0.62 1.86 1.66 2.03
GRN ENST00000053867 51.46 24.80 36.26 0.59 1.33 0.85 1.86 1.05 1.84

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