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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
UPP2 ENST00000605860 69.84 48.16 59.18 0.53 0.63 0.49 0.95 1.97 1.68
NOLC1 ENST00000605788 59.87 31.57 44.17 0.63 0.94 0.61 1.37 1.44 2.05
NBPF11 ENST00000605317 89.33 94.00 94.42 0.18 0.25 0.10 0.32 0.26 0.12
SEPT1 ENST00000605106 26.73 61.34 42.30 1.30 0.54 0.70 1.34 1.40 2.01
ARMCX5 ENST00000604957 52.86 46.51 48.59 0.66 0.73 0.67 1.77 2.02 1.85
MTRNR2L6 ENST00000604952 93.19 99.41 98.10 0.15 0.16 0.09 0.16 0.12 0.05
MTRNR2L2 ENST00000604882 92.89 99.29 98.22 0.15 0.15 0.09 0.16 0.12 0.05
MGAT4C ENST00000604798 14.22 45.17 27.83 1.61 0.70 0.87 0.73 1.98 1.28
RP11-57H12.6 ENST00000604534 42.60 45.41 42.23 0.76 0.68 0.70 1.77 2.01 2.01
HSPE1-MOB4 ENST00000604458 1.32 5.61 1.48 4.37 3.00 4.35 0.17 0.33 0.22
FXYD3 ENST00000604255 78.29 73.60 79.26 0.35 0.52 0.38 0.67 1.03 0.54
KCNE4 ENST00000604125 39.86 72.49 55.84 0.89 0.47 0.51 1.75 1.03 1.75
MTRNR2L13 ENST00000604093 92.53 99.06 98.35 0.15 0.15 0.10 0.18 0.14 0.05
RNF103-CHMP3 ENST00000604011 17.14 48.14 30.88 1.46 0.63 0.78 0.86 1.98 1.49
RP11-407N17.3 ENST00000603904 38.65 31.13 33.05 0.92 1.01 0.85 1.74 1.36 1.67
OC90 ENST00000603859 77.59 67.13 75.28 0.34 0.54 0.37 0.67 1.22 0.67
SMAGP ENST00000603798 55.57 71.87 65.17 0.61 0.51 0.52 1.66 1.07 1.31
URGCP-MRPS24 ENST00000603700 64.73 72.25 70.84 0.54 0.51 0.43 1.17 1.04 0.86
VWA2 ENST00000603594 62.99 75.03 71.54 0.58 0.52 0.44 1.27 0.92 0.83
ADAM21 ENST00000603540 55.19 78.31 68.77 0.61 0.43 0.46 1.69 0.74 1.05
HADH ENST00000603302 30.71 53.41 40.33 0.96 0.65 0.80 1.63 1.70 2.00
DUOX2 ENST00000603300 47.49 70.30 59.05 0.57 0.52 0.49 1.80 1.10 1.66
TERF2 ENST00000603068 9.30 11.25 7.62 2.24 2.13 2.72 0.47 0.55 0.33
DENND4C ENST00000602925 39.32 18.86 27.22 0.89 1.53 0.99 1.76 0.74 1.24
HIATL2 ENST00000602917 83.82 70.21 80.33 0.29 0.53 0.38 0.49 1.12 0.52

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