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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
FGL1 ENST00000398056 81.74 96.16 91.76 0.32 0.21 0.15 0.60 0.20 0.18
ITIH6 ENST00000218436 81.75 80.48 84.45 0.32 0.37 0.33 0.59 0.58 0.40
AANAT ENST00000250615 81.75 69.58 78.96 0.32 0.52 0.39 0.59 1.10 0.52
MAMSTR ENST00000318083 81.76 47.19 66.14 0.32 0.66 0.52 0.59 2.01 1.20
COL20A1 ENST00000358894 81.76 61.44 74.51 0.32 0.54 0.40 0.59 1.39 0.68
BHLHE23 ENST00000370346 81.77 82.00 85.22 0.32 0.35 0.34 0.59 0.50 0.37
SH2D4A ENST00000265807 81.77 75.73 82.13 0.32 0.44 0.35 0.58 0.88 0.45
APEX2 ENST00000374987 81.78 11.70 45.44 0.32 2.09 0.70 0.58 0.57 1.99
OR2A2 ENST00000408979 81.78 80.33 84.37 0.32 0.37 0.33 0.58 0.58 0.40
FAM86A ENST00000427587 81.79 86.15 87.13 0.32 0.27 0.28 0.59 0.42 0.30
ZNF134 ENST00000396161 81.79 71.10 79.75 0.32 0.49 0.38 0.59 1.07 0.53
C9orf43 ENST00000288462 81.80 56.88 71.92 0.32 0.56 0.43 0.59 1.54 0.81
RAX2 ENST00000555633 81.80 89.23 88.64 0.32 0.27 0.20 0.59 0.36 0.28
MFSD7 ENST00000322224 81.81 84.77 86.49 0.32 0.27 0.30 0.59 0.42 0.33
OR5AN1 ENST00000313940 81.81 91.19 89.65 0.32 0.23 0.18 0.59 0.35 0.23
NAT16 ENST00000300303 81.82 80.75 84.63 0.32 0.37 0.34 0.59 0.57 0.40
KLRF1 ENST00000279544 81.82 80.33 84.40 0.32 0.37 0.33 0.59 0.58 0.40
ZDHHC24 ENST00000310442 81.83 75.72 82.15 0.32 0.44 0.35 0.59 0.88 0.45
TNFRSF9 ENST00000377507 81.83 33.57 57.68 0.32 0.85 0.49 0.59 1.53 1.66
SERPINB11 ENST00000544088 81.84 64.55 76.29 0.32 0.47 0.37 0.59 1.21 0.61
MRPS6 ENST00000399312 81.84 81.30 84.92 0.32 0.33 0.34 0.58 0.54 0.40
GGT5 ENST00000398292 81.85 58.92 73.12 0.32 0.53 0.42 0.57 1.42 0.79
SP110 ENST00000258381 81.86 51.32 68.57 0.32 0.63 0.47 0.57 1.90 1.05
IL2RB ENST00000216223 81.86 26.67 53.68 0.32 1.18 0.62 0.57 1.12 1.80
C16orf90 ENST00000437192 81.87 80.09 84.28 0.32 0.37 0.34 0.57 0.60 0.42

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