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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
KIF23 ENST00000260363 20.15 1.96 8.43 1.53 3.75 2.54 1.00 0.25 0.38
B4GALT3 ENST00000319769 20.15 34.77 25.56 1.53 0.77 1.05 1.00 1.55 1.19
NDST2 ENST00000309979 20.16 22.43 19.30 1.53 1.52 1.53 1.00 0.82 0.85
ERO1LB ENST00000354619 20.16 46.92 31.74 1.53 0.71 0.89 1.01 1.94 1.58
SRCAP ENST00000262518 20.17 0.72 7.80 1.53 4.09 2.63 1.00 0.28 0.34
HDAC5 ENST00000225983 20.17 1.65 8.26 1.53 3.85 2.57 1.00 0.26 0.37
ZNF217 ENST00000371471 20.18 2.76 8.82 1.52 3.52 2.49 1.00 0.28 0.38
COL4A1 ENST00000375820 20.18 2.10 8.49 1.52 3.69 2.51 1.00 0.28 0.37
RPL17 ENST00000418495 20.19 16.29 16.06 1.53 1.78 1.70 1.00 0.70 0.66
COPS7B ENST00000350033 20.20 24.01 20.17 1.53 1.38 1.48 1.00 0.96 0.87
KBTBD6 ENST00000379485 20.20 13.51 14.58 1.53 2.07 1.97 1.00 0.61 0.59
KDM4B ENST00000159111 20.21 2.79 8.87 1.53 3.52 2.47 1.00 0.28 0.38
ARHGAP39 ENST00000377307 20.21 19.65 17.85 1.54 1.43 1.66 1.00 0.74 0.77
MAPK8IP1 ENST00000241014 20.22 4.37 9.81 1.54 3.27 2.29 1.00 0.32 0.40
PPP1R2 ENST00000328432 20.22 39.77 28.18 1.54 0.65 0.82 1.00 1.66 1.28
INPP4B ENST00000513000 20.23 15.80 15.85 1.53 1.90 1.77 1.00 0.68 0.66
TMOD1 ENST00000259365 20.23 26.12 21.26 1.53 1.20 1.39 1.00 1.09 0.90
KCNJ11 ENST00000339994 20.24 69.22 43.10 1.53 0.56 0.65 1.00 1.12 2.01
RBM12B ENST00000399300 20.24 26.61 21.56 1.53 1.20 1.28 1.00 1.12 0.93
CTDSP1 ENST00000273062 20.25 6.31 10.90 1.53 2.69 2.21 1.00 0.36 0.44
MARCH4 ENST00000273067 20.25 24.72 20.60 1.53 1.32 1.48 1.00 1.05 0.88
FKBP4 ENST00000001008 20.26 23.88 20.12 1.53 1.39 1.49 1.00 0.95 0.86
LPCAT4 ENST00000314891 20.26 20.01 18.06 1.53 1.43 1.71 1.00 0.73 0.78
LTBP3 ENST00000301873 20.27 13.57 14.68 1.53 2.05 1.96 1.00 0.59 0.61
NIPSNAP1 ENST00000216121 20.27 28.08 22.34 1.53 1.19 1.16 1.01 1.20 0.97

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