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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
HEATR5A ENST00000382464 92.20 84.00 91.25 0.15 0.28 0.15 0.18 0.46 0.18
AC079354.2 ENST00000594829 92.21 98.84 97.89 0.15 0.16 0.09 0.18 0.14 0.04
REXO1L1 ENST00000379010 92.21 98.84 98.09 0.15 0.16 0.09 0.18 0.14 0.05
PTPRQ ENST00000266688 92.22 35.49 65.68 0.15 0.77 0.51 0.18 1.57 1.27
RP11-10A14.4 ENST00000518496 92.22 93.73 95.92 0.15 0.28 0.07 0.18 0.26 0.10
ST7-OT4 ENST00000397750 92.23 80.25 89.59 0.15 0.37 0.18 0.18 0.58 0.23
MTRNR2L12 ENST00000600213 92.23 98.85 97.10 0.15 0.16 0.08 0.18 0.14 0.07
TBC1D3C ENST00000457979 92.24 96.98 97.46 0.15 0.24 0.08 0.18 0.19 0.07
RP11-276H1.3 ENST00000312019 92.24 96.01 97.45 0.15 0.23 0.08 0.18 0.20 0.07
ZNF787 ENST00000270459 92.25 20.30 54.59 0.15 1.43 0.56 0.18 0.75 1.74
PAPPA-AS1 ENST00000445861 92.25 92.76 95.49 0.15 0.29 0.08 0.18 0.30 0.11
STRA13 ENST00000392359 92.26 66.84 83.15 0.15 0.53 0.29 0.18 1.24 0.40
FLJ20306 ENST00000601673 92.26 95.43 95.29 0.15 0.24 0.08 0.18 0.20 0.10
RP11-67H2.1 ENST00000521500 92.27 96.63 97.01 0.15 0.23 0.08 0.18 0.20 0.07
RP11-116D17.1 ENST00000547948 92.27 98.87 97.29 0.15 0.17 0.08 0.18 0.14 0.07
RP11-156E8.1 ENST00000607453 92.28 98.87 98.22 0.15 0.17 0.09 0.19 0.14 0.05
AC132216.1 ENST00000330381 92.28 87.27 92.74 0.15 0.22 0.14 0.19 0.41 0.15
ERVV-1 ENST00000602168 92.29 98.88 97.85 0.15 0.17 0.09 0.19 0.14 0.04
KRTAP2-4 ENST00000394015 92.29 92.12 95.16 0.15 0.24 0.09 0.19 0.32 0.10
CTAGE4 ENST00000486333 92.30 98.90 98.23 0.15 0.17 0.09 0.19 0.14 0.05
AP001631.10 ENST00000433840 92.30 90.27 94.85 0.15 0.25 0.09 0.19 0.38 0.11
RP11-347C12.1 ENST00000520915 92.31 98.91 98.24 0.15 0.17 0.09 0.19 0.14 0.05
CTD-3148I10.1 ENST00000576655 92.31 29.12 59.97 0.15 1.14 0.49 0.19 1.34 1.61
SLC22A31 ENST00000562855 92.32 90.54 94.02 0.15 0.25 0.09 0.19 0.37 0.12
RP11-126K1.2 ENST00000447795 92.32 83.53 91.08 0.15 0.27 0.15 0.19 0.47 0.20

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