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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
RNMTL1 ENST00000304478 59.14 76.88 70.28 0.53 0.43 0.43 1.47 0.80 0.91
CASS4 ENST00000371336 59.15 22.61 39.24 0.53 1.48 0.77 1.48 0.86 2.04
SOAT2 ENST00000301466 59.16 80.00 72.25 0.53 0.37 0.43 1.48 0.61 0.82
BEST2 ENST00000549706 59.16 73.05 68.11 0.53 0.52 0.51 1.47 1.03 1.10
IGFBP7 ENST00000295666 59.17 63.37 62.01 0.53 0.48 0.49 1.47 1.30 1.44
EFCAB7 ENST00000371088 59.17 64.70 62.93 0.53 0.48 0.51 1.47 1.24 1.40
NPHP1 ENST00000316534 59.18 52.92 55.74 0.53 0.63 0.53 1.47 1.79 1.74
LGMN ENST00000393218 59.18 34.97 45.77 0.53 0.76 0.68 1.46 1.55 1.98
HDDC3 ENST00000330334 59.19 79.94 72.22 0.53 0.37 0.43 1.46 0.61 0.82
CIDEB ENST00000336557 59.19 94.51 80.18 0.53 0.23 0.35 1.46 0.24 0.52
BTBD19 ENST00000450269 59.20 32.13 44.08 0.53 0.87 0.61 1.46 1.46 2.04
CD9 ENST00000382518 59.20 45.76 51.63 0.54 0.75 0.62 1.46 2.02 1.92
GPR87 ENST00000260843 59.21 80.47 72.51 0.54 0.37 0.44 1.46 0.59 0.83
TMC6 ENST00000590602 59.21 37.96 47.33 0.54 0.78 0.66 1.46 1.70 1.87
OLFML2A ENST00000373580 59.22 56.50 57.89 0.54 0.52 0.48 1.46 1.54 1.66
GRIN2C ENST00000293190 59.22 39.82 48.40 0.54 0.65 0.67 1.46 1.68 1.88
HIST1H3D ENST00000377831 59.23 92.42 79.15 0.54 0.27 0.39 1.46 0.30 0.54
LGALS8 ENST00000526589 59.23 58.68 59.13 0.54 0.54 0.51 1.46 1.43 1.68
ALB ENST00000295897 59.24 18.16 36.90 0.56 1.51 0.81 1.46 0.74 1.94
CYB5R3 ENST00000361740 59.24 48.18 53.16 0.56 0.63 0.61 1.46 1.98 1.87
TMEM254 ENST00000372281 59.25 78.90 71.64 0.56 0.40 0.44 1.46 0.70 0.83
CHRNA4 ENST00000370263 59.25 42.48 49.85 0.56 0.59 0.65 1.46 1.89 1.89
ANAPC1 ENST00000341068 59.26 12.65 34.16 0.56 2.10 0.89 1.46 0.58 1.75
COBLL1 ENST00000342193 59.26 20.64 38.25 0.56 1.46 0.85 1.46 0.78 2.04
SPDL1 ENST00000265295 59.27 60.79 60.57 0.56 0.56 0.44 1.46 1.39 1.58

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