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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
NDUFV3 ENST00000354250 98.61 90.18 97.11 0.10 0.25 0.08 0.11 0.38 0.07
CTA-299D3.8 ENST00000407505 97.33 85.05 93.96 0.10 0.25 0.09 0.11 0.45 0.11
ADAM2 ENST00000265708 98.61 64.03 84.67 0.10 0.49 0.34 0.11 1.20 0.40
ZNF117 ENST00000282869 97.33 87.73 95.26 0.10 0.24 0.08 0.11 0.37 0.10
C2orf57 ENST00000313965 98.62 92.66 98.06 0.10 0.29 0.09 0.11 0.31 0.05
NLRP5 ENST00000390649 97.34 42.54 72.59 0.10 0.59 0.46 0.11 1.88 0.81
MUC13 ENST00000311075 99.90 37.26 70.95 0.10 0.76 0.43 0.14 1.66 0.85
TEX101 ENST00000602198 98.62 69.71 87.37 0.10 0.53 0.28 0.11 1.13 0.31
JSRP1 ENST00000300961 97.35 93.52 97.93 0.10 0.28 0.09 0.11 0.28 0.04
ZNF841 ENST00000389534 97.35 75.68 89.64 0.10 0.44 0.18 0.11 0.89 0.23
NLRP9 ENST00000332836 98.63 73.50 89.15 0.10 0.53 0.19 0.11 1.03 0.25
ZNF93 ENST00000343769 99.90 89.98 97.55 0.10 0.25 0.08 0.14 0.37 0.07
CT62 ENST00000449977 97.36 95.71 98.65 0.10 0.23 0.10 0.11 0.20 0.05
RFPL4B ENST00000441065 98.63 98.78 99.82 0.10 0.16 0.12 0.11 0.14 0.04
C1orf61 ENST00000368243 99.91 91.26 98.04 0.10 0.23 0.09 0.14 0.34 0.05
RLN1 ENST00000223862 97.36 91.90 97.30 0.10 0.23 0.08 0.11 0.32 0.07
OR7G2 ENST00000305456 98.64 98.66 99.79 0.10 0.20 0.12 0.11 0.15 0.04
SLCO6A1 ENST00000506729 97.37 53.19 78.51 0.10 0.66 0.38 0.11 1.75 0.55
CD4 ENST00000011653 99.91 39.67 72.48 0.10 0.68 0.44 0.14 1.66 0.83
CSN1S1 ENST00000246891 98.64 87.96 96.03 0.10 0.25 0.07 0.11 0.37 0.11
PBOV1 ENST00000527246 97.37 99.14 99.62 0.10 0.15 0.12 0.11 0.14 0.05
C11orf72 ENST00000333139 99.92 99.44 99.89 0.10 0.16 0.12 0.14 0.12 0.04
OR14I1 ENST00000342623 98.65 98.02 99.65 0.10 0.20 0.12 0.11 0.16 0.04
DAOA ENST00000375936 97.38 85.62 94.25 0.10 0.27 0.10 0.11 0.44 0.12
ZBP1 ENST00000371173 97.38 82.01 92.38 0.10 0.35 0.14 0.11 0.50 0.15

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