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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
MTMR12 ENST00000382142 23.64 10.65 14.93 1.34 2.14 1.90 1.10 0.51 0.63
TSPYL4 ENST00000420283 23.64 68.94 44.96 1.34 0.54 0.68 1.10 1.16 2.04
VDAC3 ENST00000521158 23.65 5.28 12.04 1.34 3.11 2.30 1.11 0.32 0.47
TTC7B ENST00000328459 23.65 3.59 11.29 1.34 3.37 2.16 1.11 0.30 0.45
NRM ENST00000259953 23.66 54.30 37.28 1.34 0.62 0.84 1.11 1.69 2.01
APP ENST00000346798 23.66 19.37 19.52 1.34 1.48 1.54 1.11 0.74 0.84
TRAPPC1 ENST00000303731 23.67 47.14 33.59 1.34 0.66 0.87 1.12 1.99 1.72
ST6GALNAC6 ENST00000373146 23.67 43.84 31.96 1.34 0.61 0.90 1.12 1.96 1.58
C14orf166 ENST00000261700 23.68 30.04 24.91 1.33 1.09 1.02 1.12 1.43 1.11
SEC31A ENST00000395310 23.68 21.02 20.43 1.33 1.44 1.51 1.12 0.83 0.88
TOE1 ENST00000372090 23.69 78.23 49.94 1.34 0.43 0.61 1.12 0.74 1.89
SLC17A5 ENST00000355773 23.69 56.65 38.45 1.34 0.53 0.84 1.12 1.55 2.04
TAC1 ENST00000319273 23.70 27.11 23.50 1.35 1.23 1.18 1.12 1.13 1.01
GDAP1 ENST00000220822 23.70 62.55 41.35 1.35 0.52 0.73 1.12 1.31 2.02
RABGGTB ENST00000319942 23.71 32.15 26.10 1.35 0.87 0.99 1.12 1.46 1.25
PAPPA ENST00000328252 23.71 15.57 17.51 1.35 1.87 1.62 1.12 0.67 0.75
RHBDF2 ENST00000313080 23.72 25.64 22.81 1.35 1.24 1.19 1.12 1.05 0.98
ZFYVE27 ENST00000356257 23.72 66.65 43.55 1.35 0.56 0.62 1.12 1.22 2.01
INPP4A ENST00000074304 23.73 7.49 13.21 1.35 2.53 2.10 1.12 0.40 0.53
RABEP1 ENST00000262477 23.73 10.05 14.65 1.35 2.35 1.97 1.12 0.49 0.59
ANAPC5 ENST00000261819 23.74 40.72 30.44 1.35 0.63 0.80 1.12 1.78 1.46
FKBP8 ENST00000608443 23.74 3.49 11.28 1.35 3.39 2.16 1.12 0.29 0.45
ACBD5 ENST00000396271 23.75 24.87 22.48 1.35 1.33 1.16 1.12 1.05 0.97
UBIAD1 ENST00000376810 23.75 60.98 40.56 1.35 0.54 0.80 1.12 1.41 2.04
TSEN15 ENST00000361641 23.76 42.21 31.20 1.35 0.61 0.85 1.12 1.88 1.55

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