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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
PABPC4 ENST00000372858 8.01 7.46 5.02 2.59 2.54 3.68 0.42 0.39 0.25
SESN3 ENST00000536441 8.02 18.85 11.07 2.59 1.53 2.20 0.42 0.74 0.45
GPR61 ENST00000527748 8.02 23.23 13.23 2.59 1.43 2.09 0.42 0.92 0.53
CACNB4 ENST00000539935 8.03 23.77 13.54 2.59 1.38 2.05 0.42 0.93 0.57
ZBTB10 ENST00000430430 8.03 9.77 6.16 2.58 2.42 3.20 0.42 0.50 0.30
CBLN4 ENST00000064571 8.04 58.30 31.39 2.58 0.54 0.87 0.43 1.43 1.56
CASR ENST00000498619 8.04 21.49 12.35 2.58 1.42 2.24 0.43 0.79 0.50
KEAP1 ENST00000171111 8.05 32.36 18.16 2.58 0.87 1.66 0.43 1.46 0.79
RPL8 ENST00000262584 8.05 12.59 7.67 2.58 2.10 2.69 0.43 0.58 0.33
SFPQ ENST00000357214 8.06 3.03 2.96 2.58 3.47 3.99 0.43 0.28 0.23
SLC4A8 ENST00000453097 8.06 8.92 5.73 2.58 2.44 3.33 0.43 0.48 0.28
PTGER4 ENST00000302472 8.07 14.73 8.77 2.57 1.97 2.49 0.43 0.62 0.37
CACYBP ENST00000367679 8.07 17.32 10.26 2.57 1.61 2.21 0.43 0.75 0.42
RPS27A ENST00000272317 8.08 18.74 11.05 2.57 1.52 2.20 0.43 0.74 0.45
KCNH2 ENST00000262186 8.08 11.85 7.33 2.56 2.09 2.81 0.43 0.58 0.34
LIN52 ENST00000555028 8.09 16.65 9.91 2.56 1.72 2.29 0.43 0.71 0.41
FGF10 ENST00000264664 8.09 16.66 9.94 2.56 1.72 2.29 0.43 0.71 0.42
PHF1 ENST00000374516 8.10 6.41 4.57 2.56 2.64 3.70 0.43 0.37 0.25
XRCC6 ENST00000359308 8.10 7.28 4.97 2.56 2.58 3.69 0.43 0.37 0.25
BAI2 ENST00000373658 8.11 8.96 5.79 2.56 2.44 3.33 0.43 0.47 0.28
BANF1 ENST00000312175 8.11 57.20 30.89 2.56 0.56 0.80 0.43 1.49 1.49
ITGB1 ENST00000396033 8.12 8.01 5.38 2.56 2.54 3.50 0.43 0.44 0.25
LRRTM4 ENST00000409093 8.12 24.75 14.15 2.57 1.32 1.99 0.43 1.05 0.60
TRPC5 ENST00000262839 8.13 4.02 3.50 2.57 3.26 3.84 0.43 0.32 0.23
C1QL3 ENST00000298943 8.13 40.64 22.58 2.57 0.63 1.18 0.43 1.77 0.96

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