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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
MAGEA12 ENST00000393900 97.43 98.51 99.31 0.10 0.21 0.11 0.11 0.15 0.04
POM121L12 ENST00000408890 98.02 99.46 99.81 0.11 0.16 0.12 0.11 0.13 0.04
ZNF99 ENST00000596209 96.27 75.14 88.81 0.12 0.51 0.19 0.11 0.91 0.28
BLACE ENST00000378120 98.60 97.53 99.53 0.10 0.22 0.12 0.11 0.19 0.05
C21orf54 ENST00000451980 96.85 90.33 96.31 0.09 0.25 0.07 0.11 0.38 0.09
C11orf21 ENST00000456145 97.44 60.85 82.56 0.10 0.56 0.32 0.11 1.41 0.43
RIPPLY3 ENST00000329553 96.28 75.10 88.79 0.12 0.51 0.19 0.11 0.91 0.28
SMLR1 ENST00000541421 98.02 80.14 91.86 0.11 0.37 0.14 0.11 0.60 0.17
ZNF846 ENST00000397902 96.86 95.66 98.47 0.09 0.23 0.10 0.11 0.20 0.05
NDUFV3 ENST00000354250 98.61 90.18 97.11 0.10 0.25 0.08 0.11 0.38 0.07
ZNF701 ENST00000540331 97.44 95.78 98.69 0.10 0.22 0.10 0.11 0.20 0.05
LILRB1 ENST00000324602 96.28 59.42 81.20 0.12 0.51 0.38 0.11 1.41 0.49
IRGM ENST00000522154 98.03 97.95 99.51 0.11 0.20 0.12 0.11 0.17 0.05
DYDC2 ENST00000372198 96.86 84.81 93.60 0.09 0.27 0.13 0.11 0.42 0.15
ADAM2 ENST00000265708 98.61 64.03 84.67 0.10 0.49 0.34 0.11 1.20 0.40
ZNF600 ENST00000338230 97.45 97.90 99.35 0.10 0.20 0.11 0.11 0.17 0.04
KLRC1 ENST00000544822 96.29 71.12 86.89 0.12 0.49 0.29 0.11 1.07 0.31
ZNF468 ENST00000595646 96.87 96.07 98.63 0.09 0.21 0.10 0.11 0.20 0.05
NFAM1 ENST00000329021 98.03 67.04 85.85 0.11 0.54 0.33 0.11 1.24 0.33
POTEG ENST00000409832 96.29 78.65 90.54 0.12 0.40 0.15 0.11 0.74 0.21
ZNF469 ENST00000437464 97.45 17.28 57.26 0.10 1.61 0.52 0.11 0.75 1.70
C2orf57 ENST00000313965 98.62 92.66 98.06 0.10 0.29 0.09 0.11 0.31 0.05
ICAM3 ENST00000160262 96.88 96.42 98.71 0.09 0.22 0.10 0.11 0.19 0.05
KRTAP12-4 ENST00000391618 98.04 99.31 99.79 0.11 0.16 0.12 0.11 0.12 0.04
RP11-998D10.1 ENST00000531638 96.30 92.80 97.25 0.12 0.29 0.08 0.11 0.30 0.07

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