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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
FAM206A ENST00000322940 60.05 76.61 70.67 0.63 0.42 0.43 1.39 0.83 0.88
KCNK15 ENST00000372861 60.05 58.00 59.23 0.63 0.54 0.49 1.39 1.44 1.69
CHAC1 ENST00000446533 60.06 66.93 64.92 0.63 0.53 0.51 1.39 1.25 1.33
LHX3 ENST00000371746 60.06 42.52 50.35 0.63 0.59 0.66 1.39 1.87 1.92
TNFRSF19 ENST00000382258 60.07 38.35 48.07 0.63 0.75 0.67 1.39 1.72 1.88
CA2 ENST00000285379 60.07 76.07 70.37 0.63 0.43 0.43 1.39 0.86 0.91
ARHGEF28 ENST00000545377 60.08 35.58 46.49 0.62 0.77 0.67 1.39 1.58 1.91
MYO19 ENST00000431794 60.08 64.53 63.53 0.62 0.47 0.49 1.39 1.22 1.39
THOC6 ENST00000326266 60.09 35.52 46.47 0.62 0.77 0.67 1.39 1.57 1.91
ID1 ENST00000376112 60.10 90.65 78.63 0.62 0.25 0.38 1.39 0.36 0.55
AGXT2 ENST00000231420 60.10 83.55 74.72 0.62 0.27 0.40 1.39 0.47 0.67
SYTL2 ENST00000354566 60.11 57.41 58.83 0.61 0.54 0.51 1.39 1.49 1.65
ANPEP ENST00000300060 60.11 33.28 45.41 0.61 0.84 0.70 1.40 1.49 2.01
C9orf40 ENST00000376854 60.12 78.66 72.00 0.61 0.40 0.42 1.39 0.74 0.81
USO1 ENST00000538159 60.12 14.45 35.49 0.61 2.04 0.87 1.39 0.61 1.77
SLX1A ENST00000251303 60.13 67.64 65.44 0.61 0.53 0.52 1.39 1.19 1.31
DNAJC5G ENST00000296097 60.13 82.32 74.05 0.61 0.34 0.38 1.39 0.53 0.69
DNAJC12 ENST00000225171 60.14 73.04 68.56 0.61 0.51 0.47 1.39 1.03 1.05
MT1X ENST00000394485 60.14 93.72 80.25 0.61 0.28 0.37 1.39 0.26 0.51
ITIH4 ENST00000266041 60.15 40.97 49.48 0.61 0.61 0.67 1.40 1.79 1.83
C11orf42 ENST00000316375 60.15 77.35 71.21 0.61 0.42 0.44 1.40 0.76 0.86
UCK1 ENST00000372211 60.16 66.90 64.94 0.61 0.53 0.51 1.39 1.25 1.32
KYNU ENST00000264170 60.16 69.62 66.55 0.61 0.53 0.51 1.40 1.10 1.20
FAM107A ENST00000394481 60.17 94.84 80.81 0.61 0.23 0.39 1.40 0.24 0.52
GOLGA3 ENST00000204726 60.17 16.94 36.71 0.61 1.66 0.82 1.40 0.71 1.93

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