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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
COL2A1 ENST00000380518 10.59 2.42 3.84 1.99 3.60 3.77 0.57 0.29 0.24
LRP1 ENST00000243077 10.60 0.23 2.83 1.99 4.12 4.03 0.57 0.28 0.23
ZNF711 ENST00000373165 10.60 7.72 6.50 1.99 2.53 3.05 0.57 0.43 0.32
FBXO38 ENST00000394370 10.61 9.79 7.57 1.99 2.40 2.75 0.57 0.50 0.33
CIRBP ENST00000588030 10.61 32.50 19.59 1.99 0.86 1.53 0.57 1.48 0.85
ZFP82 ENST00000392161 10.62 20.19 12.97 1.99 1.43 2.09 0.57 0.75 0.53
RAB18 ENST00000356940 10.62 20.09 12.90 1.99 1.43 2.10 0.57 0.74 0.53
PPP1R10 ENST00000376511 10.63 3.21 4.20 1.99 3.45 3.77 0.57 0.28 0.24
FGF17 ENST00000359441 10.63 12.78 9.13 1.99 2.09 2.37 0.57 0.59 0.38
PIP5K1B ENST00000265382 10.64 44.61 25.72 1.99 0.66 1.05 0.57 1.97 1.22
ADAM11 ENST00000200557 10.65 27.25 16.80 1.99 1.25 1.70 0.57 1.15 0.70
MAP2K5 ENST00000178640 10.65 23.30 14.72 1.97 1.43 1.95 0.57 0.93 0.62
UBAP2L ENST00000428931 10.66 0.54 3.03 1.97 4.16 3.96 0.57 0.27 0.24
KCNIP1 ENST00000411494 10.66 38.41 22.71 1.97 0.75 1.18 0.57 1.70 0.98
KCNT2 ENST00000294725 10.67 16.58 11.31 1.97 1.77 2.16 0.57 0.71 0.45
PSMA7 ENST00000370873 10.67 7.24 6.20 1.97 2.58 3.15 0.57 0.37 0.32
TUBA1C ENST00000301072 10.68 44.71 25.81 1.97 0.66 1.01 0.57 1.98 1.23
FAF1 ENST00000396153 10.68 9.21 7.31 1.96 2.47 2.81 0.57 0.47 0.34
HMGA2 ENST00000403681 10.69 21.62 13.81 1.96 1.44 2.09 0.57 0.81 0.57
CBLB ENST00000264122 10.69 10.41 7.91 1.96 2.23 2.61 0.57 0.50 0.35
TET1 ENST00000373644 10.70 4.24 4.77 1.96 3.26 3.68 0.57 0.32 0.25
ABCD3 ENST00000370214 10.70 19.95 12.89 1.95 1.47 2.10 0.57 0.73 0.53
PTPN1 ENST00000371621 10.71 18.10 12.01 1.95 1.53 2.29 0.57 0.74 0.47
MAB21L1 ENST00000379919 10.71 36.01 21.50 1.94 0.80 1.30 0.57 1.59 0.91
DESI1 ENST00000263256 10.72 64.76 35.86 1.94 0.48 0.86 0.57 1.24 1.79

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