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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
SUMO3 ENST00000332859 17.31 60.42 37.09 1.46 0.53 0.80 0.87 1.41 1.95
PDGFC ENST00000502773 17.31 5.70 8.89 1.46 2.92 2.49 0.87 0.34 0.38
RNF217 ENST00000359704 17.32 54.63 34.20 1.46 0.58 0.87 0.87 1.66 1.76
AP3B2 ENST00000261722 17.32 14.86 13.75 1.46 1.92 2.06 0.87 0.62 0.57
MAP4K1 ENST00000591517 17.33 12.15 12.34 1.47 2.07 2.25 0.87 0.57 0.50
VPS36 ENST00000378060 17.33 25.74 19.55 1.47 1.24 1.53 0.87 1.05 0.84
DOCK9 ENST00000376460 17.34 5.21 8.64 1.47 3.16 2.54 0.87 0.32 0.36
LDLRAD4 ENST00000361205 17.34 26.57 19.97 1.47 1.19 1.47 0.87 1.12 0.85
BAG2 ENST00000370693 17.35 62.91 38.43 1.47 0.51 0.84 0.87 1.31 2.04
DRAP1 ENST00000312515 17.35 43.59 28.63 1.47 0.62 0.80 0.87 1.95 1.34
ECT2 ENST00000392692 17.36 30.79 22.23 1.47 1.06 1.15 0.87 1.38 0.96
KDR ENST00000263923 17.36 9.10 10.83 1.47 2.45 2.19 0.87 0.47 0.43
ALKBH6 ENST00000378875 17.37 37.39 25.45 1.47 0.76 1.02 0.87 1.66 1.18
UBL5 ENST00000358666 17.38 82.44 48.80 1.47 0.34 0.70 0.87 0.52 1.86
C16orf70 ENST00000219139 17.38 13.40 12.95 1.47 2.05 2.09 0.87 0.60 0.53
IGSF11 ENST00000393775 17.39 41.87 27.79 1.47 0.61 0.90 0.87 1.80 1.27
RNF121 ENST00000361756 17.39 25.62 19.51 1.47 1.24 1.54 0.87 1.05 0.83
RFXAP ENST00000255476 17.40 45.62 29.70 1.47 0.73 0.86 0.87 2.00 1.41
VRK1 ENST00000216639 17.40 32.30 23.02 1.47 0.86 1.20 0.87 1.46 0.98
SLC11A2 ENST00000394904 17.41 27.25 20.40 1.46 1.25 1.51 0.87 1.15 0.88
LSM10 ENST00000315732 17.41 94.33 55.53 1.46 0.24 0.52 0.87 0.24 1.74
MYO6 ENST00000369977 17.42 19.94 16.51 1.46 1.47 1.71 0.87 0.73 0.69
GREM1 ENST00000300177 17.42 41.99 27.87 1.46 0.59 0.86 0.87 1.83 1.29
JAK3 ENST00000458235 17.43 25.10 19.22 1.46 1.32 1.54 0.87 1.03 0.86
NCK1 ENST00000481752 17.43 38.70 26.23 1.46 0.70 1.00 0.87 1.67 1.26

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