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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
ZNF197 ENST00000396058 44.04 51.88 46.65 0.73 0.59 0.66 1.78 1.87 1.87
TFR2 ENST00000462107 44.04 39.29 40.03 0.73 0.70 0.82 1.78 1.65 1.98
FZD9 ENST00000344575 44.05 40.59 40.52 0.72 0.63 0.80 1.78 1.77 2.04
LMTK2 ENST00000297293 44.05 8.15 24.11 0.72 2.54 1.11 1.78 0.44 1.06
CASC5 ENST00000346991 44.06 13.33 26.86 0.73 2.06 0.97 1.78 0.61 1.27
FRZB ENST00000295113 44.06 48.61 45.00 0.73 0.63 0.70 1.78 2.00 2.05
FBXW9 ENST00000393261 44.07 57.21 49.56 0.72 0.56 0.67 1.78 1.49 1.85
CRX ENST00000221996 44.07 29.95 35.19 0.72 1.09 0.86 1.78 1.41 1.75
SLC26A3 ENST00000340010 44.08 51.12 46.27 0.72 0.66 0.67 1.78 1.92 1.92
LIPG ENST00000261292 44.08 62.26 52.47 0.72 0.53 0.61 1.78 1.34 1.92
COL7A1 ENST00000328333 44.09 32.70 36.49 0.71 0.84 0.85 1.78 1.45 1.90
PON2 ENST00000222572 44.09 55.85 48.86 0.71 0.52 0.71 1.78 1.58 1.85
MAP3K10 ENST00000253055 44.10 19.34 29.91 0.71 1.49 0.86 1.77 0.74 1.44
REC8 ENST00000311457 44.10 32.18 36.26 0.71 0.86 0.85 1.77 1.46 1.85
BOD1L1 ENST00000040738 44.11 9.22 24.73 0.71 2.47 1.05 1.77 0.47 1.10
PLSCR1 ENST00000342435 44.11 35.66 38.20 0.71 0.78 0.85 1.78 1.58 2.04
ECHDC1 ENST00000531967 44.12 82.54 64.71 0.71 0.34 0.49 1.78 0.51 1.33
TBC1D8 ENST00000376840 44.12 36.65 38.64 0.71 0.77 0.82 1.78 1.66 2.01
PLXNA3 ENST00000369682 44.13 17.85 29.15 0.71 1.51 0.84 1.78 0.72 1.32
CCDC112 ENST00000379611 44.14 17.35 28.91 0.71 1.59 0.81 1.77 0.75 1.31
MRPL15 ENST00000260102 44.14 75.37 60.20 0.71 0.47 0.48 1.77 0.89 1.61
MYF5 ENST00000228644 44.15 69.15 56.47 0.71 0.56 0.52 1.78 1.12 1.70
GPX2 ENST00000389614 44.15 86.63 67.14 0.71 0.24 0.52 1.78 0.40 1.17
PPP2R3A ENST00000264977 44.16 16.57 28.51 0.71 1.77 0.78 1.78 0.71 1.31
MAP3K7CL ENST00000399947 44.16 82.67 64.80 0.71 0.34 0.51 1.78 0.50 1.32

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