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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
TUB ENST00000305253 51.78 29.48 38.96 0.58 1.10 0.80 1.82 1.39 2.06
PRRT2 ENST00000567659 52.06 29.31 39.02 0.59 1.14 0.78 1.84 1.36 2.06
SEMA4B ENST00000411539 52.80 28.70 39.10 0.66 1.16 0.77 1.77 1.29 2.06
C15orf39 ENST00000360639 53.57 28.00 39.15 0.62 1.20 0.77 1.75 1.18 2.06
LOXL2 ENST00000389131 53.62 31.78 40.90 0.62 0.94 0.78 1.77 1.48 2.06
ZNF804A ENST00000302277 59.93 21.40 39.00 0.63 1.43 0.80 1.39 0.80 2.06
SMOC2 ENST00000354536 60.40 31.74 44.64 0.59 0.95 0.62 1.38 1.48 2.06
GFRA2 ENST00000524240 60.57 31.72 44.73 0.58 0.95 0.63 1.35 1.47 2.06
HAUS7 ENST00000370211 74.16 7.11 38.98 0.35 2.58 0.80 0.82 0.37 2.06
MAGEL2 ENST00000532292 79.20 12.92 44.63 0.33 2.07 0.62 0.61 0.59 2.06
RBFOX3 ENST00000415831 88.22 3.90 44.65 0.20 3.28 0.62 0.34 0.31 2.06
GMFB ENST00000358056 23.56 61.86 40.92 1.37 0.57 0.78 1.10 1.35 2.06
SDCBP ENST00000260130 25.83 59.52 40.87 1.34 0.51 0.80 1.21 1.41 2.06
C9orf114 ENST00000361256 29.53 55.82 40.88 1.08 0.52 0.80 1.53 1.58 2.06
ISCU ENST00000311893 29.72 62.40 44.62 1.08 0.53 0.62 1.58 1.32 2.06
SLC2A2 ENST00000314251 30.51 50.66 38.91 0.99 0.63 0.80 1.62 1.95 2.06
PTAFR ENST00000373857 30.76 50.67 39.06 0.96 0.63 0.78 1.64 1.95 2.06
SOAT1 ENST00000367619 32.52 49.12 39.20 0.96 0.66 0.78 1.70 2.04 2.06
TBX19 ENST00000367821 33.81 51.94 41.09 0.92 0.61 0.76 1.73 1.85 2.06
LOXL3 ENST00000264094 34.82 46.37 38.92 0.94 0.73 0.80 1.83 2.04 2.06
ARHGEF25 ENST00000333972 35.67 45.50 38.91 0.95 0.71 0.80 1.90 1.98 2.06
MCMDC2 ENST00000422365 36.43 49.28 41.06 0.95 0.65 0.75 1.81 2.02 2.06
KIAA0895 ENST00000297063 36.71 55.43 44.62 0.95 0.58 0.62 1.75 1.60 2.06
C3orf38 ENST00000318887 36.82 55.45 44.71 0.94 0.58 0.62 1.75 1.60 2.06
GFI1B ENST00000339463 37.39 48.01 40.90 0.94 0.63 0.78 1.74 2.00 2.06

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