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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
ZNF736 ENST00000423484 91.30 91.78 94.44 0.15 0.23 0.10 0.20 0.32 0.12
PAICS ENST00000399688 91.30 45.15 70.79 0.15 0.70 0.43 0.20 1.98 0.86
RP11-210M15.2 ENST00000559008 91.31 93.46 95.33 0.15 0.28 0.08 0.20 0.28 0.10
AL645730.2 ENST00000448346 91.31 98.37 97.75 0.15 0.21 0.09 0.20 0.14 0.04
TSPY10 ENST00000428845 91.32 93.85 94.59 0.15 0.25 0.09 0.20 0.26 0.11
KCNG2 ENST00000316249 91.32 36.07 66.29 0.15 0.80 0.52 0.20 1.59 1.21
RP1-66C13.4 ENST00000582441 91.33 80.72 89.37 0.15 0.37 0.18 0.20 0.57 0.24
SPANXN4 ENST00000446864 91.33 89.71 92.55 0.15 0.27 0.14 0.20 0.37 0.15
BEAN1 ENST00000536005 91.34 81.85 90.18 0.15 0.35 0.18 0.20 0.51 0.21
SFT2D3 ENST00000310981 91.34 93.46 96.06 0.15 0.28 0.07 0.20 0.28 0.11
C20orf202 ENST00000400633 91.35 90.04 93.68 0.15 0.25 0.11 0.20 0.37 0.14
SCGB3A1 ENST00000292641 91.35 90.84 94.08 0.15 0.25 0.09 0.20 0.35 0.12
KB-1980E6.3 ENST00000523572 91.36 94.54 94.89 0.15 0.23 0.09 0.20 0.24 0.11
AC021860.1 ENST00000436901 91.36 98.39 98.17 0.15 0.21 0.09 0.20 0.14 0.05
C16orf74 ENST00000284245 91.37 77.89 88.21 0.15 0.42 0.23 0.20 0.79 0.30
ANKRD20A3 ENST00000254835 91.37 96.13 96.79 0.15 0.21 0.08 0.20 0.20 0.08
AL391421.1 ENST00000372387 91.38 94.91 96.10 0.15 0.23 0.07 0.20 0.23 0.11
ZNF580 ENST00000543039 91.38 69.96 83.29 0.15 0.53 0.32 0.20 1.14 0.40
C9orf57 ENST00000377024 91.39 88.17 92.66 0.15 0.23 0.14 0.20 0.38 0.15
DDC8 ENST00000322630 91.40 88.20 92.77 0.15 0.23 0.14 0.20 0.37 0.15
C10orf131 ENST00000423344 91.40 86.48 91.06 0.15 0.24 0.15 0.20 0.42 0.20
LGALS7 ENST00000378626 91.41 88.67 92.28 0.15 0.24 0.14 0.20 0.35 0.15
FP15737 ENST00000399967 91.41 98.40 97.79 0.15 0.21 0.09 0.20 0.14 0.04
C19orf68 ENST00000328759 91.42 15.27 52.92 0.15 1.89 0.61 0.20 0.67 1.87
AL590822.1 ENST00000545087 91.42 98.40 97.80 0.15 0.21 0.09 0.20 0.14 0.04

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