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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
TEX19 ENST00000333437 98.34 97.84 99.56 0.09 0.21 0.12 0.10 0.17 0.05
PKDREJ ENST00000253255 97.00 64.04 83.87 0.09 0.49 0.35 0.11 1.20 0.43
ARMS2 ENST00000528446 98.33 96.64 99.24 0.09 0.23 0.11 0.10 0.20 0.04
CDR1 ENST00000370532 96.99 97.74 99.17 0.09 0.21 0.11 0.11 0.17 0.04
ZNF878 ENST00000547628 98.33 75.53 90.01 0.09 0.44 0.18 0.10 0.90 0.22
IL36B ENST00000259213 96.99 66.83 85.25 0.09 0.53 0.34 0.11 1.23 0.36
C22orf34 ENST00000400023 98.32 85.90 94.87 0.09 0.28 0.09 0.10 0.43 0.11
ZNF705A ENST00000359286 96.98 82.92 92.71 0.09 0.32 0.14 0.11 0.49 0.15
PROM1 ENST00000510224 96.98 54.10 78.77 0.09 0.65 0.39 0.11 1.68 0.53
CRISP3 ENST00000433368 98.32 62.35 83.74 0.09 0.53 0.34 0.10 1.33 0.41
LILRB2 ENST00000391749 96.97 62.36 83.02 0.09 0.53 0.32 0.11 1.33 0.40
NKG2-E ENST00000539033 98.31 86.87 95.30 0.09 0.22 0.08 0.10 0.41 0.10
SPANXN1 ENST00000370493 96.97 86.56 94.49 0.09 0.24 0.10 0.11 0.42 0.12
C8orf86 ENST00000358138 98.31 86.94 95.37 0.09 0.22 0.08 0.10 0.40 0.10
CEACAM5 ENST00000221992 96.96 54.31 78.91 0.09 0.62 0.39 0.11 1.69 0.52
FCER1A ENST00000368115 98.30 75.29 89.89 0.09 0.49 0.18 0.10 0.90 0.23
LILRA3 ENST00000251390 96.96 59.73 81.72 0.09 0.52 0.35 0.11 1.38 0.47
ZNF320 ENST00000595635 98.30 79.48 91.73 0.09 0.38 0.14 0.10 0.66 0.18
PRG3 ENST00000287143 96.95 62.49 83.07 0.09 0.53 0.30 0.11 1.31 0.40
TAS2R20 ENST00000538986 96.95 99.87 99.33 0.09 0.17 0.11 0.11 0.11 0.04
APOBEC3G ENST00000407997 98.29 85.89 94.80 0.09 0.28 0.09 0.10 0.43 0.11
C9orf129 ENST00000375419 96.94 92.02 97.20 0.09 0.24 0.08 0.11 0.33 0.06
RP11-404P21.8 ENST00000553811 98.29 93.96 98.40 0.09 0.25 0.10 0.10 0.26 0.05
HMSD ENST00000408945 96.94 84.66 93.56 0.09 0.27 0.13 0.11 0.42 0.15
SPRR3 ENST00000331860 98.28 98.33 99.56 0.09 0.21 0.12 0.10 0.14 0.05

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