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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
MAN2B2 ENST00000285599 79.03 55.28 69.27 0.32 0.57 0.43 0.64 1.62 0.98
CMC2 ENST00000219400 79.04 81.32 83.54 0.32 0.33 0.33 0.64 0.54 0.40
OAS3 ENST00000228928 79.04 70.54 77.98 0.32 0.52 0.38 0.64 1.08 0.54
METTL22 ENST00000381920 79.05 73.41 79.49 0.32 0.54 0.38 0.64 1.03 0.52
ZNF674 ENST00000523374 79.05 71.71 78.64 0.32 0.51 0.38 0.64 1.07 0.55
PPP1R27 ENST00000330261 79.06 89.97 87.63 0.32 0.25 0.25 0.64 0.37 0.31
TUSC1 ENST00000358022 79.06 88.61 87.03 0.32 0.24 0.28 0.64 0.35 0.30
C16orf92 ENST00000300575 79.07 72.38 79.04 0.32 0.51 0.39 0.64 1.03 0.53
CLDN22 ENST00000323319 79.07 70.89 78.23 0.32 0.49 0.37 0.64 1.07 0.55
OR51Q1 ENST00000300778 79.08 89.53 87.46 0.32 0.27 0.28 0.64 0.36 0.30
CSMD1 ENST00000537824 79.08 6.48 41.00 0.32 2.63 0.76 0.64 0.37 2.04
TAC4 ENST00000334568 79.09 84.69 85.23 0.32 0.27 0.34 0.63 0.42 0.36
OR8J1 ENST00000303039 79.09 94.32 89.80 0.32 0.24 0.18 0.63 0.24 0.23
OR1F1 ENST00000304646 79.10 95.61 90.40 0.32 0.23 0.15 0.62 0.21 0.21
AKNA ENST00000307564 79.10 21.04 48.96 0.32 1.44 0.71 0.62 0.83 1.84
GPX4 ENST00000354171 79.11 66.92 76.03 0.32 0.53 0.38 0.62 1.25 0.62
TEX35 ENST00000319416 79.11 74.14 79.96 0.32 0.53 0.35 0.62 1.03 0.52
DNPH1 ENST00000230431 79.12 63.43 74.09 0.32 0.49 0.39 0.62 1.27 0.69
TMC4 ENST00000376591 79.12 54.95 69.12 0.32 0.57 0.43 0.62 1.63 1.00
ALDH3B2 ENST00000349015 79.13 84.10 84.97 0.32 0.27 0.33 0.62 0.45 0.39
PPP1R14A ENST00000301242 79.13 62.73 73.72 0.32 0.51 0.42 0.62 1.31 0.71
LY6G6D ENST00000375825 79.14 68.89 77.17 0.32 0.54 0.35 0.62 1.17 0.59
PRF1 ENST00000441259 79.14 67.75 76.51 0.32 0.52 0.38 0.62 1.18 0.61
FCGBP ENST00000221347 79.15 39.56 59.70 0.32 0.68 0.49 0.62 1.65 1.66
BPIFB1 ENST00000253354 79.15 51.59 67.13 0.32 0.62 0.51 0.62 1.87 1.17

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