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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
ZNF418 ENST00000396147 98.58 80.20 92.08 0.10 0.37 0.14 0.11 0.59 0.16
DDTL ENST00000215770 98.57 91.57 97.66 0.10 0.23 0.09 0.11 0.33 0.06
LCN10 ENST00000497771 98.57 73.56 89.16 0.10 0.52 0.19 0.11 1.03 0.25
C6orf195 ENST00000296847 98.56 99.71 99.92 0.10 0.17 0.12 0.11 0.11 0.04
SPATA31D1 ENST00000344803 98.56 77.90 91.19 0.10 0.42 0.15 0.11 0.79 0.18
PAGE2 ENST00000374968 98.55 83.85 93.99 0.10 0.28 0.09 0.11 0.47 0.11
DEFB126 ENST00000382398 98.55 85.09 94.55 0.10 0.25 0.09 0.11 0.45 0.12
IGFL2 ENST00000434646 98.54 83.25 93.66 0.10 0.28 0.11 0.11 0.47 0.15
APOBEC3C ENST00000361441 98.54 52.03 78.51 0.10 0.61 0.38 0.11 1.86 0.55
CALML5 ENST00000380332 98.53 98.56 99.76 0.10 0.20 0.12 0.11 0.15 0.04
CATSPERD ENST00000381624 98.53 51.35 78.20 0.10 0.63 0.39 0.11 1.90 0.55
PRB2 ENST00000389362 98.52 97.34 99.46 0.10 0.23 0.11 0.11 0.19 0.05
CX3CL1 ENST00000006053 98.52 19.84 59.42 0.10 1.42 0.49 0.11 0.74 1.71
CTAG2 ENST00000247306 98.51 92.16 97.87 0.10 0.25 0.09 0.11 0.32 0.04
GZMH ENST00000216338 98.51 88.90 96.48 0.10 0.25 0.07 0.11 0.35 0.08
GIMAP6 ENST00000328902 98.50 77.04 90.84 0.10 0.42 0.15 0.11 0.78 0.20
ZNF560 ENST00000301480 98.50 61.60 83.41 0.10 0.54 0.33 0.11 1.41 0.40
COLCA1 ENST00000532918 98.49 97.87 99.59 0.10 0.21 0.12 0.11 0.17 0.05
GSDMD ENST00000526406 98.49 75.44 90.06 0.10 0.46 0.18 0.11 0.90 0.22
OR14A16 ENST00000357627 98.48 99.12 99.68 0.10 0.15 0.12 0.11 0.14 0.04
IVL ENST00000368764 98.48 99.18 99.85 0.10 0.15 0.12 0.11 0.13 0.04
RAET1G ENST00000367360 98.47 76.00 90.27 0.10 0.43 0.16 0.11 0.86 0.22
TAS2R8 ENST00000240615 98.47 99.56 99.88 0.10 0.16 0.12 0.11 0.13 0.04
DPPA3 ENST00000345088 98.46 46.98 75.72 0.10 0.71 0.38 0.11 1.95 0.64
C7orf69 ENST00000258776 98.46 91.39 97.52 0.10 0.23 0.08 0.11 0.33 0.07

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