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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
NPAS1 ENST00000602212 80.36 8.47 42.71 0.33 2.52 0.68 0.58 0.46 2.02
MAGEB5 ENST00000602297 87.89 98.51 95.66 0.23 0.21 0.07 0.36 0.15 0.11
EIF4G3 ENST00000602326 8.53 1.54 2.58 2.45 3.89 4.01 0.44 0.26 0.23
COMMD3-BMI1 ENST00000602390 10.96 30.92 18.94 1.87 1.06 1.54 0.58 1.36 0.83
DNAJC3 ENST00000602402 17.96 27.50 20.87 1.53 1.25 1.47 0.89 1.16 0.87
ZNF658 ENST00000602553 94.60 91.41 95.78 0.10 0.23 0.07 0.12 0.33 0.11
HIST1H2AC ENST00000602637 28.26 55.24 40.06 1.16 0.57 0.82 1.48 1.62 1.99
MINOS1-NBL1 ENST00000602662 41.01 73.00 56.84 0.85 0.51 0.52 1.71 1.03 1.70
OAZ1 ENST00000602676 83.61 37.75 61.36 0.29 0.80 0.44 0.52 1.70 1.48
APITD1 ENST00000602787 84.23 87.54 89.00 0.30 0.23 0.19 0.47 0.37 0.27
NELFCD ENST00000602795 19.26 20.96 18.05 1.57 1.44 1.70 0.95 0.83 0.78
HIATL2 ENST00000602917 83.82 70.21 80.33 0.29 0.53 0.38 0.49 1.12 0.52
DENND4C ENST00000602925 39.32 18.86 27.22 0.89 1.53 0.99 1.76 0.74 1.24
TERF2 ENST00000603068 9.30 11.25 7.62 2.24 2.13 2.72 0.47 0.55 0.33
DUOX2 ENST00000603300 47.49 70.30 59.05 0.57 0.52 0.49 1.80 1.10 1.66
HADH ENST00000603302 30.71 53.41 40.33 0.96 0.65 0.80 1.63 1.70 2.00
ADAM21 ENST00000603540 55.19 78.31 68.77 0.61 0.43 0.46 1.69 0.74 1.05
VWA2 ENST00000603594 62.99 75.03 71.54 0.58 0.52 0.44 1.27 0.92 0.83
URGCP-MRPS24 ENST00000603700 64.73 72.25 70.84 0.54 0.51 0.43 1.17 1.04 0.86
SMAGP ENST00000603798 55.57 71.87 65.17 0.61 0.51 0.52 1.66 1.07 1.31
OC90 ENST00000603859 77.59 67.13 75.28 0.34 0.54 0.37 0.67 1.22 0.67
RP11-407N17.3 ENST00000603904 38.65 31.13 33.05 0.92 1.01 0.85 1.74 1.36 1.67
RNF103-CHMP3 ENST00000604011 17.14 48.14 30.88 1.46 0.63 0.78 0.86 1.98 1.49
MTRNR2L13 ENST00000604093 92.53 99.06 98.35 0.15 0.15 0.10 0.18 0.14 0.05
KCNE4 ENST00000604125 39.86 72.49 55.84 0.89 0.47 0.51 1.75 1.03 1.75

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