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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
RGL4 ENST00000290691 99.23 73.02 89.23 0.11 0.51 0.19 0.12 1.03 0.25
APOL1 ENST00000319136 99.22 87.21 95.95 0.11 0.20 0.07 0.12 0.41 0.10
ZNF415 ENST00000500065 99.21 77.66 91.36 0.11 0.42 0.15 0.12 0.79 0.18
SPZ1 ENST00000296739 99.21 97.62 99.67 0.11 0.22 0.12 0.12 0.20 0.04
KIAA1210 ENST00000402510 99.20 22.94 61.81 0.11 1.47 0.47 0.12 0.90 1.46
DEFB118 ENST00000253381 99.20 92.87 98.35 0.11 0.29 0.10 0.12 0.30 0.05
ADAM30 ENST00000369400 99.19 99.77 99.80 0.11 0.17 0.12 0.12 0.11 0.04
TAS2R14 ENST00000537503 99.19 97.83 99.70 0.11 0.21 0.12 0.12 0.17 0.04
BEND2 ENST00000380033 99.18 27.57 64.76 0.11 1.25 0.49 0.12 1.17 1.32
DCD ENST00000293371 99.18 86.50 95.62 0.11 0.24 0.08 0.12 0.42 0.11
SLAMF6 ENST00000368057 99.17 31.95 67.35 0.11 0.92 0.52 0.12 1.48 1.15
SPATA31E1 ENST00000325643 99.17 74.04 89.71 0.11 0.53 0.18 0.12 1.03 0.23
CST9 ENST00000376971 99.16 93.94 98.66 0.11 0.25 0.10 0.12 0.26 0.05
CEACAM18 ENST00000451626 99.16 87.46 96.04 0.11 0.23 0.07 0.12 0.40 0.11
C7orf76 ENST00000356686 99.15 80.05 92.29 0.11 0.37 0.14 0.12 0.60 0.15
ZNF160 ENST00000429604 99.15 71.44 88.43 0.11 0.53 0.22 0.12 1.06 0.30
CFHR3 ENST00000367425 99.14 82.90 93.82 0.11 0.32 0.10 0.12 0.49 0.13
FLJ14816 ENST00000593290 99.14 99.73 99.97 0.11 0.17 0.13 0.12 0.11 0.04
CD8A ENST00000409511 99.13 80.51 92.55 0.11 0.37 0.14 0.12 0.58 0.15
WFDC12 ENST00000372785 99.13 86.16 95.40 0.11 0.27 0.08 0.12 0.42 0.11
AC007952.5 ENST00000428928 99.12 71.97 88.67 0.11 0.51 0.20 0.12 1.05 0.28
PRR4 ENST00000228811 99.12 87.10 95.84 0.11 0.22 0.07 0.12 0.41 0.11
ZNF347 ENST00000452676 99.11 91.06 97.68 0.11 0.25 0.09 0.12 0.36 0.06
IFI16 ENST00000368131 99.11 53.81 79.78 0.11 0.63 0.38 0.12 1.71 0.53
AC092687.4 ENST00000418835 99.10 79.41 91.99 0.11 0.38 0.14 0.12 0.67 0.16

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