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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
PSG11 ENST00000401740 94.96 92.68 96.61 0.10 0.29 0.08 0.12 0.30 0.08
CARD17 ENST00000375707 95.38 92.25 96.61 0.11 0.25 0.08 0.11 0.31 0.08
AMY1B ENST00000330330 90.93 96.28 96.60 0.16 0.22 0.08 0.21 0.20 0.08
AP000695.1 ENST00000595927 87.83 99.74 96.60 0.23 0.17 0.08 0.36 0.11 0.08
C11orf45 ENST00000310799 99.25 88.36 96.59 0.11 0.23 0.08 0.12 0.37 0.07
SPATA12 ENST00000334325 88.64 98.71 96.59 0.19 0.18 0.08 0.34 0.15 0.07
RP11-93B14.6 ENST00000370520 92.13 95.01 96.58 0.15 0.23 0.08 0.19 0.21 0.07
NBPF12 ENST00000442909 94.67 92.89 96.58 0.10 0.29 0.08 0.11 0.30 0.07
CFHR2 ENST00000367415 97.16 90.42 96.57 0.10 0.25 0.08 0.11 0.37 0.07
DMRTC1 ENST00000373529 93.37 93.92 96.57 0.14 0.25 0.07 0.15 0.26 0.07
VCX3A ENST00000381089 95.02 92.52 96.56 0.10 0.29 0.07 0.12 0.31 0.07
C9orf153 ENST00000376001 95.91 91.62 96.55 0.11 0.23 0.07 0.11 0.32 0.07
RFPL4A ENST00000434937 99.93 87.56 96.55 0.10 0.23 0.07 0.14 0.37 0.07
C20orf201 ENST00000308906 91.93 93.55 96.54 0.15 0.28 0.07 0.20 0.28 0.07
ZNF788 ENST00000339302 89.60 97.82 96.54 0.16 0.21 0.07 0.30 0.18 0.07
AL445989.1 ENST00000453638 89.48 97.93 96.53 0.16 0.20 0.07 0.30 0.17 0.07
C20orf187 ENST00000378252 92.06 94.92 96.53 0.15 0.23 0.07 0.20 0.23 0.07
C2orf27B ENST00000303798 93.29 94.97 96.52 0.15 0.23 0.07 0.15 0.21 0.07
CTD-2228K2.5 ENST00000342584 89.99 97.33 96.52 0.16 0.23 0.07 0.27 0.19 0.07
SPRN ENST00000541506 94.17 93.32 96.51 0.10 0.28 0.07 0.13 0.29 0.07
RP11-386G21.1 ENST00000522186 93.96 93.48 96.51 0.11 0.28 0.07 0.13 0.28 0.07
PRR21 ENST00000408934 89.40 99.51 96.50 0.16 0.16 0.07 0.32 0.13 0.07
LRRC66 ENST00000343457 96.61 90.83 96.50 0.11 0.25 0.07 0.11 0.35 0.07
PPIAL4A ENST00000539781 89.74 97.60 96.49 0.16 0.22 0.07 0.28 0.20 0.07
PRAMEF3 ENST00000376173 93.36 93.81 96.49 0.15 0.27 0.07 0.15 0.26 0.08

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