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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
CAPN12 ENST00000328867 77.87 80.92 82.79 0.32 0.35 0.32 0.67 0.57 0.42
ST6GALNAC2 ENST00000225276 77.87 87.14 85.81 0.32 0.22 0.33 0.67 0.41 0.33
IQCF2 ENST00000333127 77.88 65.16 74.43 0.32 0.51 0.40 0.67 1.24 0.70
ZNF573 ENST00000590414 77.88 69.39 76.73 0.32 0.56 0.34 0.67 1.14 0.60
SAC3D1 ENST00000398846 77.89 82.60 83.62 0.32 0.34 0.33 0.66 0.51 0.40
TMEM140 ENST00000275767 77.89 84.09 84.30 0.32 0.27 0.34 0.66 0.45 0.41
FAHD1 ENST00000382666 77.90 97.13 90.58 0.32 0.24 0.15 0.66 0.18 0.20
NPHP4 ENST00000378156 77.90 53.93 67.82 0.32 0.65 0.51 0.67 1.70 1.12
FHIT ENST00000468189 77.91 72.37 78.39 0.32 0.51 0.38 0.67 1.03 0.54
PLAUR ENST00000340093 77.91 44.11 61.75 0.32 0.59 0.46 0.67 1.99 1.46
CCDC12 ENST00000425441 77.92 47.12 63.75 0.32 0.67 0.49 0.67 2.01 1.38
LRIT2 ENST00000372113 77.92 82.29 83.46 0.32 0.34 0.33 0.67 0.53 0.40
SUSD2 ENST00000358321 77.93 60.80 71.99 0.33 0.56 0.42 0.67 1.39 0.81
CD99L2 ENST00000370377 77.94 59.57 71.20 0.33 0.52 0.44 0.67 1.41 0.86
RNF135 ENST00000328381 77.94 75.71 80.16 0.33 0.44 0.35 0.67 0.88 0.53
NUDT16 ENST00000502852 77.95 93.84 88.98 0.33 0.25 0.19 0.67 0.26 0.27
LCE1E ENST00000368770 77.95 83.52 84.02 0.33 0.27 0.35 0.67 0.47 0.42
CDX1 ENST00000231656 77.96 63.06 73.28 0.33 0.48 0.43 0.67 1.30 0.79
SLC2A11 ENST00000398356 77.96 71.77 78.07 0.33 0.51 0.39 0.67 1.07 0.55
CCDC151 ENST00000356392 77.97 60.18 71.60 0.33 0.52 0.44 0.67 1.37 0.83
ZBED2 ENST00000317012 77.97 89.04 86.69 0.33 0.27 0.30 0.67 0.35 0.33
CEACAM16 ENST00000587331 77.98 49.44 65.15 0.33 0.66 0.52 0.67 2.01 1.31
OR10H5 ENST00000308940 77.98 78.64 81.71 0.33 0.40 0.35 0.67 0.74 0.47
MX1 ENST00000398600 77.99 68.37 76.25 0.33 0.52 0.37 0.67 1.21 0.61
ACPT ENST00000270593 77.99 79.11 81.94 0.33 0.39 0.37 0.67 0.69 0.47

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