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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
COL18A1 ENST00000355480 77.48 25.82 50.73 0.34 1.21 0.66 0.67 1.07 1.84
FOXH1 ENST00000377317 77.49 44.06 61.46 0.34 0.61 0.44 0.67 1.97 1.47
RPLP1 ENST00000260379 77.49 54.02 67.57 0.34 0.65 0.51 0.67 1.69 1.13
EIF2S3L ENST00000322446 77.50 70.79 77.30 0.34 0.49 0.35 0.67 1.08 0.58
ACOX3 ENST00000356406 77.50 59.48 70.85 0.34 0.51 0.43 0.67 1.40 0.86
ADH1A ENST00000209668 77.51 81.65 82.93 0.34 0.33 0.32 0.67 0.52 0.40
OPN1MW ENST00000369935 77.51 90.46 87.15 0.34 0.25 0.28 0.67 0.37 0.30
CERS1 ENST00000427170 77.52 36.38 56.80 0.34 0.82 0.52 0.67 1.63 1.71
SFT2D1 ENST00000361731 77.52 58.51 70.25 0.34 0.54 0.43 0.68 1.39 0.91
OR13D1 ENST00000318763 77.53 78.30 81.26 0.34 0.43 0.38 0.68 0.74 0.48
ADAMTS7 ENST00000388820 77.53 32.59 54.63 0.34 0.86 0.56 0.68 1.48 1.73
NFKBIL1 ENST00000376148 77.54 23.42 49.34 0.34 1.42 0.70 0.68 0.93 1.84
OR4D10 ENST00000530162 77.54 81.97 83.13 0.34 0.35 0.30 0.69 0.50 0.40
CHGA ENST00000216492 77.55 29.01 52.59 0.34 1.15 0.61 0.69 1.31 1.89
ACTL9 ENST00000324436 77.55 61.62 72.24 0.34 0.54 0.43 0.69 1.40 0.82
VNN2 ENST00000326499 77.56 82.97 83.65 0.34 0.30 0.34 0.69 0.49 0.40
ENGASE ENST00000579016 77.56 72.12 78.07 0.34 0.52 0.39 0.69 1.04 0.55
C19orf53 ENST00000588234 77.57 85.27 84.78 0.34 0.25 0.34 0.68 0.46 0.40
UNC93A ENST00000230256 77.57 85.30 84.80 0.34 0.25 0.34 0.67 0.46 0.40
MAGOHB ENST00000320756 77.58 39.70 58.75 0.34 0.66 0.52 0.67 1.66 1.65
WIPF3 ENST00000409290 77.58 41.32 59.82 0.34 0.62 0.49 0.67 1.82 1.63
LEFTY1 ENST00000272134 77.59 85.06 84.66 0.34 0.25 0.34 0.67 0.45 0.40
OC90 ENST00000603859 77.59 67.13 75.28 0.34 0.54 0.37 0.67 1.22 0.67
OC90 ENST00000254627 77.60 67.16 75.30 0.34 0.54 0.37 0.67 1.22 0.66
OR6C76 ENST00000328314 77.60 87.50 85.83 0.34 0.23 0.33 0.67 0.38 0.33

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